Miracle-dz/UniFAR-FTUs huggingface dataset:
Mkp1 Is a c-Jun Target Gene That Antagonizes JNK-Dependent Apoptosis in Sympathetic Neurons

Developing sympathetic neurons depend on NGF for survival. When sympathetic neurons are deprived of NGF in vitro, a well documented series of events, including c-Jun N-terminal kinase (JNK) pathway activation, release of cytochrome c from the mitochondria, and caspase activation, culminates in the death of the neuron by apoptosis within 24–48 h. This process requires de novo gene expression, suggesting that increased expression of specific genes activates the cell death program. Using rat gene microarrays, we found that NGF withdrawal induces the expression of many genes, including mkp1, which encodes a MAPK phosphatase that can dephosphorylate JNKs. The increase in mkp1 mRNA level requires the MLK-JNK-c-Jun pathway, and we show that Mkp1 is an important regulator of JNK-dependent apoptosis in sympathetic neurons. In microinjection experiments, Mkp1 overexpression can inhibit JNK-mediated phosphorylation of c-Jun and protect sympathetic neurons from apoptosis, while Mkp1 knockdown accelerates NGF withdrawal-induced death. Accordingly, the number of superior cervical ganglion (SCG) neurons is reduced in mkp1−/− mice at P1 during the period of developmental sympathetic neuron death. We also show that c-Jun and ATF2 bind to two conserved ATF binding sites in the mkp1 promoter in vitro and in chromatin. Both of these ATF sites contribute to basal promoter activity and are required for mkp1 promoter induction after NGF withdrawal. These results demonstrate that Mkp1 is part of a negative feedback loop induced by the MLK-JNK-c-Jun signaling pathway that modulates JNK activity and the rate of neuronal death in rat sympathetic neurons following NGF withdrawal.
Symbolic Computations based on Grid Services

The widespread adoption of the current Grid technologies is still impeded by a number of problems, one of which is difficulty of developing and implementing Grid-enabled applications. In another dimension, symbolic computation, aiming to automatize the steps of mathematical problem solving, has become in the last years a basis for advanced applications in many areas of computer science. In this context we have recently analyzed and developed grid-extensions of known tools for symbolic computations. We further present in this paper a case study of a Web service-based Grid application for symbolic computations.
Active Contour Based Visual Tracking UsingLevel Sets

The visual tracking is the major process in finding the spot of moving object over time using a camera. Object tracking is challenging task when the object moves fast relative to the frame rate. The active contour algorithm is used for tracking the object in a given frame of an image sequence. In videos particular object motion can be tracked by using stationary cameras but in moving camera the particular object cannot be extracted from background subtraction. Active contour based visual tracking using level sets is proposed which does not consider the camera is stationary (or) moving . The optical flow based algorithm is used for initializing contours at first frame. The correlations between the values of neighbouring pixels for posterior probability estimation is done by Markov random field theory in the color based contour evolution. The Independent Component Analysis (ICA) is used to deal with noise (or) partial occlusion to obtain the more accurate contours in the shape based contour. To handle the abrupt motions the particle swarm optimization is used to track the object from first frame to last frame and it is applied to current frame to produce an initial contour in next frame. This visual tracking can be used in real time applications like vehicle guidance and control, surveillance and identification, user interface, video processing and medical applications.
Solving Lasso: Extended ADMM is more efficient than ADMM

The least absolute shrinkage and selection operator (Lasso) has become very popular and attractive approach for regularization and variable selection for high-dimensional data in machine learning. In this paper, we present an extended alternating direction method of multipliers (ADMM) for solving the Lasso. The extended ADMM is global convergent, and all the subproblems can easily get the solutions. It can also be implemented in distributed manner, which is beneficial for storage and computation requirement. Numerical experiments demonstrated that the extended ADMM outperforms other popular algorithms.
Design of Distributed Multi-Edge Type LDPC Codes for Two-Way Relay Channels

This paper studies the problem of determining the optimum degree distribution for distributed LDPC codes in two-way relay channels. Based on the framework of multi-edge type (MET) LDPC codes, we propose a methodology to asymptotically optimize the code's ensemble when different segments within the distributed codeword have been transmitted through different channels and experience different SNRs. An average noise threshold is formulated to compute the convergence threshold of the distributed LDPC codes under density evolution and acts as the performance gap between the optimized distributed codes and the theoretical limit. We demonstrate that the optimized distributed LDPC code using our proposed method performs asymptotically within a fraction of a dB away from the theoretical limit.
The molecular mechanism of G2/M cell cycle arrest induced by AFB1 in the jejunum

Aflatoxin B1 (AFB1) has potent hepatotoxic, carcinogenic, genotoxic, immunotoxic and other adverse effects in human and animals. The aim of this study was to investigate the molecular mechanism of G2/M cell cycle arrest induced by AFB1 in the jejunum of broilers. Broilers, as experimental animals, were fed 0.6 mg/kg AFB1 diet for 3 weeks. Our results showed that AFB1 reduced the jejunal villus height, villus height/crypt ratio and caused G2/M cell cycle arrest. The G2/M cell cycle was accompanied by the increase of ataxia telangiectasia mutated (ATM), p53, Chk2, p21 protein and mRNA expression, and the decrease of Mdm2, cdc25C, cdc2, cyclin B and proliferating cell nuclear antigen protein and mRNA expression. In conclusion, AFB1 blocked G2/M cell cycle by ATM pathway in the jejunum of broilers.
A coarse-grained reconfigurable wavelet denoiser exploiting the Multi-Dataflow Composer tool

In the last few years, efficient resource management turned out to be one of the major challenges for hardware designers. Strategies of reusability through reconfiguration have demonstrated interesting potentials to address it, providing also power and area minimization. The Multi-Dataflow Composer (MDC) tool has been presented to the scientific community to automatically build-up runtime coarse-grained reconfigurable platforms. Originally conceived in the field of Reconfigurable Video Coding (RVC), the MDC allows achieving attractive results also for hardware designers operating in different application fields. In this work, we intend to demonstrate the potential orthogonality of the MDC approach with respect to the RVC domain. A runtime reconfigurable wavelet denoiser, targeted for biomedical applications, has been developed and prototyped onto an FPGA Development Board Spartan 3E 1600. Impressive results in terms of resource minimization have been achieved with respect to more traditional solutions.
A preamble allocation method for M2M traffics in 3GPP LTE-A networks

The number of Machine-to-Machine (M2M) traffics is rapidly increasing in cellular communication systems. In order to ensure a maximum system capacity, the communication resources should be allocated appropriately to M2M traffics and common Human-to-Human (H2H) traffics. In this paper, a preamble allocation method for M2M services in 3GPP LTE system is presented. This method splits the set of available random access preambles into three subsets: the first one is for H2H services only, the second is for both H2H and M2M services and the third is for M2M services only. We model and analyze the throughput performance of the proposed method, and compare it with the two major candidate preamble allocation methods under consideration for possible adoption in LTE-Advanced networks. It is shown that the proposed method performs much better in most practical situations.
An algebraic theory of infinite classical lattices

We present an algebraic theory of the states of the infinite classical lattices. The construction follows the Haag-Kastler axioms from quantum field theory (QFT). By comparison, the *-algebras of the quantum theory are replaced here with the Banach lattices (MI-spaces) to have real-valued measurements, and the GNS construction with the structure theorem for MI-spaces to represent the Segal algebra as C(X). The theory represents any compact convex set of states as a decomposition problem of states on an abstract Segal algebra C(X), where X is isomorphic with the space of extremal states of the set. Three examples are treated, the study of groups of symmetries and symmetry breakdown, the Gibbs states, and the set of all stationary states on the lattice. For relating the theory to standard problems of statistical mechanics, it is shown that every thermodynamic-limit (TL) state is uniquely identified by expectation values with an algebraic state.
Simultaneous topology, shape and size optimization of truss structures by fully stressed design based on evolution strategy

The most effective scheme of truss optimization considers the combined effect of topology, shape and size (TSS); however, most available studies on truss optimization by metaheuristics concentrated on one or two of the above aspects. The presence of diverse design variables and constraints in TSS optimization may account for such limited applicability of metaheuristics to this field. In this article, a recently proposed algorithm for simultaneous shape and size optimization, fully stressed design based on evolution strategy (FSD-ES), is enhanced to handle TSS optimization problems. FSD-ES combines advantages of the well-known deterministic approach of fully stressed design with potential global search of the state-of-the-art evolution strategy. A comparison of results demonstrates that the proposed optimizer reaches the same or similar solutions faster and/or is able to find lighter designs than those previously reported in the literature. Moreover, the proposed variant of FSD-ES requires no user-based tuning effort, which is desired in a practical application. The proposed methodology has been tested on a number of problems and is now ready to be applied to more complex TSS problems.
Are Small GTPases Signal Hubs in Sugar-Mediated Induction of Fructan Biosynthesis?

External sugar initiates biosynthesis of the reserve carbohydrate fructan, but the molecular processes mediating this response remain obscure. Previously it was shown that a phosphatase and a general kinase inhibitor hamper fructan accumulation. We use various phosphorylation inhibitors both in barley and in Arabidopsis and show that the expression of fructan biosynthetic genes is dependent on PP2A and different kinases such as Tyr-kinases and PI3-kinases. To further characterize the phosphorylation events involved, comprehensive analysis of kinase activities in the cell was performed using a PepChip, an array of >1000 kinase consensus substrate peptide substrates spotted on a chip. Comparison of kinase activities in sugar-stimulated and mock(sorbitol)-treated Arabidopsis demonstrates the altered phosphorylation of many consensus substrates and documents the differences in plant kinase activity upon sucrose feeding. The different phosphorylation profiles obtained are consistent with sugar-mediated alterations in Tyr phosphorylation, cell cycling, and phosphoinositide signaling, and indicate cytoskeletal rearrangements. The results lead us to infer a central role for small GTPases in sugar signaling.
Intergenerational equity and the investing of rents from exhaustible resources

The present generation's ethical dilemma over shortchanging future generations by overconsuming exhaustible resources could be relieved by a program of converting the capital from these resources into machines and living off the current flow of machines and labor. If the stock of machines is assumed not to depreciate, then the stock of productive capital and resources is not depleted. Cobb-Douglas technology is used to determine what will happen to consumption if only the rents from exhaustible resources are invested in reproducible capital goods. An important feature of Cobb-Douglas technology is that input in the form of minerals from an exhaustible resource is needed to get a positive output of the single produced commodity. Results of the model indicate that a savings investment rule will not provide for the maintenance of per capita consumption constant over time. Further studies have explored the effects of depreciations and intergenerational equity. 7 references.
CK2 Inhibitor CX-4945 Blocks TGF-β1-Induced Epithelial-to-Mesenchymal Transition in A549 Human Lung Adenocarcinoma Cells

Background The epithelial-to-mesenchymal transition (EMT) is a major phenotype of cancer metastasis and invasion. As a druggable cancer target, the inhibition of protein kinase CK2 (formally named to casein kinase 2) has been suggested as a promising therapeutic strategy to treat EMT-controlled cancer metastasis. This study aimed to evaluate the effect of the CK2 inhibitor CX-4945 on the processes of cancer migration and invasion during the EMT in A549 human lung adenocarcinoma cells. Materials and Methods The effect of CX-4945 on TGF-β1-induced EMT was evaluated in A549 cells treated with TGF-β1 (5 ng/ml) and CX-4945. The effect of CX-4945 on TGF-β1-induced cadherin switch and activation of key signaling molecules involved in Smad, non-Smad, Wnt and focal adhesion signaling pathways were investigated by Western blot analysis, immunocytochemistry and reporter assay. Additionally, the effect of CX-4945 on TGF-β1-induced migration and invasion was investigated by wound healing assay, Boyden chamber assay, gelatin zymography, and the quantitative real-time PCR. Results CX-4945 inhibits the TGF-β1-induced cadherin switch and the activation of key signaling molecules involved in Smad (Smad2/3, Twist and Snail), non-Smad (Akt and Erk), Wnt (β-catenin) and focal adhesion signaling pathways (FAK, Src and paxillin) that cooperatively regulate the overall process of EMT. As a result, CX-4945 inhibits the migration and invasion of A549 cells accompanied with the downregulation of MMP-2 and 9. Conclusions Clinical evaluation of CX-4945 in humans as a single agent in solid tumors and multiple myeloma has established its promising pharmacokinetic, pharmacodynamic, and safety profiles. Beyond regression of tumor mass, CX-4945 may be advanced as a new therapy for cancer metastasis and EMT-related disorders.
Paracrine Effects of Bone Marrow Mononuclear Cells in Survival and Cytokine Expression after 90% Partial Hepatectomy

Acute liver failure is a complex and fatal disease. Cell-based therapies are a promising alternative therapeutic approach for liver failure due to relatively simple technique and lower cost. The use of semipermeable microcapsules has become an interesting tool for evaluating paracrine effects in vivo. In this study, we aimed to assess the paracrine effects of bone marrow mononuclear cells (BMMC) encapsulated in sodium alginate to treat acute liver failure in an animal model of 90% partial hepatectomy (90% PH). Encapsulated BMMC were able to increase 10-day survival without enhancing liver regeneration markers. Gene expression of Il-6 and Il-10 in the remnant liver was markedly reduced at 6 h after 90% PH in animals receiving encapsulated BMMC compared to controls. This difference, however, was neither reflected by changes in the number of CD68+ cells nor by serum levels of IL6. On the other hand, treated animals presented increased caspase activity and gene expression in the liver. Taken together, these results suggest that BMMC regulate immune response and promote apoptosis in the liver after 90% PH by paracrine factors. These changes ultimately may be related to the higher survival observed in treated animals, suggesting that BMMC may be a promising alternative to treat acute liver failure.
Characterization of protein import channel-forming proteins in chloroplasts

Most chloroplast proteins are encoded for in the nucleus and have to be transported into the organelle after translation in the cytoplasm. The TOC and TIC machineries (Translocon at the Outer/Inner envelope membrane of Chloroplasts) mediate the import of these proteins across the chloroplast membranes. The major aim of this work was to characterize two TIC translocon components: Tic110, the main protein translocation channel in the inner envelope, and Tic20, which was proposed to also form a protein import channel. After a detailed study of Tic110, a topological model could be established, demonstrating that the protein is inserted into the membrane with two hydrophobic and four amphipathic helices, placing residues both to the intermembrane space and to the stromal side. The presence of highly conserved cysteine residues and experiments demonstrating that Tic110 possess a redox active disulfide bridge, which could be reduced by stromal thioredoxins in vitro, indicated that Tic110 might be a possible target for thioredoxin regulation. To explore which cysteines are involved in disulfide bridge formation, mutations were generated for conserved cysteines in Tic110. As a result, Cys492 and Cys890 were identified as possible candidates. To define the functional role of disulfide bridge(s), components of the TIC motor complex were overexpressed and purified and their interaction was analysed with Tic110 via different approaches. The second part of this work focuses on the channel activity of Tic20. Although both Tic110 and Tic20 are clearly important for plant viability and preprotein translocation, there were neither electrophysiological nor biochemical data supporting that Tic20 can form a channel. After inserting the heterologously overexpressed and purified protein into liposomes, swelling assays and electrophysiological measurements provided the first experimental evidence for the channel activity of Tic20, being a cation selective channel with a pore size of about 8-14 A. Therefore, it was concluded that the TIC translocon consists of at least two distinct translocation channels: Firstly, Tic110 forms the main translocation pore and therefore facilitates import of most of the chloroplast-targeted preproteins. Secondly, Tic20 might be specifically required for the translocation of some possibly essential proteins. To gain further insight into the structure and function of both proteins, preliminary tests were performed for crystallization in lipidic phases. The large sample of grown crystals observed under different conditions will presumably enable to crystallize these proteins and resolve their crystal structures in the future.
Generalized Fault Trees: from reliability to security

Fault Trees (FT) are widespread models in the reliability ﬁeld, but they lack of modelling power. So, in the literature, several extensions have been proposed and introduced speciﬁc new modelling primitives. Attack Trees (AT) have gained acceptance in the ﬁeld of security. They follow the same notation of standard FT, but they represent the combinations of actions necessary for the success of an attack to a computing system. In this paper, we extend the AT formalism by exploiting the new primitives introduced in speciﬁc FT extensions. This leads to more accurate models. The approach is applied to a case study: the AT is exploited to represent the attack mode and compute speciﬁc quantitative measures about the system security.
Identifying Liver Cancer-Related Enhancer SNPs by Integrating GWAS and Histone Modification ChIP-seq Data

Many disease-related single nucleotide polymorphisms (SNPs) have been inferred from genome-wide association studies (GWAS) in recent years. Numerous studies have shown that some SNPs located in protein-coding regions are associated with numerous diseases by affecting gene expression. However, in noncoding regions, the mechanism of how SNPs contribute to disease susceptibility remains unclear. Enhancer elements are functional segments of DNA located in noncoding regions that play an important role in regulating gene expression. The SNPs located in enhancer elements may affect gene expression and lead to disease. We presented a method for identifying liver cancer-related enhancer SNPs through integrating GWAS and histone modification ChIP-seq data. We identified 22 liver cancer-related enhancer SNPs, 9 of which were regulatory SNPs involved in distal transcriptional regulation. The results highlight that these enhancer SNPs may play important roles in liver cancer.
A GPU based trafficparallel simulation module of artificial transportation systems

Traffic micro-simulation is an important tool in the Intelligent Transportation Systems (ITS) research. In the microsimulation, a bottom up system can be built up by the interactions of vehicle agents, road agents, traffic lights agents, etc. The Artificial societies, Computational experiments, and Parallel execution (ACP) approach suggests integrating other metropolitan systems such as logistic, infrastructure, legal and regulatory, weather and environmental systems to build an Artificial Transportation System (ATS) to help solve ITS problems. This is reasonable as the transportation system is complex that is affected by many systems interacting with each other. However, there is a challenge that the computing burden can be very heavy as there can be many agents of different kinds interacting in parallel in ATS. In recent years, the Graphics Processing Units (GPUs) have been applied successfully in many areas for parallel computing. Compared with the traditional CPU cluster, GPU has an obvious advantage of low cost of hardware and electricity consumption. In this paper, we build a parallel traffic simulation module of ATS with GPU. The simulation results are reasonable and a maximum speedup factor of 105 is obtained compared with the CPU implementations.
A reduction in Drp1-mediated fission compromises mitochondrial health in autosomal recessive spastic ataxia of Charlevoix Saguenay

The neurodegenerative disease autosomal recessive spastic ataxia of Charlevoix Saguenay (ARSACS) is caused by loss of function of sacsin, a modular protein that is required for normal mitochondrial network organization. To further understand cellular consequences of loss of sacsin, we performed microarray analyses in sacsin knockdown cells and ARSACS patient fibroblasts. This identified altered transcript levels for oxidative phosphorylation and oxidative stress genes. These changes in mitochondrial gene networks were validated by quantitative reverse transcription PCR. Functional impairment of oxidative phosphorylation was then demonstrated by comparison of mitochondria bioenergetics through extracellular flux analyses. Moreover, staining with the mitochondrial-specific fluorescent probe MitoSox suggested increased levels of superoxide in patient cells with reduced levels of sacsin. Key to maintaining mitochondrial health is mitochondrial fission, which facilitates the dynamic exchange of mitochondrial components and separates damaged parts of the mitochondrial network for selective elimination by mitophagy. Fission is dependent on dynamin-related protein 1 (Drp1), which is recruited to prospective sites of division where it mediates scission. In sacsin knockdown cells and ARSACS fibroblasts, we observed a decreased incidence of mitochondrial associated Drp1 foci. This phenotype persists even when fission is induced by drug treatment. Mitochondrial-associated Drp1 foci are also smaller in sacsin knockdown cells and ARSACS fibroblasts. These data suggest a model for ARSACS where neurons with reduced levels of sacsin are compromised in their ability to recruit or retain Drp1 at the mitochondrial membrane leading to a decline in mitochondrial health, potentially through impaired mitochondrial quality control.