THE LEGACY OF GN 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.

Multiscale Symmetry Detection in Scalar Fields by Clustering Contours

The complexity in visualizing volumetric data often limits the scope of direct exploration of scalar fields. Isocontour extraction is a popular method for exploring scalar fields because of its simplicity in presenting features in the data. In this paper, we present a novel representation of contours with the aim of studying the similarity relationship between the contours. The representation maps contours to points in a high-dimensional transformation-invariant descriptor space. We leverage the power of this representation to design a clustering based algorithm for detecting symmetric regions in a scalar field. Symmetry detection is a challenging problem because it demands both segmentation of the data and identification of transformation invariant segments. While the former task can be addressed using topological analysis of scalar fields, the latter requires geometry based solutions. Our approach combines the two by utilizing the contour tree for segmenting the data and the descriptor space for determining transformation invariance. We discuss two applications, query driven exploration and asymmetry visualization, that demonstrate the effectiveness of the approach.

Solid state structure of p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside and an analysis of non-covalent interactions

The solid state structure of a new seven-membered sugar oxepane derivative, namely, p-bromo phenyl 4,5,7-tri-O-benzyl-beta-D-glycero-D-talo-septanoside is discussed, as determined through single crystal X-ray structural determination and in relation to their conformational features. The molecule adopts twist-chair as the preferred conformation, with conformational descriptor (TC2,3)-T-0,1. The solid state packing of molecules is governed by a rich network of non-covalent bonding originating from O-H center dot center dot center dot O, C-H center dot center dot center dot pi, C-H center dot center dot center dot Br and aromatic pi center dot center dot center dot pi interactions that stabilize the packing of molecules in the crystal. (C) 2015 Elsevier Ltd. All rights reserved.

Do we see what we should see? Describing non-covalent interactions in protein structures including precision

The power of X-ray crystal structure analysis as a technique is to `see where the atoms are'. The results are extensively used by a wide variety of research communities. However, this `seeing where the atoms are' can give a false sense of security unless the precision of the placement of the atoms has been taken into account. Indeed, the presentation of bond distances and angles to a false precision (i.e. to too many decimal places) is commonplace. This article has three themes. Firstly, a basis for a proper representation of protein crystal structure results is detailed and demonstrated with respect to analyses of Protein Data Bank entries. The basis for establishing the precision of placement of each atom in a protein crystal structure is non-trivial. Secondly, a knowledge base harnessing such a descriptor of precision is presented. It is applied here to the case of salt bridges, i.e. ion pairs, in protein structures; this is the most fundamental place to start with such structure-precision representations since salt bridges are one of the tenets of protein structure stability. Ion pairs also play a central role in protein oligomerization, molecular recognition of ligands and substrates, allosteric regulation, domain motion and alpha-helix capping. A new knowledge base, SBPS (Salt Bridges in Protein Structures), takes these structural precisions into account and is the first of its kind. The third theme of the article is to indicate natural extensions of the need for such a description of precision, such as those involving metalloproteins and the determination of the protonation states of ionizable amino acids. Overall, it is also noted that this work and these examples are also relevant to protein three-dimensional structure molecular graphics software.

Lesion Detection in Breast Ultrasound Images Using Tissue Transition Analysis

Breast cancer is one of the leading cause of cancer related deaths in women and early detection is crucial for reducing mortality rates. In this paper, we present a novel and fully automated approach based on tissue transition analysis for lesion detection in breast ultrasound images. Every candidate pixel is classified as belonging to the lesion boundary, lesion interior or normal tissue based on its descriptor value. The tissue transitions are modeled using a Markov chain to estimate the likelihood of a candidate lesion region. Experimental evaluation on a clinical dataset of 135 images show that the proposed approach can achieve high sensitivity (95 %) with modest (3) false positives per image. The approach achieves very similar results (94 % for 3 false positives) on a completely different clinical dataset of 159 images without retraining, highlighting the robustness of the approach.

A Cause and Effect Analysis of Motion Trajectories for Modeling Actions

An action is typically composed of different parts of the object moving in particular sequences. The presence of different motions (represented as a 1D histogram) has been used in the traditional bag-of-words (BoW) approach for recognizing actions. However the interactions among the motions also form a crucial part of an action. Different object-parts have varying degrees of interactions with the other parts during an action cycle. It is these interactions we want to quantify in order to bring in additional information about the actions. In this paper we propose a causality based approach for quantifying the interactions to aid action classification. Granger causality is used to compute the cause and effect relationships for pairs of motion trajectories of a video. A 2D histogram descriptor for the video is constructed using these pairwise measures. Our proposed method of obtaining pairwise measures for videos is also applicable for large datasets. We have conducted experiments on challenging action recognition databases such as HMDB51 and UCF50 and shown that our causality descriptor helps in encoding additional information regarding the actions and performs on par with the state-of-the art approaches. Due to the complementary nature, a further increase in performance can be observed by combining our approach with state-of-the-art approaches.

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.

Efficient topological localization using orientation adjacency coherence histograms

This paper describes an efficient vision-based global topological localization approach that uses a coarse-to-fine strategy. Orientation Adjacency Coherence Histogram (OACH), a novel image feature, is proposed to improve the coarse localization. The coarse localization results are taken as inputs for the fine localization which is carried out by matching Harris-Laplace interest points characterized by the SIFT descriptor. Computation of OACHs and interest points is efficient due to the fact that these features are computed in an integrated process. We have implemented and tested the localization system in real environments. The experimental results demonstrate that our approach is efficient and reliable in both indoor and outdoor environments. © 2006 IEEE.

Combining interest points and edges for content-based image retrieval

This paper presents a novel approach using combined features to retrieve images containing specific objects, scenes or buildings. The content of an image is characterized by two kinds of features: Harris-Laplace interest points described by the SIFT descriptor and edges described by the edge color histogram. Edges and corners contain the maximal amount of information necessary for image retrieval. The feature detection in this work is an integrated process: edges are detected directly based on the Harris function; Harris interest points are detected at several scales and Harris-Laplace interest points are found using the Laplace function. The combination of edges and interest points brings efficient feature detection and high recognition ratio to the image retrieval system. Experimental results show this system has good performance. © 2005 IEEE.

Efecto de la densidad poblacional y la época de siembra en el rendimiento y la calidad de la semilla de una población de caupi rojo (Vigna unguiculata (L.) Walp) en la Finca El Plantel

El presente ensayo se realizó en la Finca El Plantel, Zambrano, departamento de Masaya, Nicaragua durante las épocas de siembra de primera, postrera y de riego (Junio 2005-Marzo 2006) con el objetivo de determinar el efecto de la densidad poblacional y la época de siembra sobre el rendimiento y la calidad de semilla de una población de caupí rojo. Fue establecido un diseño bifactorial de bloques completos al azar (BCA), con cuatro bloques, cinco distancias de siembra (0.40, 0.60, 0.80, 1.00, 1.20) y tres épocas de siembra. Se realizó el análisis de varianza y separación de medias por Tukey al 5% de confianza, utilizando el programa Statistical Analysis System (SAS). La medición de las variables se basó en el descriptor de Vignas sp y en la tabla de colores de Methuen. Las variables cuantitativas medidas fueron longitud del foliolo central, longitud del pecíolo, longitud del pecíolulo, longitud del pedúnculo de la vaina, longitud de la rama, longitud de la vaina, diámetro del tallo, altura de la planta, número de ramas por planta, contenido de humedad de la semilla, materia seca, germinación, número de semilla por vainas, número de vainas por parcela, peso de 1000 semillas, y rendimiento. De acuerdo con los resultados no se encontró interacción entre épocas y distancias de siembra. Se determinó que hubo efecto entre épocas de siembra sobre las variables medidas a excepción de número de ramas y diámetro del tallo. El mayor rendimiento se obtuvo en postrera con 1228.8 kg.ha-1, seguida de riego con 452.8 kg.ha-1 y primera 361.6kgha-1. La siembra con riego presentó el primer lugar en las variables peso de 1000 semillas (146.0 g), materia seca (1.8 g) y germinación (87.2 %). Respecto a distancia de siembra la variable número de vainas por parcela presentó efecto significativo correspondiente a la distancia de 1.20m con 406 vainas. De acuerdo a estos resultados se puede decir que la mejor época para producir semilla de caupí es riego por la calidad alcanzada de este insumo.

Caracterización y evaluación preliminar de 14 accesiones de Chile (Capsicum spp)

La presente investigación se llevó a cabo en el Programa de Recursos Genéticos Nicaragüenses (REGEN) de la Universidad Nacional Agraria, durante el período Octubre 2002-Abril-2003. El objetivo fue estudiar y evaluar gennoplasma nativo e introducido de chile {Capsicum spp.) en condiciones del trópico seco de Nicaragua. La caracterización de las 14 accesiones en base a la guía de descriptores propuesta por IBPGR (lt¡83) y mediante el análisis estadístico univariado y multivariados permitió identificar los principales descriptores cualitatí vos ( fonna del fruto, pungencía y forma del fruto en la unión con el pedúnculo) y cuantitativos (diámetro de semillas, diámetro del fruto y peso del fruto) que son de gran utilidad para el estudio de la variación genética de chile. Además se logró conformar un catálogo con las características de cada uno de los material.es. Las accesiones de mayor variación fueron Bacatum, Diente de perro, Pico de pájaro, Alfilerillo y Chile ancho. El resto de materiales tienen características más uniformes. Las accesiones evaluadas presentaron características morfológicas propias de las especies C. annuum, C. frutescens y C. baccatum. En el germopla.sma de Capsicum evaluado se encontraron materiales que poseen diferente reacción a plagas y enfermedades. Palabras claves: Capsicum; accesión; germoplasma; descriptor.

Small scale, grain size and substrate effects in nano-indentation experiment of film-substrate systems

The mechanical properties of film-substrate systems have been investigated through nano-indentation experiments in our former paper (Chen, S.H., Liu, L., Wang, T.C., 2005. Investigation of the mechanical properties of thin films by nano-indentation, considering the effects of thickness and different coating-substrate combinations. Surf. Coat. Technol., 191, 25-32), in which Al-Glass with three different film thicknesses are adopted and it is found that the relation between the hardness H and normalized indentation depth h/t, where t denotes the film thickness, exhibits three different regimes: (i) the hardness decreases obviously with increasing indentation depth; (ii) then, the hardness keeps an almost constant value in the range of 0.1-0.7 of the normalized indentation depth h/t; (iii) after that, the hardness increases with increasing indentation depth. In this paper, the indentation image is further investigated and finite element method is used to analyze the nano-indentation phenomena with both classical plasticity and strain gradient plasticity theories. Not only the case with an ideal sharp indenter tip but also that with a round one is considered in both theories. Finally, we find that the classical plasticity theory can not predict the experimental results, even considering the indenter tip curvature. However, the strain gradient plasticity theory can describe the experimental data very well not only at a shallow indentation depth but also at a deep depth. Strain gradient and substrate effects are proved to coexist in film-substrate nano-indentation experiments. (c) 2006 Elsevier Ltd. All rights reserved.

Sediment budget: principals and applications

The framework of sediment budget concepts provides a formalized procedure to account for the various components of sediment flux and the changes of volume that occur within a given region. Sediment budget methodology can be useful in a number of coastal engineering and research applications, including: inferring the amount of onshore sediment transport for a nearshore system that contains an "excess of sediment", determining sediment deficits to downdrift beaches as a result of engineering works at navigational entrances, evaluating the performance of a beach nourishment project, inferring the distribution of longshore sediment transport across the surf zone, etc. This chapter reviews briefly the governing equations for sediment budget calculations, considers various measurement and other bases for determining the sediment flux components necessary to apply the sediment budget concept and finally for illustration purposes, applies the sediment budget concept to several examples. (PDF contains 52 pages.)