Miracle-dz/UniFAR-FTUs huggingface dataset:
Elastic–plastic transition in three-dimensional random materials: massively parallel simulations, fractal morphogenesis and scaling functions

Elastic–plastic transitions were investigated in three-dimensional (3D) macroscopically homogeneous materials, with microscale randomness in constitutive properties, subjected to monotonically increasing, macroscopically uniform loadings. The materials are cubic-shaped domains (of up to 100 × 100 × 100 grains), each grain being cubic-shaped, homogeneous, isotropic and exhibiting elastic–plastic hardening with a J 2 flow rule. The spatial assignment of the grains’ elastic moduli and/or plastic properties is a strict-white-noise random field. Using massively parallel simulations, we find the set of plastic grains to grow in a partially space-filling fractal pattern with the fractal dimension reaching 3, whereby the sharp kink in the stress–strain curve of individual grains is replaced by a smooth transition in the macroscopically effective stress–strain curve. The randomness in material yield limits is found to have a stronger effect than that in elastic moduli. The elastic–plastic transitions in 3D simulations are observed to progress faster than those in 2D models. By analogy to the scaling analysis of phase transitions in condensed matter physics, we recognize the fully plastic state as a critical point and, upon defining three order parameters (the ‘reduced von-Mises stress’, ‘reduced plastic volume fraction’ and ‘reduced fractal dimension’), three scaling functions are introduced to unify the responses of different materials. The critical exponents are universal regardless of the randomness in various constitutive properties and their random noise levels.
Ion imprinted beads embedded cryogels for in vitro removal of iron from β‐thalassemic human plasma

Molecular recognition based Fe3+ imprinted poly(GMA-MAC) (MIP) beads embedded PHEMA composite cryogel was prepared for selective removal of Fe3+ ions from β-thalassemia patient plasma. The precomplexation was achieved by the coordination of Fe3+ ions with N-methacryloyl-(L)-cysteine methyl ester (MAC-Fe3+). MIP beads were prepared by dispersion polymerization in the presence of MAC-Fe3+ complex and glycidyl methacrylate (GMA) monomer. Then the MIP beads were embedded into poly(hydroxyethyl methacrylate) (PHEMA) cryogel. The specific surface area and the swelling degree of the PHEMA-MIP composite cryogel were found to be 76.8 m2/g and 7.7 g H2O/g cryogel, respectively. The maximum adsorption amount of Fe3+ ions was 2.23 mg/g. The relative selectivity of PHEMA-MIP composite cryogel towards the Fe3+ ions was 135.0, 61.4, and 57.0 times greater than that of the PHEMA-NIP cryogel as compared with the Ni2+, Zn2+, and Fe2+ ions, respectively. PHEMA-MIP composite cryogel was recovered and reused many times without any significant decrease in its adsorption capacity. © 2011 Wiley Periodicals, Inc. J Appl Polym Sci, 2012
Chaperone‐rich tumor cell lysate‐mediated activation of antigen‐presenting cells resists regulatory T cell suppression

CD4+CD25+ regulatory T lymphocytes (Tregs) critically contribute to the mechanisms of cancer‐induced tolerance. These cells suppress anti‐tumoral CD8+ and CD4+ T lymphocytes and can also restrain the function of APCs. We have previously documented the immunostimulatory effects of a chaperone‐rich cell lysate (CRCL) anti‐cancer vaccine. Tumor‐derived CRCL induces tumor immunity in vivo, partly by promoting dendritic cell (DC) and macrophage activation. In the current study, we evaluated the effects of CD4+CD25+forkhead box P3+ Tregs isolated from mice bearing 12B1 bcr‐abl+ leukemia on DC and macrophages that had been activated by 12B1‐derived CRCL. CRCL‐activated DC and macrophages resisted Treg suppression, as the production of proinflammatory cytokines, the activation of transcription factor NF‐κB, and their immunostimulatory potential was unaffected by Tregs. Our results thus highlight CRCL as a powerful adjuvant endowed with the capacity to overcome tumor‐induced Treg‐inhibitory effects on APCs.
Interactive Simulation of Deformable Bodies on GPUs

We present a mass-spring system for interactive simulation of deformable bodies. For the amount of springs we target, numerical time integration of spring displacements needs to be accelerated and the transfer of displaced point positions for rendering must be avoided. To fulfill these requirements, we exploit features of recent graphics accelerators to simulate spring elongation and compression in the graphics processing unit (GPU), saving displaced point masses in graphics memory, and then sending these positions through the GPU again to render the deformed body. This approach allows for interactive simulation and rendering of about one hundred thousand elements and it enables the display of internal properties of the deformed body. To further increase the physical realism of this simulation, we have integrated volume preservation and additional physics based constraints into the GPU mass-spring system.
Plastic optical fibres (POF) in sensing: current status and prospects (Invited Paper)

POF has found wide use in multimode intensity-based sensor applications. The characteristics of POF, limit the link (sensor)length to a few tens of meters and the sensor operational temperature cannot exceed 80°C. However, when these limitations are not important, POF sensors can offer their most significant advantage over corresponding glass fibre sensors, and this is a significantly lower system cost. Following recent new developments in POF technology, such as fibre gratings and microstructured POF, one looks forward to new and more exciting POF sensor applications. The future of POF sensors is concluded as optimistic.
DB-OLS: An Approach for IDS

An intrusion detection system plays a major role in network security. We propose a model “DB-OLS: An Approach for IDS” which is a Deviation Based-Outlier approach for Intrusion detection using Self Organizing Maps. In this model “Self Organizing Map” approach is to be used for behavior learning and “Outlier mining” approach, for detecting an intruder by calculating deviation from known user profile. This model aims to improve the capability of detecting intruders.
Finite volume effects in thermal field theory

We analyze the effect of a finite volume on the thermodynamic potentials of a relativistic quantum field theory defined on a hypertorus at vanishing chemical potential. Using the symmetries of the Euclidean partition function, we interpret the thermodynamic observables as the expectation value of the energy-momentum tensor in the same theory living on a β × L2 volume. In the case where the screening correlation lengths in the thermal system are finite, we obtain a closed formula for the leading finite volume effects in terms of the smallest screening mass. This formula can be used to estimate, and possibly correct for, the leading finite volume effects in lattice calculations of QCD thermodynamics.
Implications of trust, fear, and reciprocity for modeling economic behavior

This paper reports three experiments with triadic or dyadic designs. The experiments include the moonlighting game in which first-mover actions can elicit positively or negatively reciprocal reactions from second movers. First movers can be motivated by trust in positive reciprocity or fear of negative reciprocity, in addition to unconditional other-regarding preferences. Second movers can be motivated by unconditional other-regarding preferences as well as positive or negative reciprocity. The experimental designs include control treatments that discriminate among actions with alternative motivations. Data from our three experiments and a fourth one are used to explore methodological questions, including the effects on behavioral hypothesis tests of within-subjects vs. across-subjects designs, single-blind vs. double-blind payoffs, random vs. dictator first-mover control treatments, and strategy responses vs. sequential play.
NTPT: On the end-to-end traffic prediction in the on-chip networks

Power and thermal distribution are critical issues in chip multiprocessors (CMPs). Most previous studies focus on cores and on-chip memory subsystems and discuss how to reduce their power and control thermal distribution by using dynamic voltage/frequency scaling. However, the on-chip interconnection network, or network-on-chip (NoC), is also an important source of power consumption and heat generation. Particularly, the traffic flowing through the NoC affects directly its power and thermal distribution. Unfortunately, very few works discuss the dynamism of NoC. A key technique for NoC management is to capture its traffic patterns and predict future behaviors. In this paper, we propose a table-driven predictor called Network Traffic Prediction Table (NTPT) for recording and predicting traffic in NoC. The most unique feature of NTPT is its ability to predict end-to-end traffic, rather than switch-to-switch traffic. Thus, more application behaviors can be captured and monitored. Evaluations on Tilera's TILE64 show that NTPT has very high prediction accuracy. Analyses also show that it incurs a low area overhead and is very feasible.
Patterns of Saccharina latissima Recruitment

The lack of recovery in Norwegian populations of the kelp Saccharina latissima (Linnaeus) C. E. Lane, C. Mayes, Druehl & G. W. Saunders after a large-scale disturbance that occurred sometime between the late 1990s and early 2000s has raised considerable concerns. Kelp forests are areas of high production that serve as habitats for numerous species, and their continued absence may represent the loss of an entire ecosystem. Some S. latissima populations remain as scattered patches within the affected areas, but today, most of the areas are completely devoid of kelp. The question is if natural recolonization by kelp and the reestablishment of the associated ecosystem is possible. Previous studies indicate that a high degree of reproductive synchrony in macrophytes has a positive effect on their potential for dispersal and on the connectivity between populations, but little is known about the patterns of recruitment in Norwegian S. latissima. More is, however, known about the development of fertile tissue (sori) on adult individuals, which is easily observed. The present study investigated the degree of coupling between the appearance of sori and the recruitment on clean artificial substrate beneath adult specimens. The pattern of recruitment was linked to the retreat of visible sori (i.e. spore release) and a seasonal component unrelated to the fertility of the adults. The formation and the retreat of visible sori are processes that seem synchronized along the south coast of Norway, and the link between sori development and recruitment may therefore suggest that the potential for S. latissima dispersal is relatively large. These results support the notion that the production and dispersal of viable spores is unlikely to be the bottleneck preventing recolonization in the south of Norway, but studies over larger temporal and spatial scales are still needed to confirm this hypothesis.
Human Action Recognition using Improved Vector of Locally Aggregated Descriptors

Recently, two high-dimensional encoding techniques for human action recognition, namely, Fisher vector (FV) and vector of locally aggregated descriptors (VLAD), are widely employed. In this study, a new human action recognition approach using improved VLAD with localized soft assignment (LSA) and second-order statistics is proposed. When encoding videos into VLAD, instead of considering only the nearest one, we utilize localized soft assignment, i.e., considering multiple nearest visual words. In general, LSA-VLAD captures only the first-order statistics of descriptors and visual words. In this study, LSA and second-order statistics are encoded into VLADlike form, namely, LSA2-VLAD. Based on the experimental results obtained in this study, in terms of average accuracy, the performance of the proposed approach combining LSA-VLAD and LSA2-VLAD is better than those of 10 comparison approaches.
Soil-Water Characteristics of Saline Soil in Northwest China

Geotechnical engineers have become increasingly aware of salt damages caused by water-salt migration.The soil water characteristic curve (SWCC) is a very important tool for determining the engineering properties of unsaturated soil. Using pressure plate extractors, This paper carried out a research on soil-water characteristics of saline soil in northwest China. Then, The relationship between matrix suction and water content was analyzed, the unsaturated hydraulic conductivity in different water content was calculated through predicting model of Van Genuchten(1980). Based on the measurement and calculation, the correlation between unsaturated hydraulic conductivity and water content was established. Research results show that unsaturated hydraulic conductivity of saline soil decreases in non-linear trend with the water content reducing, while it decline linearly by a certain specific rate with the matrix suction increasing at a high-suction section (100kpa ~ 100000kpa) in double logarithmic coordinates.
Software Support for Atomicity and Persistence in Non-volatile Memory

Advances in memory technology are promising the availability of byte-addressable persistent memory as an integral component of future computing platforms. This change has significant implications for software that has traditionally made a sharp distinction between durable and volatile storage. In this paper we describe a software framework for persistent memory that provides atomicity and durability while simultaneously ensuring that fast paths through the cache, DRAM, and persistent memory layers are not slowed down.
Three Dimensional Forming Simulation of the Shielded Slot Plate for the MCFC Using a Ductile Fracture Criterion

The shielded slot plate, which has a sheared corrugated trapezoidal pattern, is a component of the metallic bipolar plate for the molten carbonate fuel cell (MCFC). In order to increase the efficiency of the fuel cell, the unit cell of the shielded slot plate should have a relatively large upper area. Additionally, defects from the forming process should be minimized. In order to simulate the slitting process, whereby sheared corrugated patterns are formed, ductile fracture criteria based on the histories of stress and strain are employed. The user material subroutine VUMAT is employed for implementation of the material and ductile fracture criteria in the commercial FEM software ABAQUS. The variables of the ductile fracture criteria were determined by comparing the simulation results and the experimental results of the tension test and the shearing test. Parametric studies were conducted to determine the critical value of the ductile fracture criterion. Employing these ductile fracture criteria, the thre.
The Crystal Structure and RNA-Binding of an Orthomyxovirus Nucleoprotein

Genome packaging for viruses with segmented genomes is often a complex problem. This is particularly true for influenza viruses and other orthomyxoviruses, whose genome consists of multiple negative-sense RNAs encapsidated as ribonucleoprotein (RNP) complexes. To better understand the structural features of orthomyxovirus RNPs that allow them to be packaged, we determined the crystal structure of the nucleoprotein (NP) of a fish orthomyxovirus, the infectious salmon anemia virus (ISAV) (genus Isavirus). As the major protein component of the RNPs, ISAV-NP possesses a bi-lobular structure similar to the influenza virus NP. Because both RNA-free and RNA-bound ISAV NP forms stable dimers in solution, we were able to measure the NP RNA binding affinity as well as the stoichiometry using recombinant proteins and synthetic oligos. Our RNA binding analysis revealed that each ISAV-NP binds ∼12 nts of RNA, shorter than the 24–28 nts originally estimated for the influenza A virus NP based on population average. The 12-nt stoichiometry was further confirmed by results from electron microscopy and dynamic light scattering. Considering that RNPs of ISAV and the influenza viruses have similar morphologies and dimensions, our findings suggest that NP-free RNA may exist on orthomyxovirus RNPs, and selective RNP packaging may be accomplished through direct RNA-RNA interactions.
Optimal variational perturbations for the inference of stochastic reaction dynamics

Although single-cell techniques are advancing rapidly, quantitative assessment of kinetic parameters is still characterized by ill-posedness and a large degree of uncertainty. In many standard experiments, where transcriptional activation is recorded upon application of a step-like external perturbation, cells almost instantaneously adapt such that only a few informative measurements can be obtained. Consequently, the information gain between subsequent experiments or time points is comparably low, which is reflected in a hardly decreasing parameter uncertainty. However, novel microfluidic techniques can be applied to synthesize more sophisticated perturbations to increase the informativeness of such time-course experiments. Here we introduce a mathematical framework to design optimal perturbations for the inference of stochastic reaction dynamics. Based on Bayesian statistics, we formulate a variational problem to find optimal temporal perturbations and solve it using a stochastic approximation algorithm. Simulations are provided for the realistic scenario of noisy and discrete-time measurements using two simple reaction networks.
Data-Driven High-Throughput Prediction of the 3-D Structure of Small Molecules: Review and Progress

Accurate prediction of the 3-D structure of small molecules is essential in order to understand their physical, chemical, and biological properties, including how they interact with other molecules. Here, we survey the field of high-throughput methods for 3-D structure prediction and set up new target specifications for the next generation of methods. We then introduce COSMOS, a novel data-driven prediction method that utilizes libraries of fragment and torsion angle parameters. We illustrate COSMOS using parameters extracted from the Cambridge Structural Database (CSD) by analyzing their distribution and then evaluating the system's performance in terms of speed, coverage, and accuracy. Results show that COSMOS represents a significant improvement when compared to state-of-the-art prediction methods, particularly in terms of coverage of complex molecular structures, including metal-organics. COSMOS can predict structures for 96.4% of the molecules in the CSD (99.6% organic, 94.6% metal-organic), whereas the widely used commercial method CORINA predicts structures for 68.5% (98.5% organic, 51.6% metal-organic). On the common subset of molecules predicted by both methods, COSMOS makes predictions with an average speed per molecule of 0.15 s (0.10 s organic, 0.21 s metal-organic) and an average rmsd of 1.57 Å (1.26 Å organic, 1.90 Å metal-organic), and CORINA makes predictions with an average speed per molecule of 0.13s (0.18s organic, 0.08s metal-organic) and an average rmsd of 1.60 Å (1.13 Å organic, 2.11 Å metal-organic). COSMOS is available through the ChemDB chemoinformatics Web portal at http://cdb.ics. uci.edu/ .
Nonlinear droop charging control of a supercapacitor with a bi-directional hybrid DC-DC converter

In microgrid systems, a high power density storage unit is needed in order to take quick bursts of power provided by the renewable sources. A supercapacitor (SC) is ideal for this purpose therefore a charge/discharge regulation is needed for the energy management system. This paper presents a novel nonlinear droop control strategy used for this purpose. Usually, droop control is implemented as a load sharing scheme, but in this case it will be used to do the opposite and it will command the charge/discharge of the SC only when it is required by the grid. Also, the converter-supercapacitor unit (CSU) will have the advantage of being independently controlled therefore the autonomous characteristic of the microgrid is preserved. The converter used for this task is a bi-directional hybrid DC-DC topology (HBDC) with a high voltage conversion ratio, which connects the SC to a DC microgrid. The converter high voltage conversion ratio is helpful in order to use an extended range of the SC energy storage capacity.
Investigation on nonlinear dynamics of ZnO using time-resolved pump-probe technique with phase object

The nonlinear absorptive and refractive dynamics of semiconductor zinc oxide (ZnO) are investigated using a modified time-resolved pump-probe system with phase object performed at 532 nm on picosecond timescale. The measurement method is based on method with a phase object for measurement of optical nonlinearities and standard time-resolved pump-probe system. The sample's nonlinear optical properties can be determined by measuring the normalized transmittance with/without an aperture in the far field. The experimental results show that the nonlinear response of ZnO is a combination of bound-electronic and free-carrier nonlinearities mechanism. With the theory of two-photon induced free-carrier nonlinearity, we fitted the experimental results and the nonlinear parameters of ZnO, such as two-photon absorption coefficient β, two-photon induced free-carrier absorption cross sectionσ and life time of the free-carrier τr are obtained.
Loss of estrogen-related receptor α promotes hepatocarcinogenesis development via metabolic and inflammatory disturbances

Significance This study shows that absence of the orphan nuclear receptor estrogen-related receptor α (ERRα), a master regulator of cellular energy metabolism, predisposes mice to hepatocellular cancer development when exposed to a known carcinogen. Biochemical and metabolomics studies revealed that loss of ERRα promotes hepatocyte necrosis over apoptosis in response to a carcinogen due to a deficiency in energy production. In addition, we demonstrate that loss of ERRα-dependent regulation of the nuclear factor κB (NF-κB) inhibitor IκBα leads to enhanced NF-κB activity and cytokine gene activation. These findings have particular biological significance in view that rapamycin, a drug currently in use in various clinical settings, has been shown recently to decrease ERRα protein levels and activity in mouse liver. Estrogen-related receptor α (ERRα) is a key regulator of mitochondrial function and metabolism essential for energy-driven cellular processes in both normal and cancer cells. ERRα has also been shown to mediate bone-derived macrophage activation by proinflammatory cytokines. However, the role of ERRα in cancer in which inflammation acts as a tumor promoter has yet to be investigated. Herein we show that global loss of ERRα accelerates the development of diethylnitrosamine (DEN)-induced hepatocellular carcinoma. Biochemical and metabolomics studies revealed that loss of ERRα promotes hepatocyte necrosis over apoptosis in response to DEN due to a deficiency in energy production. We further show that increased hepatocyte death and associated compensatory proliferation observed in DEN-injured ERRα-null livers is concomitant with increased nuclear factor κB (NF-κB)–dependent transcriptional control of cytokine expression in Kupffer cells. In particular, we demonstrate that loss of ERRα-dependent regulation of the NF-κB inhibitor IκBα leads to enhanced NF-κB activity and cytokine gene activation. Our work thus shows that global loss of ERRα activity promotes hepatocellular carcinoma by independent but synergistic mechanisms in hepatocytes and Kupffer cells, implying that pharmacological manipulation of ERRα activity may have a significant clinical impact on carcinogen-induced cancers.