Miracle-dz/UniFAR-FTUs huggingface dataset:
Rac1 Mediates Collapsin-1-Induced Growth Cone Collapse

Collapsin-1 or semaphorin III(D) inhibits axonal outgrowth by collapsing the lamellipodial and filopodial structures of the neuronal growth cones. Because growth cone collapse is associated with actin depolymerization, we considered whether small GTP-binding proteins of the rho subfamily might participate in collapsin-1 signal transduction. Recombinant rho, rac1, and cdc42 proteins were triturated into embryonic chick (DRG) neurons. Constitutively active rac1 increases the proportion of collapsed growth cones, and dominant negative rac1 inhibits collapsin-1-induced collapse of growth cones and collapsin-1 inhibition of neurite outgrowth. DRG neurons treated with dominant negative rac1 remain sensitive to myelin-induced growth cone collapse. Similar mutants of cdc42 do not alter growth cone structure, neurite elongation, or collapsin-1 sensitivity. Whereas the addition of activated rho has no effect, the inhibition of rho withClostridium botulinum C3 transferase stimulates the outgrowth of DRG neurites. C3 transferase-treated growth cones exhibit little or no lamellipodial spreading and are minimally responsive to collapsin-1 and myelin. These data demonstrate a prominent role for rho and rac1 in modulating growth cone motility and indicate that rac1 may mediate collapsin-1 action.
Caspase-3 Is Required for α-Fodrin Cleavage but Dispensable for Cleavage of Other Death Substrates in Apoptosis*

Although the commonly activated death protease caspase-3 appears not to be essential for apoptosis during development except in the brain, it was not shown whether substrates known to be cleaved by caspase-3 are still proteolyzed in its absence. We have addressed this question with MCF-7 breast carcinoma cells that we recently showed lack caspase-3 owing to the functional deletion of theCASP-3 gene. Tumor necrosis factor- or staurosporine-induced apoptosis of caspase-3-deficient MCF-7 cells resulted in cleavage of the death substrates PARP, Rb, PAK2, DNA-PKcs, gelsolin, and DFF-45, but not α-fodrin. In contrast, all these substrates including α-fodrin were cleaved in apoptotic HeLa cells expressing caspase-3. Introduction ofCASP-3 cDNA, but not CASP-10 cDNA, into MCF-7 cells restored α-fodrin cleavage. In addition, tumor necrosis factor- or staurosporine-induced apoptosis of MCF-7 cells stably expressing pro-caspase-3 also resulted in α-fodrin cleavage. Although the specific caspase inhibitory peptides Z-VAD-fmk and Z-DEVD-fmk prevented apoptosis of MCF-7 cells, we were unable to detect activation of caspases 2 and 7, which are known to be inhibited by Z-DEVD-fmk. Together our results suggest that caspase-3 is essential for cleavage of α-fodrin, but dispensable for the cleavage of PARP, Rb, PAK2, DNA-PKcs, gelsolin, and DFF-45 and imply that one or more caspases other than caspases 2, 3, and 7 is activated and plays a crucial role in the cleavage of these substrates in MCF-7 cells.
Oxidative Stress in Hemodialysis Patients: A Review of the Literature

Hemodialysis (HD) patients are at high risk for all-cause mortality and cardiovascular events. In addition to traditional risk factors, excessive oxidative stress (OS) and chronic inflammation emerge as novel and major contributors to accelerated atherosclerosis and elevated mortality. OS is defined as the imbalance between antioxidant defense mechanisms and oxidant products, the latter overwhelming the former. OS appears in early stages of chronic kidney disease (CKD), advances along with worsening of renal failure, and is further exacerbated by the HD process per se. HD patients manifest excessive OS status due to retention of a plethora of toxins, subsidized under uremia, nutrition lacking antioxidants and turn-over of antioxidants, loss of antioxidants during renal replacement therapy, and leukocyte activation that leads to accumulation of oxidative products. Duration of dialysis therapy, iron infusion, anemia, presence of central venous catheter, and bioincompatible dialyzers are several factors triggering the development of OS. Antioxidant supplementation may take an overall protective role, even at early stages of CKD, to halt the deterioration of kidney function and antagonize systemic inflammation. Unfortunately, clinical studies have not yielded unequivocal positive outcomes when antioxidants have been administered to hemodialysis patients, likely due to their heterogeneous clinical conditions and underlying risk profile.
Mechanical resistance of proteins explained using simple molecular models.

Recent experiments have demonstrated that proteins unfold when two atoms are mechanically pulled apart, and that this process is different to when heated or when a chemical denaturant is added to the solution. Experiments have also shown that the response of proteins to external forces is very diverse, some of them being "hard," and others "soft. " Mechanical resistance originates from the presence of barriers on the energy landscape; together, experiment and simulation have demonstrated that unfolding occurs through alternative pathways when different pairs of atoms undergo mechanical extension. Here we use simulation to probe the mechanical resistance of six structurally diverse proteins when pulled in different directions. For this, we use two very different models: a detailed, transferable one, and a coarse-grained, structure-based one. The coarse-grained model gives results that are surprisingly similar to the detailed one and qualitatively agree with experiment; i.e., the mechanical resistance of different proteins or of a single protein pulled in different directions can be predicted by simulation. The results demonstrate the importance of pulling direction relative to the local topology in determining mechanical stability, and rationalize the effect of the location of importation/degradation tags on the rates of mitochondrial import or protein degradation in vivo.
Iterative Construction of Cayley Expander Graphs

We construct a sequence of groups Gn, and explicit sets of generators Yn Gn, such that all generating sets have bounded size, and the associated Cayley graphs are all expanders. The group G1 is the alternating group Ad, the set of even permutations on the elements {1, 2,. , d}. The group Gn is the group of all even symmetries of the rooted d-regular tree of depth n. Our results hold for any large enough d. We also describe a finitely generated infinite group G∞ with generating set Y∞, given with a mapping fn from G∞ to Gn for every n, which sends Y∞ to Yn. In particular, under the assumption described above, G∞ has property (t) with respect to the family of subgroups ker( fn). The proof is elementary, using only simple combinatorics and linear algebra. The re- cursive structure of the groups Gn (iterated wreath products of the alternating group Ad) allows for an inductive proof of expansion, using the group theoretic analogue (of Alon et
A Quick Look at Cognitive Theory

There are many questions about multimedia development that seem to be appropriate to frame as issues of cognitive psychology. This very brief introduction to some of the principles of cognitive theory is intended primarily to provide a framework for understanding one origin for some recommendations concerning interface design and choice of illustration. A couple of other more focused papers should provide further insights.
Injecting Discrimination and Privacy Awareness Into Pattern Discovery

Data mining is gaining societal momentum due to the ever increasing availability of large amounts of human data, easily collected by a variety of sensing technologies. Data mining comes with unprecedented opportunities and risks: a deeper understanding of human behavior and how our society works is darkened by a greater chance of privacy intrusion and unfair discrimination based on the extracted patterns and profiles. Although methods independently addressing privacy or discrimination in data mining have been proposed in the literature, in this context we argue that privacy and discrimination risks should be tackled together, and we present a methodology for doing so while publishing frequent pattern mining results. We describe a combined pattern sanitization framework that yields both privacy and discrimination-protected patterns, while introducing reasonable (controlled) pattern distortion.
Particle filtering for joint data-channel estimation in fast fading channels

In this paper, we propose to use the particle filtering methods in order to estimate jointly the data and the channel coefficients in fast fading conditions. We compare the obtained reduced complexity maximum likelihood detector with the state-of-the-art solution represented by the per-survivor processing (PSP) detector. We show that the proposed particle detector (PD) presents a better trade-off between performance and computational complexity than the reduced complexity PSP detector. Moreover, we observe that the computational complexity of the PD is adapted according to the signal-to-noise ratio.
DCU-UVT: Word-Level Language Classification with Code-Mixed Data

This paper describes the DCU-UVT team’s participation in the Language Identification in Code-Switched Data shared task in the Workshop on Computational Approaches to Code Switching. Word-level classification experiments were carried out using a simple dictionary-based method, linear kernel support vector machines (SVMs) with and without contextual clues, and a k-nearest neighbour approach. Based on these experiments, we select our SVM-based system with contextual clues as our final system and present results for the Nepali-English and Spanish-English datasets.
A Hybrid Multiview Stereo Algorithm for Modeling Urban Scenes

We present an original multiview stereo reconstruction algorithm which allows the 3D-modeling of urban scenes as a combination of meshes and geometric primitives. The method provides a compact model while preserving details: Irregular elements such as statues and ornaments are described by meshes, whereas regular structures such as columns and walls are described by primitives (planes, spheres, cylinders, cones, and tori). We adopt a two-step strategy consisting first in segmenting the initial mesh-based surface using a multilabel Markov Random Field-based model and second in sampling primitive and mesh components simultaneously on the obtained partition by a Jump-Diffusion process. The quality of a reconstruction is measured by a multi-object energy model which takes into account both photo-consistency and semantic considerations (i.e., geometry and shape layout). The segmentation and sampling steps are embedded into an iterative refinement procedure which provides an increasingly accurate hybrid representation. Experimental results on complex urban structures and large scenes are presented and compared to state-of-the-art multiview stereo meshing algorithms.
Energy Efficient Home Gateway Based on User Service Traffic in Always-On Home Network Environment

Home gateway (HG) is a device that connects multiple home network devices to an access network. The HG is to be always in operating state for providing any requested digital home services without suspension and user's waiting because these services can be started at any time, by any device and from any network. Furthermore, most home network devices are also required to be ready to operate at any time in the digital home environment. We call this characterized digital home network by 'always-on home network'. The characteristic of the 'always-on' in home network environment gives rise to consume more electrical power. In this paper, we propose a novel scheme to reduce the power consumed by a HG and the architecture to implement the proposed HG. The proposed scheme uses sleep and wake-up mechanism based on existence of real data traffic for user service. In the proposed scheme, almost hardware components of the HG are working, power-on, only in the period that some user service traffic is in the proposed HG; wake-up state or normal stat. On the other hand, some hardware components such as network protocol agent (NPA) with low power consumption are working in the period of no user service traffic. The NPA controls these sleep and wake-up for the proposed HG with cooperating with CPU.
Quantized kernel least mean mixed-norm algorithm

Quantized kernel least mean square (QKLMS) algorithm is an effective up-to-date adaptive nonlinear learning algorithm which also has good performance for kernel structure growing control. It achieves good results under Gaussian noise environment. In this paper, a new algorithm, quantized kernel least mean mixed norm (QKLMMN), is proposed for adaptive nonlinear learning with non-Gaussian additive noise statistical distribution models (including combination). As an alternative of conventional squared error criteria, mixed-norm criteria is utilized for our algorithm. A comprehensive convergence analysis is carried out. Experiments for nonlinear time series prediction and nonlinear system identification are conducted. Experimental results verified the effectiveness and superiority of our proposed algorithm compared with other kernel based adaptive nonlinear learning algorithms under non-Gaussian noise environment.
Role of methylation in aerotaxis in Bacillus subtilis

Taxis to oxygen (aerotaxis) in Bacillus subtilis was characterized in a capillary assay and in a temporal assay in which the concentration of oxygen in a flow chamber was changed abruptly. A strong aerophilic response was present, but there was no aerophobic response to high concentrations of oxygen. Adaptation to a step increase in oxygen concentration was impaired when B. subtilis cells were depleted of methionine to prevent methylation of the methyl-accepting chemotaxis proteins. There was a transient increase in methanol release when wild-type B. subtilis, but not a cheR mutant that was deficient in methyltransferase activity, was stimulated by a step increase or a step decrease in oxygen concentration. The methanol released was quantitatively correlated with demethylation of methyl-accepting chemotaxis proteins. This indicated that methylation is involved in aerotaxis in B. subtilis in contrast to aerotaxis in Escherichia coli and Salmonella typhimurium, which is methylation independent.
Aurora-A expressing tumour cells are deficient for homology-directed DNA double strand-break repair and sensitive to PARP inhibition

The protein kinase Aurora‐A is a major regulator of the cell cycle that orchestrates mitotic entry and is required for the assembly of a functional mitotic spindle. Overexpression of Aurora‐A has been strongly linked with oncogenesis and this has led to considerable efforts at therapeutic targeting of the kinase activity of this protein. However, the exact mechanism by which Aurora‐A promotes oncogenesis remains unclear. Here, we show that Aurora‐A modulates the repair of DNA double‐strand breaks (DSBs). Aurora‐A expression inhibits RAD51 recruitment to DNA DSBs, decreases DSB repair by homologous recombination and sensitizes cancer cells to PARP inhibition. This impairment of RAD51 function requires inhibition of CHK1 by Polo‐like kinase 1 (PLK1). These results identify a novel function of Aurora‐A in modulating the response to DNA DSB that likely contributes to carcinogenesis and suggest a novel therapeutic approach to the treatment of cancers overexpressing this protein.
Context-Sensitive Decision Forests for Object Detection

In this paper we introduce Context-Sensitive Decision Forests - A new perspective to exploit contextual information in the popular decision forest framework for the object detection problem. They are tree-structured classifiers with the ability to access intermediate prediction (here: classification and regression) information during training and inference time. This intermediate prediction is available for each sample and allows us to develop context-based decision criteria, used for refining the prediction process. In addition, we introduce a novel split criterion which in combination with a priority based way of constructing the trees, allows more accurate regression mode selection and hence improves the current context information. In our experiments, we demonstrate improved results for the task of pedestrian detection on the challenging TUD data set when compared to state-of-the-art methods.
NOVEL BLOCKER OF NFAT ACTIVATION INHIBITS INTERLEUKIN-6 PRODUCTION IN HUMAN MYOMETRIAL ARTERIES AND REDUCES VASCULAR SMOOTH MUSCLE CELL PROLIFERATION

The calcineurin/NFAT signaling pathway has been found to play a role in regulating growth and differentiation in several cell types. However, the functional significance of NFAT in the vasculature is largely unclear. Here we show that NFATc1, NFATc3 and NFATc4 are expressed in human myometrial arteries. Confocal immunofluorescence and western blot analysis revealed that endothelin-1 efficiently increases NFATc3 nuclear accumulation in native arteries. Endothelin-1 also stimulates NFAT-dependent transcriptional activity, as shown by a luciferase reporter assay. Both the agonist-induced NFAT nuclear accumulation and transcriptional activity were prevented by the calcineurin inhibitor CsA and by the novel NFAT blocker A-285222. Chronic inhibition of NFAT significantly reduced IL-6 production in intact myometrial arteries and inhibited cell proliferation in vascular smooth muscle cells cultured from explants from the same arteries. Further, using small-interfering-RNAmediated reduction of NFATc3, we show that this isoform is involved in the regulation of cell proliferation. Protein synthesis in intact arteries was investigated using autoradiography of [S]methionine incorporation in serum-free culture. Inhibition of NFAT signaling did not affect overall protein synthesis or specifically the synthesis rates of major proteins associated with the contractile/cytoskeletal system. An intact contractile phenotype under these conditions was also shown by unchanged force response to depolarization or agonist stimulation. Our results demonstrate NFAT expression and activation in native human vessels and point out A-285222 as a powerful pharmacological blocker of NFAT signaling in the vasculature.
Magnesium-binding architectures in RNA crystal structures: validation, binding preferences, classification and motif detection

The ubiquitous presence of magnesium ions in RNA has long been recognized as a key factor governing RNA folding, and is crucial for many diverse functions of RNA molecules. In this work, Mg2+-binding architectures in RNA were systematically studied using a database of RNA crystal structures from the Protein Data Bank (PDB). Due to the abundance of poorly modeled or incorrectly identified Mg2+ ions, the set of all sites was comprehensively validated and filtered to identify a benchmark dataset of 15 334 ‘reliable’ RNA-bound Mg2+ sites. The normalized frequencies by which specific RNA atoms coordinate Mg2+ were derived for both the inner and outer coordination spheres. A hierarchical classification system of Mg2+ sites in RNA structures was designed and applied to the benchmark dataset, yielding a set of 41 types of inner-sphere and 95 types of outer-sphere coordinating patterns. This classification system has also been applied to describe six previously reported Mg2+-binding motifs and detect them in new RNA structures. Investigation of the most populous site types resulted in the identification of seven novel Mg2+-binding motifs, and all RNA structures in the PDB were screened for the presence of these motifs.
Simulation of Enhanced Gate Control in a Double Gate Quantum Domain InAlAs/InGaAs/InP HEMT

Electron concentration profiles are simulated for the double-gate (DG) InAlAs/InGaAs/InP HEMT for nanometer gate dimension with two separate gate controls on either side of the double heterostructure. A Quantum Moments model has been used to account for the quantization effects in the device. The quantum simulation of the confinement of the charge carriers in the nano-dimensional channel formed between the two hetero structures reveals a single peak for electron concentration in the channel with enhanced gate control. Moreover, simulated quantum results obtained for ID-VDS are verified by comparing them with the experimental 100nm Double-gate InAlAs/InGaAs/InP HEMT and are in good agreement.
Para‐Graph: Graph‐Based Parameterization of Triangle Meshes with Arbitrary Genus

This paper describes a novel approach to the parameterization of triangle meshes representing 2‐manifolds with an arbitrary genus. A topology‐based decomposition of the shape is computed and used to segment the shape into primitives, which define a chart decomposition of the mesh. Then, each chart is parameterized using an extension of the barycentric coordinates method. The charts are all 0‐genus and can be of three types only, depending on the number of boundary components. The chart decomposition and the parameterization are used to define a shape graph where each node represents one primitive and the arcs code the adjacency relationships between the primitives. Conical and cylindrical primitives are coded together with their skeletal lines that are computed from and aligned with their parameterization. The application of the parameterization approach to remeshing guarantees that extraordinary vertices are localized only where two patches share a boundary and they are not scattered on the whole surface.
Integrin-dependent induction of early growth response genes in capillary endothelial cells.

Studies were carried out to explore how extracellular matrix molecules, such as fibronectin (FN), promote capillary endothelial (CE) cell growth. When G0-synchronized cells were plated on FN-coated dishes, expression of the immediate-early mRNAs, c-fos, c-myc and c-jun, was rapidly induced, even in the absence of serum or soluble growth factors. Moreover, plating cells on different FN densities (5-200 micrograms/150 mm dish), resulted in a dose-dependent increase in the steady state levels of these mRNAs. Addition of FGF potentiated gene activation and was required for maximal DNA synthesis, however, the overall steady-state level of gene induction was dictated primarily by the density of immobilized FN. Expression of junB also was induced when suspended cells bound RGD-peptide coated microbeads that promote integrin clustering, but not when the suspended cells bound beads coated with other receptor ligands (e.g. acetylated low density protein) or when they were stimulated by soluble FN or FGF in the absence of substrate adhesion. c-Jun exhibited a similar requirement for gene induction except that it also was partially induced by binding to soluble FN alone. In contrast, c-fos expression was induced by all stimuli tested. Interestingly, inhibition of Na+/H+ exchange using hexamethylene-amiloride prevented most of the FN-induced increase in c-jun expression whereas it was relatively ineffective when cells were simultaneously stimulated by both FN and FGF. These data demonstrate that cell adhesion to extracellular matrix and associated integrin binding can directly activate signaling cascades in quiescent CE cells that lead to induction of immediate-early genes associated with the G0/G1 transition and thereby, stimulate these cells to reenter the growth cycle.
An Arabidopsis Homolog of the Bacterial Cell Division Inhibitor SulA Is Involved in Plastid Division

Plastids have evolved from an endosymbiosis between a cyanobacterial symbiont and a eukaryotic host cell. Their division is mediated both by proteins of the host cell and conserved bacterial division proteins. Here, we identified a new component of the plastid division machinery, Arabidopsis thaliana SulA. Disruption of its cyanobacterial homolog (SSulA) in Synechocystis and overexpression of an AtSulA-green fluorescent protein fusion in Arabidopsis demonstrate that these genes are involved in cell and plastid division, respectively. Overexpression of AtSulA inhibits plastid division in planta but rescues plastid division defects caused by overexpression of AtFtsZ1-1 and AtFtsZ2-1, demonstrating that its role in plastid division may involve an interaction with AtFtsZ1-1 and AtFtsZ2-1.