Matrix Configurations Research Articles

A fast and unbiased procedure to randomize ecological binary matrices with fixed row and column totals.

A well-known problem in numerical ecology is how to recombine presence-absence matrices without altering row and column totals. A few solutions have been proposed, but all of them present some issues in terms of statistical robustness (that is, their capability to generate different matrix configurations with the same probability) and their performance (that is, the computational effort that they require to generate a null matrix). Here we introduce the 'Curveball algorithm', a new procedure that differs from existing methods in that it focuses rather on matrix information content than on matrix structure. We demonstrate that the algorithm can sample uniformly the set of all possible matrix configurations requiring a computational effort orders of magnitude lower than that required by available methods, making it possible to easily randomize matrices larger than 10(8) cells.

The use of bi-layer silk fibroin scaffolds and small intestinal submucosa matrices to support bladder tissue regeneration in a rat model of spinal cord injury

Adverse side-effects associated with enterocystoplasty for neurogenic bladder reconstruction have spawned the need for the development of alternative graft substitutes. Bi-layer silk fibroin (SF) scaffolds and small intestinal submucosa (SIS) matrices were investigated for their ability to support bladder tissue regeneration and function in a rat model of spinal cord injury (SCI). Bladder augmentation was performed with each scaffold configuration in SCI animals for 10 wk of implantation and compared to non-augmented control groups (normal and SCI alone). Animals subjected to SCI alone exhibited a 72% survival rate (13/18) while SCI rats receiving SIS and bi-layer SF scaffolds displayed respective survival rates of 83% (10/12) and 75% (9/12) over the course of the study period. Histological (Masson's trichrome analysis) and immunohistochemical (IHC) evaluations demonstrated both implant groups supported de novo formation of smooth muscle layers with contractile protein expression [α-smooth muscle actin (α-SMA) and SM22α] as well as maturation of multi-layer urothelia expressing cytokeratin (CK) and uroplakin 3A proteins. Histomorphometric analysis revealed bi-layer SF and SIS scaffolds respectively reconstituted 64% and 56% of the level of α-SMA+ smooth muscle bundles present in SCI-alone controls, while similar degrees of CK+ urothelium across all experimental groups were detected. Parallel evaluations showed similar degrees of vascular area and synaptophysin+ boutons in all regenerated tissues compared to SCI-alone controls. In addition, improvements in certain urodynamic parameters in SCI animals, such as decreased peak intravesical pressure, following implantation with both matrix configurations were also observed. The data presented in this study detail the ability of acellular SIS and bi-layer SF scaffolds to support formation of innervated, vascularized smooth muscle and urothelial tissues in a neurogenic bladder model.

An e-Learning Collaborative Filtering Approach to Suggest Problems to Solve in Programming Online Judges

The paper proposes a recommender system approach to cover online judge's domains. Online judges are e-learning tools that support the automatic evaluation of programming tasks done by individual users, and for this reason they are usually used for training students in programming contest and for supporting basic programming teachings. The proposal pretends to suggest problems assuming that a user must try to solve those problems already successfully solved by similar users. With this goal, the authors adopt the traditional collaborative filtering method with a new similarity measure adapted to the current domain, and the authors propose several transformations in the user-problem matrix to incorporate specific online judge's information. The authors evaluate the effect of the matrix configurations using Precision and Recall metrics, getting better results comparing with the authors method without transformations and with a representative state-of-art approach. Finally, the authors outline possible extensions to the current work.

FUZZY GESTURES RECOGNITION METHOD IN DEVELOPMENT OF CONTACTLESS INTERFACES

The article discusses the gesture recognition system based on head distributed multiagent network. A model of head movement in 3D space. Head position described by the matrix configurations. Developed a method of recognition of fuzzy gestures, based on recognition of the graph constructed on the basis of fuzzy nodes. Graph is generated for each dynamic gesture, perfect head. It is shown that the recognition process can be performed by a fuzzy neural network. Software agents implement recognition system. Presented work distributed recognition system in real time.

Gradient generation platforms: new directions for an established microfluidic technology

Microscale platforms are enabling for cell-based studies as they allow the recapitulation of physiological conditions such as extracellular matrix (ECM) configurations and soluble factors interactions. Gradient generation platforms have been one of the few applications of microfluidics that have begun to be translated to biological laboratories and may become a new "gold standard". Though gradient generation platforms are now established, their full potential has not yet been realized. Here, we will provide our perspective on milestones achieved in the development of gradient generation and cell migration platforms, as well as emerging directions such as using cell migration as a diagnostic readout and attaining mechanistic information from cell migration models.

Probability distribution over some phenomenological models in the matrix model compactified on a torus

We study some phenomenological models in a matrix model corresponding to the IIB matrix model compactified on a six-dimensional torus with magnetic fluxes. Extending our previous works, we examine a wider class of models: a Pati–Salam-like model with a gauge group U(4)×UL(2)×UR(2), and models where the gauge group U(4) is broken down to Uc(3)×U(1) and/or UR(2) is broken down to |${\mathrm {U}}(1)^2$|⁠. We find all the matrix configurations that yield matter content of all the phenomenological models whose gauge group is a subgroup of U(8). We then estimate semiclassically a probability distribution for the appearance of the phenomenological models.

Bladder tissue regeneration using acellular bi-layer silk scaffolds in a large animal model of augmentation cystoplasty

Acellular scaffolds derived from Bombyx mori silk fibroin were investigated for their ability to support functional tissue regeneration in a porcine model of augmentation cystoplasty. Two bi-layer matrix configurations were fabricated by solvent-casting/salt leaching either alone (Group 1) or in combination with silk film casting (Group 2) to yield porous foams buttressed by heterogeneous surface pore occlusions or homogenous silk films, respectively. Bladder augmentation was performed with each scaffold group (6 × 6 cm2) in juvenile Yorkshire swine for 3 m of implantation. Augmented animals exhibited high rates of survival (Group 1: 5/6, 83%; Group 2: 4/4, 100%) and voluntary voiding over the course of the study period. Urodynamic evaluations demonstrated mean increases in bladder capacity over pre-operative levels (Group 1: 277%; Group 2: 153%) which exceeded nonsurgical control gains (144%) encountered due to animal growth. Similarly, elevations in bladder compliance were substantially higher in augmented animals from baseline (Group 1: 357%; Group 2: 147%) in comparison to controls (41%). Gross tissue evaluations revealed that both matrix configurations supported extensive de novo tissue formation throughout the entire original implantation site which exhibited ultimate tensile strength similar to nonsurgical counterparts. Histological and immunohistochemical analyses showed that both implant groups promoted comparable extents of smooth muscle regeneration and contractile protein (α-smooth muscle actin and SM22α) expression within defect sites similar to controls. Parallel evaluations demonstrated the formation of a transitional, multi-layered urothelium with prominent cytokeratin, uroplakin, and p63 protein expression in both matrix groups. De novo innervation and vascularization processes were evident in all regenerated tissues indicated by synaptophysin-positive neuronal cells and vessels lined with CD31 expressing endothelial cells. Ex vivo organ bath studies demonstrated that regenerated tissues supported by both silk matrices displayed contractile responses to carbachol, α,β-methylene-ATP, KCl, and electrical field stimulation similar to controls. Our data detail the ability of acellular silk scaffolds to support regeneration of innervated, vascularized smooth muscle and urothelial tissues within 3 m with structural, mechanical, and functional properties comparable to native tissue in a porcine model of bladder repair.

Real Time “2CRT” Architecture and Platform for the Experimentation of Telecommunication Terminals According to the Manhattan Mobility

In the field of technology the verification of the robustness of a system is very important. This system verification compares the actual with the origin bearing in mind that any anomaly could lead to a catastrophe. The control could be in different forms: either measure, or test the first control is done to measure the physical parameters in order to confirm system reliability as it is the case of « 2CRM » (Connection, Control, Recognition and Measure) [1]. The second control enables a remote experimentation to certify credibility of the terminal. Our article presents a new architecture of control « 2CRT » (Connection, Control, Recognition and Test). Its newness is based on the distribution of actions as it is based on multi-agent systems. The control is done remotely via the web using Real Time constraints. It meets to the functionalities of distribution, cooperation and adaptation to the changes in user behavior, environments and materials. Notably, the approach includes the test control mode of telecommunication terminals. The solution is based upon the Manhattan mobility with the possibility of integrating other topologies. This experimentation is done via the web by matrix configurations using FIFO (First In First Out) data structures. To further embody our architecture, we perfected it in the OpenAirInterface project of the Eurecom laboratory in France. Our control platform was developed using the unified process « RUP » (Rational Unified Process) [2] with the use of the UML modelization to well illustrate the system. It is implemented by an open source distribution (Java and J2ee running on Eclipse).

Probability of the standard model appearance from a matrix model

The standard model of particle physics lies in an enormous number of string vacua. In a nonperturbative formulation of string theory, various string vacua can, in principle, be compared dynamically, and the probability distribution over the vacuum space could be calculated. In this paper, we consider situations where the IIB matrix model is compactified on a six-dimensional torus with various gauge groups and various magnetic fluxes, find matrix configurations that provide the standard model matter content, and estimate semiclassically the probability of their appearance.

Particle-tracking simulations of anomalous transport in hierarchically fractured rocks

Complex topology of fracture networks and interactions between transport processes in a fracture and the ambient un-fractured rock (matrix) combine to render modeling solute transport in fractured media a challenge. Classical approaches rely on both strong assumptions of either limited or full diffusion of solutes in the matrix and simplified fracture configurations. We analyze fracture-matrix transport in two-dimensional Sierpinski lattice structures, which display a wide range of matrix block sizes. The analysis is conducted in several transport regimes that are limited by either diffusion or block sizes. Our simulation results can be used to validate the simplifying assumptions that underpin classical analytical solutions and to benchmark other numerical methods. They also demonstrate that both hydraulic and structural properties of fractured rocks control the residence time distribution.

RF MEMS ohmic switches for matrix configurations

Two different topologies of radio frequency micro-electro-mechanical system (RF MEMS) series ohmic switches (cantilever and clamped–clamped beams) in coplanar waveguide (CPW) configuration have been characterized by means of DC, environmental, and RF measurements. In particular, on-wafer checks have been followed by RF test after vibration, thermal shocks, and temperature cycles. The devices have been manufactured on high resistivity silicon substrates, as building blocks to be implemented in different single-pole 4-throw (SP4 T), double-pole double-throw (DPDT) configurations, and then integrated in Low Temperature Co-fired Ceramics (LTCC) technology for the realization of large-order Clos 3D networks.

Data driven linear algebraic methods for analysis of molecular pathways: Application to disease progression in shock/trauma

MotivationAlthough trauma is the leading cause of death for those below 45years of age, there is a dearth of information about the temporal behavior of the underlying biological mechanisms in those who survive the initial trauma only to later suffer from syndromes such as multiple organ failure. Levels of serum cytokines potentially affect the clinical outcomes of trauma; understanding how cytokine levels modulate intra-cellular signaling pathways can yield insights into molecular mechanisms of disease progression and help to identify targeted therapies. However, developing such analyses is challenging since it necessitates the integration and interpretation of large amounts of heterogeneous, quantitative and qualitative data. Here we present the Pathway Semantics Algorithm (PSA), an algebraic process of node and edge analyses of evoked biological pathways over time for in silico discovery of biomedical hypotheses, using data from a prospective controlled clinical study of the role of cytokines in multiple organ failure (MOF) at a major US trauma center. A matrix algebra approach was used in both the PSA node and PSA edge analyses with different matrix configurations and computations based on the biomedical questions to be examined. In the edge analysis, a percentage measure of crosstalk called XTALK was also developed to assess cross-pathway interference. ResultsIn the node/molecular analysis of the first 24h from trauma, PSA uncovered seven molecules evoked computationally that differentiated outcomes of MOF or non-MOF (NMOF), of which three molecules had not been previously associated with any shock/trauma syndrome. In the edge/molecular interaction analysis, PSA examined four categories of functional molecular interaction relationships – activation, expression, inhibition, and transcription – and found that the interaction patterns and crosstalk changed over time and outcome. The PSA edge analysis suggests that a diagnosis, prognosis or therapy based on molecular interaction mechanisms may be most effective within a certain time period and for a specific functional relationship.

Evaluation of fly‐ash additive for removal of dissolved organic matter during soil aquifer treatment of wastewater treatment plant Peffluent

AbstractBACKGROUND: Fly‐ash (FA) additive was evaluated for enhanced removal of organic matter during soil aquifer treatment (SAT) of a wastewater treatment plant (WWTP) effluent in five 0.50 m length columns (diameter 0.1 m) in parallel.RESULTS: The characteristic behavior of dissolved organic matter (DOM) was examined for the stratum matrix configurations of both natural soil and a mixture of soil and FA. Incubation and fractionation experiments indicated that FA additive within the SAT columns would enhance the bulk adsorption of hydrophobic fractions, but decrease the biodegradation of the hydrophilic fraction simultaneously. The configuration design of an upper 0.25 m soil layer and a mixture of FA and soil underneath could make use of the functions of both FA adsorption and biodegradation within soil, which could lead to a further fractional removal of dissolved organic carbon (DOC) and trihalomethane formation potential (THMFP). Moreover, FA additive in the SAT columns could result in a significant decrease of tryptophan‐like aromatic proteins and fulvic‐like components (CC and CO related), while the setting of the top 25 cm soil layer would lead to a further reduction of oxygen‐containing functional groups.CONCLUSIONS: Based on the results, FA might serve as a supplementary material for enhancing the reduction of DOM during SAT operation. Copyright © 2010 Society of Chemical Industry

CAPPS: A Framework for Power–Performance Tradeoffs in Bus-Matrix-Based On-Chip Communication Architecture Synthesis

On-chip communication architectures have a significant impact on the power consumption and performance of emerging chip multiprocessor (CMP) applications. However, customization of such architectures for an application requires the exploration of a large design space. Designers need tools to rapidly explore and evaluate relevant communication architecture configurations exhibiting diverse power and performance characteristics. In this paper, we present an automated framework for fast system-level, application-specific, power-performance tradeoffs in a bus matrix communication architecture synthesis (CAPPS). Our study makes two specific contributions. First, we develop energy models for system-level exploration of bus matrix communication architectures. Second, we incorporate these models into a bus matrix synthesis flow that enables designers to efficiently explore the power-performance design space of different bus matrix configurations. Experimental results show that our energy macromodels incur less than 5% average cycle energy error across 180-65 nm technology libraries. Our early system-level power estimation approach also shows a significant speedup ranging from 1000 to 2000× when compared with detailed gate-level power estimation. Furthermore, on applying our synthesis framework to three industrial networking CMP applications, a tradeoff space that exhibits up to 20% variation in power and up to 40% variation in performance is generated, demonstrating the usefulness of our approach.

In vitro engineering of transitional tissue by patterning and functional control of cells in fibrin gel

Tendon insertions show specific three-dimensional (3D) cell and matrix configurations. To fabricate this transitional tissue in vitro, the development of a cell manipulation technique that can control cell and matrix patterning in the 3D construct is crucial. Bone marrow-derived stromal cells and osteoblasts were respectively cultured in fibrin gel using a custom-made device that can apply uniaxial continuous tensile strain to the gel at different strain rates. Cells in the strained fibrin gel showed a specific orientation, which was parallel to the strain direction, because of the structural change of fibrin fibres within the strained gel. The direction of cell proliferation in the strained gel was also restricted to the same direction. Subsequently, linearly aligned cell sets, similar to the cell patterning of tendon tissue, were obtained in this culture system. Notably, linearly aligned extracellular matrix and mineral patterning, which are crucial for the fabrication of tendon insertions, were also confirmed in the strained fibrin gel. A cell proliferation assay indicated that the strained gel with a higher strain rate enhanced cell proliferation in the gel. In contrast, a Real-Time PCR study indicated that the strained gel with a lower strain rate enhanced cell differentiation in the gel. Thus, our new cell culture system enabled us to fabricate a 3D construct containing patterned cells and matrices in a controllable manner. This would be an effective tool for reproducing tendon insertions in vitro.

Dynamic dipolar interaction effect on spin-transfer switching with perpendicular anisotropy

Micromagnetic simulation is employed to study the influence of neighboring cells on spin torque switching in a matrix of nanopillars with perpendicular magnetic anisotropy. We find that with the decreased separation the critical switching current densities can be strongly modified for different matrix configurations as compared to an isolated disk element. Such variations are attributed to the stray fields rather than the resonant effect, although both of them arise from the dipolar interaction between the target and neighboring cells. The Bloch wall mediated switching process is evidenced by the magnetization snapshots, which agrees with the recent experimental results.

状態空間モデルを用いたＪＥＰＸ価格モデリングの基礎検討

Time series models are popular in attempts to model and forecast price dynamics in various markets. In this paper, we have formulated two state space models and tested them for its applicability to power price modeling and forecasting using JEPX (Japan Electric Power eXchange) data. The state space models generally have a high degree of flexibility with its time-dependent state transition matrix and system equation configurations. Based on empirical data analysis and past literatures, we used calculation assumptions to a) extract stochastic trend component to capture non-stationarity, and b) detect structural changes underlying in the market. The stepwise calculation algorithm followed that of Kalman Filter. We then evaluated the two models' forecasting capabilities, in comparison with ordinary AR (autoregressive) and ARCH (autoregressive conditional heteroskedasticity) models. By choosing proper explanatory variables, the latter state space model yielded as good a forecasting capability as that of the AR and the ARCH models for a short forecasting horizon.

Primary culture of rat hepatocytes in 96-well plates: Effects of extracellular matrix configuration on cytochrome P450 enzyme activity and inducibility, and its application in in vitro cytotoxicity screening

Basal level enzyme activities and enzyme inducibility were compared for rat hepatocytes that were cultured in 96-well plates with three different extracellular matrix configurations: single layer (SL) collagen type I, SL Matrigel, and collagen/Matrigel (C/M) sandwich. Overall, C/M sandwich and SL Matrigel plates were both superior to SL collagen type I plates in maintaining enzyme activities and inducibility and C/M sandwich plates had higher induced activity for CYP3A enzymes than SL Matrigel plates did. Cytotoxicity of nine reference compounds to rat hepatocytes (C/M sandwich configuration), rat hepatoma H4IIE and mouse fibroblast Balb/c 3T3 (3T3) cells was evaluated in 96-well plates using neutral red uptake (for 3T3) and tetrazolium salt MTS assays (for H4IIE and rat hepatocytes). For compounds chlorpromazine, quinidine, trichlorfon, thiopental, and antipyrine, the absolute differences in cytotoxicity Log IC 50 values obtained from different cell types were relatively small and without an obvious trend. The Δ Log IC 50 values between cultured hepatocytes and the cell lines were much larger for acetaminophen and cyclophosphamide (1.35 ⩽ ∣Δ Log IC 50∣ ⩽ 3.40), and for clofibrate and thioacetamide (not cytotoxic in hepatocytes at their highest dose levels). These large differences were likely the result of metabolism of these compounds in rat hepatocytes. The relationship between in vitro cytotoxicity Log IC 50 values and in vivo mouse or rat oral acute Log LD 50 values showed that compared to the cell lines, cultured rat hepatocytes improved correlation for acetaminophen and cyclophosphamide. The potential benefit of conducting in vitro cytotoxicity screening using a combination of permanent cell lines and cultured hepatocytes would allow us to obtain mechanistic insight on bioactivation, as well as improve the predictability of metabolism-mediated toxicity.

Diamagnetic Levitation With Permanent Magnets for Contactless Guiding and Trapping of Microdroplets and Particles in Air and Liquids

Diamagnetic levitation was applied to micro-positioning and trapping of diamagnetic micron-sized particles and micro-droplets. Scale reduction laws for magnetism indicate that diamagnetism is highly efficient for magnetic MEMS. We demonstrate here that diamagnetic bodies can be contactless guided along magnetic grooves or trapped in magnetic wells both in air and in liquids. Levitation of water, ethanol and oil microdroplets was achieved within a 1.6 mm bore of a cylindrical magnet and in micromachined bulk magnets. Thick permanent micromagnets were also electroplated above silicon wafers in various matrix configurations. Diamagnetic levitation on micromagnet arrays was tested with 3 mum-large diamagnetic latex beads in a paramagnetic buffered solution. Trapping and arraying of microparticles in stable spatial levitation within magnetic wells were successfully achieved

An Automated BIST Architecture for Testing and Diagnosing FPGA Interconnect Faults

We present an efficient built-in self-test (BIST) architecture for testing and diagnosing stuck-at faults, delay faults, and bridging faults in FPGA interconnect resources. The BIST structure contains self-enabling test pattern generators, self-configurable switch matrices, and response analyzers that all work together and reprogram themselves without any external intervention. This eliminates downloading configuration bitstreams into the FPGA after the start of testing and, hence, reduces test time. Our technique requires only six different switch matrix configurations to test the interconnect, which is fewer than prior methods, while retaining good diagnostic resolution. The area overhead to add self-configurable test structures to Xilinx FPGAs is as low as 0.5%.