Graph Modification Problems: A Modern Perspective

We give an overview of recent results and techniques in parameterized algorithms for graph modification problems.

Query Click and Text Similarity Graph for Query Suggestions

Query suggestion is an important feature of the search engine with the explosive and diverse growth of web contents. Different kind of suggestions like query, image, movies, music and book etc. are used every day. Various types of data sources are used for the suggestions. If we model the data into various kinds of graphs then we can build a general method for any suggestions. In this paper, we have proposed a general method for query suggestion by combining two graphs: (1) query click graph which captures the relationship between queries frequently clicked on common URLs and (2) query text similarity graph which finds the similarity between two queries using Jaccard similarity. The proposed method provides literally as well as semantically relevant queries for users' need. Simulation results show that the proposed algorithm outperforms heat diffusion method by providing more number of relevant queries. It can be used for recommendation tasks like query, image, and product suggestion.

Kinematics and dynamics of Jansen leg mechanism: A bond graph approach

The Jansen mechanism is a one degree-of-freedom, planar, 12-link, leg mechanism that can be used in mobile robotic applications and in gait analysis. This paper presents the kinematics and dynamics of the Jansen leg mechanism. The forward kinematics, accomplished using circle intersection method, determines the trajectories of various points on the mechanism in the chassis (stationary link) reference frame. From the foot point trajectory, the step length is shown to vary linearly while step height varies non-linearly with change in crank radius. A dynamic model for the Jansen leg mechanism is proposed using bond graph approach with modulated multiport transformers. For given ground reaction force pattern and crank angular speed, this model helps determine the motor torque profile as well as the link and joint stresses. The model can therefore be used to rate the actuator torque and in design of the hardware and controller for such a system. The kinematics of the mechanism can also be obtained from this dynamic model. The proposed model is thus a useful tool for analysis and design of systems based on the Jansen leg mechanism. (C) 2015 Elsevier B.V. All rights reserved.

Falcon: A Graph Manipulation Language for Heterogeneous Systems

Graph algorithms have been shown to possess enough parallelism to keep several computing resources busy-even hundreds of cores on a GPU. Unfortunately, tuning their implementation for efficient execution on a particular hardware configuration of heterogeneous systems consisting of multicore CPUs and GPUs is challenging, time consuming, and error prone. To address these issues, we propose a domain-specific language (DSL), Falcon, for implementing graph algorithms that (i) abstracts the hardware, (ii) provides constructs to write explicitly parallel programs at a higher level, and (iii) can work with general algorithms that may change the graph structure (morph algorithms). We illustrate the usage of our DSL to implement local computation algorithms (that do not change the graph structure) and morph algorithms such as Delaunay mesh refinement, survey propagation, and dynamic SSSP on GPU and multicore CPUs. Using a set of benchmark graphs, we illustrate that the generated code performs close to the state-of-the-art hand-tuned implementations.

Temperature-Dependent Photoluminescence of g-C3N4: Implication for Temperature Sensing

We report the temperature-dependent photoluminescence (PL) properties of polymeric graphite-like carbon nitride (g-C3N4) and a methodology for the determination of quantum efficiency along with the activation energy. The PL is shown to originate from three different pathways of transitions: sigma*-LP, pi*-LP, and pi*-pi, respectively. The overall activation energy is found to be similar to 73.58 meV which is much lower than the exciton binding energy reported theoretically but ideal for highly sensitive wide-range temperature sensing. The quantum yield derived from the PL data is 23.3%, whereas the absolute quantum yield is 5.3%. We propose that the temperature-dependent PL can be exploited for the evaluation of the temperature dependency of quantum yield as well as for temperature sensing. Our analysis further indicates that g-C3N4 is well-suited for wide-range temperature sensing.

Fuel-optimal G-MPSP Guidance for Powered Descent Phase of Soft Lunar Landing

A fuel optimal nonlinear sub-optimal guidance scheme is presented in this paper for soft landing of a lunar craft during the powered descent phase. The recently developed Generalized Model Predictive Static Programming (G-MPSP) is used to compute the required magnitude and angle of the thrust vector. Both terminal position and velocity vector are imposed as hard constraints, which ensures high position accuracy and facilitates initiation of vertical descent at the end of the powered descent phase. A key feature of the G-MPSP algorithm is that it converts the nonlinear dynamic programming problem into a low-dimensional static optimization problem (of the same dimension as the output vector). The control history update is done in closed form after computing a time-varying weighting matrix through a backward integration process. This feature makes the algorithm computationally efficient, which makes it suitable for on-board applications. The effectiveness of the proposed guidance algorithm is demonstrated through promising simulation results.

Targeting human telomeric G-quadruplex DNA with curcumin and its synthesized analogues under molecular crowding conditions

The formation of telomeric G-quadruplexes has been shown to inhibit telomerase activity. Indeed, a number of small molecules capable of p-stacking with G-tetrads have shown the ability to inhibit telomerase activity through the stabilization of G-quadruplexes. Curcumin displays a wide spectrum of medicinal properties ranging from anti-bacterial, anti-viral, anti-protozoal, anti-fungal and anti-inflammatory to anti-cancer activity. We have investigated the interactions of curcumin and its structural analogues with the human telomeric sequence AG(3)(T(2)AG(3))(3) under molecular crowding conditions. Experimental studies indicated the existence of a AG(3)(T(2)AG(3))(3)/curcumin complex with binding affinity of 0.72 x 10(6) M-1 under molecular crowding conditions. The results from UV-visible absorption spectroscopy, a fluorescent TO displacement assay, circular dichroism and molecular docking studies, imply that curcumin and their analogues interact with G-quadruplex DNA via groove binding. While other analogs of curcumin studied here bind to G-quadruplexes in a qualitatively similar manner their affinities are relatively lower in comparison to curcumin. The Knoevenagel condensate, a methoxy-benzylidene derivative of curcumin, also exhibited significant binding to G-quadruplex DNA, although with two times decreased affinity. Our study establishes the potential of curcumin as a promising natural product for G-quadruplex specific ligands.

The legacy of G. N. Ramachandran and the development of structural biology in India

G. N. Ramachandran is among the founding fathers of structural molecular biology. He made pioneering contributions in computational biology, modelling and what we now call bioinformatics. The triple helical coiled coil structure of collagen proposed by him forms the basis of much of collagen research at the molecular level. The Ramachandran map remains the simplest descriptor and tool for validation of protein structures. He has left his imprint on almost all aspects of biomolecular conformation. His contributions in the area of theoretical crystallography have been outstanding. His legacy has provided inspiration for the further development of structural biology in India. After a pause, computational biology and bioinformatics are in a resurgent phase. One of the two schools established by Ramachandran pioneered the development of macromolecular crystallography, which has now grown into an important component of modern biological research in India. Macromolecular NMR studies in the country are presently gathering momentum. Structural biology in India is now poised to again approach heights of the kind that Ramachandran conquered more than a generation ago.

Targeting human telomeric G-quadruplex DNA with curcumin and its synthesized analogues under molecular crowding conditions

The formation of telomeric G-quadruplexes has been shown to inhibit telomerase activity. Indeed, a number of small molecules capable of p-stacking with G-tetrads have shown the ability to inhibit telomerase activity through the stabilization of G-quadruplexes. Curcumin displays a wide spectrum of medicinal properties ranging from anti-bacterial, anti-viral, anti-protozoal, anti-fungal and anti-inflammatory to anti-cancer activity. We have investigated the interactions of curcumin and its structural analogues with the human telomeric sequence AG(3)(T(2)AG(3))(3) under molecular crowding conditions. Experimental studies indicated the existence of a AG(3)(T(2)AG(3))(3)/curcumin complex with binding affinity of 0.72 x 10(6) M-1 under molecular crowding conditions. The results from UV-visible absorption spectroscopy, a fluorescent TO displacement assay, circular dichroism and molecular docking studies, imply that curcumin and their analogues interact with G-quadruplex DNA via groove binding. While other analogs of curcumin studied here bind to G-quadruplexes in a qualitatively similar manner their affinities are relatively lower in comparison to curcumin. The Knoevenagel condensate, a methoxy-benzylidene derivative of curcumin, also exhibited significant binding to G-quadruplex DNA, although with two times decreased affinity. Our study establishes the potential of curcumin as a promising natural product for G-quadruplex specific ligands.

Framework for morphometric classification of cells in imaging flow cytometry

Imaging flow cytometry is an emerging technology that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy. It allows high-throughput imaging of cells with good spatial resolution, while they are in flow. This paper proposes a general framework for the processing/classification of cells imaged using imaging flow cytometer. Each cell is localized by finding an accurate cell contour. Then, features reflecting cell size, circularity and complexity are extracted for the classification using SVM. Unlike the conventional iterative, semi-automatic segmentation algorithms such as active contour, we propose a noniterative, fully automatic graph-based cell localization. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using custom fabricated cost-effective microfluidics-based imaging flow cytometer. The proposed system is a significant development in the direction of building a cost-effective cell analysis platform that would facilitate affordable mass screening camps looking cellular morphology for disease diagnosis. Lay description In this article, we propose a novel framework for processing the raw data generated using microfluidics based imaging flow cytometers. Microfluidics microscopy or microfluidics based imaging flow cytometry (mIFC) is a recent microscopy paradigm, that combines the statistical power of flow cytometry with spatial and quantitative morphology of digital microscopy, which allows us imaging cells while they are in flow. In comparison to the conventional slide-based imaging systems, mIFC is a nascent technology enabling high throughput imaging of cells and is yet to take the form of a clinical diagnostic tool. The proposed framework process the raw data generated by the mIFC systems. The framework incorporates several steps: beginning from pre-processing of the raw video frames to enhance the contents of the cell, localising the cell by a novel, fully automatic, non-iterative graph based algorithm, extraction of different quantitative morphological parameters and subsequent classification of cells. In order to evaluate the performance of the proposed framework, we have successfully classified unstained label-free leukaemia cell-lines MOLT, K562 and HL60 from video streams captured using cost-effective microfluidics based imaging flow cytometer. The cell lines of HL60, K562 and MOLT were obtained from ATCC (American Type Culture Collection) and are separately cultured in the lab. Thus, each culture contains cells from its own category alone and thereby provides the ground truth. Each cell is localised by finding a closed cell contour by defining a directed, weighted graph from the Canny edge images of the cell such that the closed contour lies along the shortest weighted path surrounding the centroid of the cell from a starting point on a good curve segment to an immediate endpoint. Once the cell is localised, morphological features reflecting size, shape and complexity of the cells are extracted and used to develop a support vector machine based classification system. We could classify the cell-lines with good accuracy and the results were quite consistent across different cross validation experiments. We hope that imaging flow cytometers equipped with the proposed framework for image processing would enable cost-effective, automated and reliable disease screening in over-loaded facilities, which cannot afford to hire skilled personnel in large numbers. Such platforms would potentially facilitate screening camps in low income group countries; thereby transforming the current health care paradigms by enabling rapid, automated diagnosis for diseases like cancer.

On the Geometrically Dependent Quasi-Saturation and g(m) Reduction in Advanced DeMOS Transistors

This paper reveals an early quasi-saturation (QS) effect attributed to the geometrical parameters in shallow trench isolation-type drain-extended MOS (STI-DeMOS) transistors in advanced CMOS technologies. The quasi-saturation effect leads to serious g(m) reduction in STI-DeMOS. This paper investigates the nonlinear resistive behavior of the drain-extended region and its impact on the particular behavior of the STI-DeMOS transistor. In difference to vertical DMOS or lateral DMOS structures, STI-DeMOS exhibits three distinct regions of the drain extension. A complete understanding of the physics in these regions and their impact on the QS behavior are developed in this paper. An optimization strategy is shown for an improved g(m) device in a state-of-the-art 28-nm CMOS technology node.

Direct numerical test of the B-G-K model equation by the DSMC method

In the present paper the rarefied gas how caused by the sudden change of the wall temperature and the Rayleigh problem are simulated by the DSMC method which has been validated by experiments both in global flour field and velocity distribution function level. The comparison of the simulated results with the accurate numerical solutions of the B-G-K model equation shows that near equilibrium the BG-K equation with corrected collision frequency can give accurate result but as farther away from equilibrium the B-G-K equation is not accurate. This is for the first time that the error caused by the B-G-K model equation has been revealed.

Comparación de parámetros reproductivos bajo inseminación artificial y monta natural en cerdas, (Cofradia, G.E.P.)

Este experimento se realizó en la Granja Experimental Porcina (G.E.P), Cofradía, Masaya, con 82 cerdas del cuarto parto, 30 servidas a través de inseminación artificial (I.A) y 52 cerdas por monta natural (M.N); iniciando en mayo de 1,995 hasta mayo de 1,996 con el objetivo de evaluar los parámetros reproductivos y económicos en ambos sistemas de monta. Los dos grupos de cerdas reproductoras estaban compuestos por las razas LANDRACE, YORKSHIRE y DUROC. Las variables evaluadas fueron: Tasa de concepción (T.C) y tasa de parición (T.P), números de crías por partos (N.C.P), peso vivo promedio del lechón en la camada al nacer (P.V.L.C), relación beneficio-costo (B-C). Los resultados finales comprobados al 5% de significancia estadísticas fueron: T.P en I.A con 56.66% menor que en M.N con 76.92%, en N.C.P para I.A con 7.06, menor que en M.N de 8.725, P.V.L.C en I.A de 1.85 kg, similar a 1.74 kg, en MN. Para la relación B-C en I.A fue de 0.53 córdobas y para M.N de 0.56 córdobas.