PocketMatch: A new algorithm to compare binding sites in protein structures

Background: Recognizing similarities and deriving relationships among protein molecules is a fundamental
requirement in present-day biology. Similarities can be present at various levels which can be detected through comparison of protein sequences or their structural folds. In some cases similarities obscure at these levels could be present merely in the substructures at their binding sites. Inferring functional similarities between protein molecules by comparing their binding sites is still largely exploratory and not as yet a routine protocol. One of
the main reasons for this is the limitation in the choice of appropriate analytical tools that can compare binding sites with high sensitivity. To benefit from the enormous amount of structural data that is being rapidly accumulated, it is essential to have high throughput tools that enable large scale binding site comparison.

Results: Here we present a new algorithm PocketMatch for comparison of binding sites in a frame invariant
manner. Each binding site is represented by 90 lists of sorted distances capturing shape and chemical nature of the site. The sorted arrays are then aligned using an incremental alignment method and scored to obtain PMScores for pairs of sites. A comprehensive sensitivity analysis and an extensive validation of the algorithm have been carried out. Perturbation studies where the geometry of a given site was retained but the residue types were changed randomly, indicated that chance similarities were virtually non-existent. Our analysis also demonstrates that shape information alone is insufficient to discriminate between diverse binding sites, unless
combined with chemical nature of amino acids.

Conclusions: A new algorithm has been developed to compare binding sites in accurate, efficient and
high-throughput manner. Though the representation used is conceptually simplistic, we demonstrate that along
with the new alignment strategy used, it is sufficient to enable binding comparison with high sensitivity. Novel methodology has also been presented for validating the algorithm for accuracy and sensitivity with respect to geometry and chemical nature of the site. The method is also fast and takes about 1/250th second for one comparison on a single processor. A parallel version on BlueGene has also been implemented

Mechanikal Applications of the Harmless Error Rule in Cases of Prosecutorial Grand Jury Misconduct

Even though time-interleaved analog-to-digital converters (ADCs) help to achieve higher bandwidth with simpler individual ADCs, gain, offset, and time-skew mismatch between the channels degrade the achievable resolution. Of particular interest is the time-skew error between channels which results in nonuniform samples and thereby introducing distortion tones at the output of the time-interleaved ADC. Time-varying digital reconstructors can be used to correct the time-skew errors between the channels in a time-interleaved ADC. However, the complexity of such reconstructors increases as their bandwidth approaches the Nyquist band. In addition to this, the reconstructor needs to be redesigned online every time the time-skew error varies. Design methods that result in minimum reconstructor order require expensive online redesign while those methods that simplify online redesign result in higher reconstructor complexity. This paper proposes a technique that can be used to simplify the online redesign and achieve a low complexity reconstructor at the same time

Special Considerations in Estate Planning for Same-Sex and Unmarried Couples

Sub-Nyquist sampling makes use of sparsities in analog signals to sample them at a rate lower than the Nyquist rate. The reduction in sampling rate, however, comes at the cost of additional digital signal processing (DSP) which is required to reconstruct the uniformly sampled sequence at the output of the sub-Nyquist sampling analog-to-digital converter. At present, this additional processing is computationally intensive and time consuming and offsets the gains obtained from the reduced sampling rate. This paper focuses on sparse multi-band signals where the user band locations can change from time to time and the reconstructor requires real-time redesign. We propose a technique that can reduce the computational complexity of the reconstructor. At the same time, the proposed scheme simplifies the online reconfigurability of the reconstructor

Decline of the European Entrepreneurship in the Tea Plantation Industry: A Case a study of the Darjeeling and Jalpaiguri District (1933 a 1960)

Tea plantation industry in India was originally initiated and developed by British enterprises The management of the estates of various Sterling and British Rupee Public Limited tea companies were vested on the British Managing Agency Houses of Calcutta They played an important role in converting either a personal lease or proprietary estate into a public limited company In the tea plantations the major collieries commanding greater capital and larger mining rights were joint stock firms and 89 per cent of these were controlled by Europeans mostly British managing agencies With the impact of 1930 s World wide economic depression the colonial firms fell from grace and made a hasty retreat from India In this juncture the European tea Companies were also affected by some acts which were implemented after the independence of India such as Minimum Wages Act 1947 Factory Act 1948 Plantation Labour Act 1951 This grave situation compelled the European planters to think whether they would retain their business in India or not As a result the European tea companies began to shift their business in South Africa Uganda and Rhodesia after selling their gardens to the native Indians Thus an attempt have been made here to draw a pen picture on the decline of European entrepreneurship of the tea plantation industry in the tea growing areas of Bengal such as Jalpaiguri and Darjeeling district

Drama: A Tool for Learning

AbstractTeaching and learning of business modules have always been a challenge, especially with students who have low language proficiency. Although there have been a variety of active-learning methods employed to enhance students” understanding of the subject matter, traditionally, the key approach to teaching and learning of business modules has been lecture-based. These limited approaches have not substantially improved the students” understanding of the subject matter as these approaches have not significantly improved their language proficiency. Therefore, this study aims to explore the use of drama as a teaching and learning tool not only to enhance students” language proficiency but to also improve students” learning and understanding of a business module. The study employs a qualitative method utilizing various data collection techniques, including the use of students” reflective writing, practice observations and students” assessment results. The findings show that the use of drama for business context and content has helped enhance students” language proficiency and knowledge of the subject

Sensing, Actuation, and Embedded Control for a Custom SCR Nitrogen Oxides Emissions Reduction System

Diesel engines are the main power source for medium and heavy duty on road vehicles. With the rising standards for mileage of vehicles set by the Corporate Average Fuel Economy and the Environmental Protection Agency, diesel engines should soon be considered in lieu of gas engines. Despite advantages of diesel engines, diesel emissions include harmful gasses like carbon monoxide, nitrogen oxides and particulate matter. Selective Catalytic Reduction (SCR) systems have long been used to reduce diesel emissions from medium to heavy-duty diesel engines. Primary focus of this research effort is the implementation and improvement of a SCR system on light diesel engines. To improve efficiency we implemented a control law to limit the emissions within bounds ensuring low emissions for varied drive cycles. We developed a controller network using user datagram protocol to collect engine data using Arduino. The controller network establishes communication link between sensor data collection and a raspberry pi controller to enable full control over the test station