CancerLectinDB: a database of lectins relevant to cancer

The role of lectins in mediating cancer metastasis, apoptosis as well as various other signaling events has been well established in the past few years. Data on various aspects of the role of lectins in cancer is being accumulated at a rapid pace. The data on lectins available in the literature is so diverse, that it becomes difficult and time-consuming, if not impossible to comprehend the advances in various areas and obtain the maximum benefit. Not only do the lectins vary significantly in their individual functional roles, but they are also diverse in their sequences, structures, binding site architectures, quaternary structures, carbohydrate affinities and specificities as well as their potential applications. An organization of these seemingly independent data into a common framework is essential in order to achieve effective use of all the data towards understanding the roles of different lectins in different aspects of cancer and any resulting applications. An integrated knowledge base (CancerLectinDB) together with appropriate analytical tools has therefore been developed for lectins relevant for any aspect of cancer, by collating and integrating diverse data. This database is unique in terms of providing sequence, structural, and functional annotations for lectins from all known sources in cancer and is expected to be a useful addition to the number of glycan related resources now available to the community. The database has been implemented using MySQL on a Linux platform and web-enabled using Perl-CGI and Java tools. Data for individual lectins pertain to taxonomic, biochemical, domain architecture, molecular sequence and structural details as well as carbohydrate specificities. Extensive links have also been provided for relevant bioinformatics resources and analytical tools. Availability of diverse data integrated into a common framework is expected to be of high value for various studies on lectin cancer biology.

The Skill of ECMWF Medium-Range Forecasts during the Year of Tropical Convection 2008

This study uses the European Centre for Medium-Range Weather Forecasts (ECMWF) model-generated high-resolution 10-day-long predictions for the Year of Tropical Convection (YOTC) 2008. Precipitation forecast skills of the model over the tropics are evaluated against the Tropical Rainfall Measuring Mission (TRMM) estimates. It has been shown that the model was able to capture the monthly to seasonal mean features of tropical convection reasonably. Northward propagation of convective bands over the Bay of Bengal was also forecasted realistically up to 5 days in advance, including the onset phase of the monsoon during the first half of June 2008. However, large errors exist in the daily datasets especially for longer lead times over smaller domains. For shorter lead times (less than 4-5 days), forecast errors are much smaller over the oceans than over land. Moreover, the rate of increase of errors with lead time is rapid over the oceans and is confined to the regions where observed precipitation shows large day-to-day variability. It has been shown that this rapid growth of errors over the oceans is related to the spatial pattern of near-surface air temperature. This is probably due to the one-way air-sea interaction in the atmosphere-only model used for forecasting. While the prescribed surface temperature over the oceans remain realistic at shorter lead times, the pattern and hence the gradient of the surface temperature is not altered with change in atmospheric parameters at longer lead times. It has also been shown that the ECMWF model had considerable difficulties in forecasting very low and very heavy intensity of precipitation over South Asia. The model has too few grids with ``zero'' precipitation and heavy (>40 mm day(-1)) precipitation. On the other hand, drizzle-like precipitation is too frequent in the model compared to that in the TRMM datasets. Further analysis shows that a major source of error in the ECMWF precipitation forecasts is the diurnal cycle over the South Asian monsoon region. The peak intensity of precipitation in the model forecasts over land (ocean) appear about 6 (9) h earlier than that in the observations. Moreover, the amplitude of the diurnal cycle is much higher in the model forecasts compared to that in the TRMM estimates. It has been seen that the phase error of the diurnal cycle increases with forecast lead time. The error in monthly mean 3-hourly precipitation forecasts is about 2-4 times of the error in the daily mean datasets. Thus, effort should be given to improve the phase and amplitude forecast of the diurnal cycle of precipitation from the model.

Surface Chemistry of Thiobacillus ferrooxidans Relevant to Adhesion on Mineral Surfaces

Thiobacillus ferrooxidans cells grown on sulfur, pyrite, and chalcopyrite exhibit greater hydrophobicity than ferrous ion-grown cells. The isoelectric points of sulfur-, pyrite-, and chalcopyrite-grown cells were observed to be at a pH higher than that for ferrous ion-grown cells. Microbe-mineral interactions result in change in the surface chemistry of the organism as well as that of the minerals with which it has interacted. Sulfur, pyrite, and chalcopyrite after interaction with T. ferrooxidans exhibited a significant shift in their isoelectric points from the initial values exhibited by uninteracted minerals. With antibodies raised against sulfur-grown T. ferrooxidans, pyrite- and chalcopyrite-grown cells showed immunoreactivity, whereas ferrous ion-grown cells failed to do so. Fourier transform infrared spectroscopy of sulfur-grown cells suggested that a proteinaceous new cell surface appendage synthesized in mineral-grown cells brings about adhesion to the solid mineral substrates. Such an appendage was found to be absent in ferrous ion-grown cells as it is not required during growth in liquid substrates.

Assessing design creativity

Creativity is crucial for designing products and enabling innovation. Assessing creativity can help identify innovative designers and products, and support improvement of both. The literature variously defines creativity as a function of degree of novelty, usefulness, or both. Most methods for assessing creativity, however, focus only on assessing novelty of products. This research proposes a new method for assessing the creativity of products as a function of their novelty and usefulness. We develop individual methods for assessing novelty and usefulness of products. and then combine these into a method for assessing creativity of products. The proposed methods have been evaluated by benchmarking them, and other methods available from literature, against the collective, intuitive assessment of product creativity of experienced designers. (C) 2011 Elsevier Ltd. All rights reserved.

Utilizing Model Nanostructured Porous Inorganic Compounds Such as Silica to Beneficially Confine “Bio”-Relevant Molecules and Demonstrate their Potential in Therapeutics

Abstract | The importance of well-defined inorganic porous nanostructured materials in the context of biotechnological applications such as drug delivery and biomolecular sensing is reviewed here in detail. Under optimized conditions, the confinement of “bio”-relevant molecules such as pharmaceutical drugs, enzymes or proteins inside such inorganic nanostructures may be remarkably beneficial leading to enhanced molecular stability, activity and performance. From the point of view of basic research, molecular confinement inside nanostructures poses several formidable and intriguing problems of statistical mechanics at the mesoscopic scale. The theoretical comprehension of such non-trivial issues will not only aid in the interpretation of observed phenomena but also help in designing better inorganic nanostructured materials for biotechnological applications.

Comparison of the degree of creativity in the design outcomes using different design methods

This work analyses the influence of several design methods on the degree of creativity of the design outcome. A design experiment has been carried out in which the participants were divided into four teams of three members, and each team was asked to work applying different design methods. The selected methods were Brainstorming, Functional Analysis, and SCAMPER method. The `degree of creativity' of each design outcome is assessed by means of a questionnaire offered to a number of experts and by means of three different metrics: the metric of Moss, the metric of Sarkar and Chakrabarti, and the evaluation of innovative potential. The three metrics share the property of measuring the creativity as a combination of the degree of novelty and the degree of usefulness. The results show that Brainstorming provides more creative outcomes than when no method is applied, while this is not proved for SCAMPER and Functional Analysis.

Computational investigations on covalent dimerization/oligomerization of polyacenes: Is it relevant to soot formation?

We have postulated a novel pathway that could assist in the nucleation of soot particles through covalent dimerization and oligomerizations of a variety of PAHs. DFT calculations were performed with the objective of obtaining the relative thermal stabilities and formation probabilities of oligomeric species that exploit the facile dimerization that is known to occur in linear oligoacenes. We propose that the presence of small stretches of linear oligoacence (tetracene or longer) in extended PAH, either embedded or tethered, would be adequate for enabling the formation of such dimeric and oligomeric adducts; these could then serve as nuclei for the growth of soot particles. Our studies also reveal the importance of p-stacking interactions between extended aromatic frameworks in governing the relative stabilities of the oligomeric species that are formed. (c) 2012 Wiley Periodicals, Inc.

Cross-Guided Clustering: Transfer of Relevant Supervision across Tasks

Lack of supervision in clustering algorithms often leads to clusters that are not useful or interesting to human reviewers. We investigate if supervision can be automatically transferred for clustering a target task, by providing a relevant supervised partitioning of a dataset from a different source task. The target clustering is made more meaningful for the human user by trading-off intrinsic clustering goodness on the target task for alignment with relevant supervised partitions in the source task, wherever possible. We propose a cross-guided clustering algorithm that builds on traditional k-means by aligning the target clusters with source partitions. The alignment process makes use of a cross-task similarity measure that discovers hidden relationships across tasks. When the source and target tasks correspond to different domains with potentially different vocabularies, we propose a projection approach using pivot vocabularies for the cross-domain similarity measure. Using multiple real-world and synthetic datasets, we show that our approach improves clustering accuracy significantly over traditional k-means and state-of-the-art semi-supervised clustering baselines, over a wide range of data characteristics and parameter settings.

Assessment of the Relationships Among Design Methods, Design Activities, and Creativity

This paper presents an experimental study that was conducted to compare the results obtained from using different design methods (brainstorming (BR), functional analysis (FA), and SCAMPER) in design processes. The objectives of this work are twofold. The first was to determine whether there are any differences in the length of time devoted to the different types of activities that are carried out in the design process, depending on the method that is employed; in other words, whether the design methods that are used make a difference in the profile of time spent across the design activities. The second objective was to analyze whether there is any kind of relationship between the time spent on design process activities and the degree of creativity in the solutions that are obtained. Creativity evaluation has been done by means of the degree of novelty and the level of resolution of the designed solutions using creative product semantic scale (CPSS) questionnaire. The results show that there are significant differences between the amounts of time devoted to activities related to understanding the problem and the typology of the design method, intuitive or logical, that are used. While the amount of time spent on analyzing the problem is very small in intuitive methods, such as brainstorming and SCAMPER (around 8-9% of the time), with logical methods like functional analysis practically half the time is devoted to analyzing the problem. Also, it has been found that the amount of time spent in each design phase has an influence on the results in terms of creativity, but results are not enough strong to define in which measure are they affected. This paper offers new data and results on the distinct benefits to be obtained from applying design methods. DOI: 10.1115/1.4007362]

Ideas generated in conceptual design and their effects on creativity

Search of design spaces to generate solutions affects the design outcomes during conceptual design. This research aims to understand the different types of search that occurs during conceptual design and their effect on the design outcomes. Additionally, we study the effect of other factors, such as creativity, problem-solving style, and experience of designers, on the design outcomes. Two sets of design experiments, with experienced and novice designers, are used in this study. We find that designers employ twelve different types of searches during conceptual design for problem understanding, solution generation, and solution evaluation activities. Results also suggest that creativity is influenced positively by the type and amount of searches, duration of designing, and experience of designers.