Abstract: Tandem mass spectrometry (MS/MS) is the engine
driving high-throughput protein identification. Protein mixtures possibly
representing thousands of proteins from multiple species are
treated with proteolytic enzymes, cutting the proteins into smaller
peptides that are then analyzed generating MS/MS spectra. The
task of determining the identity of the peptide from its spectrum
is currently the weak point in the process. Current approaches to de
novo sequencing are able to compute candidate peptides efficiently.
The problem lies in the limitations of current scoring functions. In this
paper we introduce the concept of proteome signature. By examining
proteins and compiling proteome signatures (amino acid usage) it is
possible to characterize likely combinations of amino acids and better
distinguish between candidate peptides. Our results strongly support
the hypothesis that a scoring function that considers amino acid usage
patterns is better able to distinguish between candidate peptides. This
in turn leads to higher accuracy in peptide prediction.
Abstract: Communication is becoming a significant tool to engage stakeholders since half of the century ago. In the recent years, there has been rapid growth of new technology developments. In tandem with such developments, there has been growing emphasis in communication strategies and management especially in determining the level of influence and management strategies among the said stakeholders on particular field. This paper presents a research conceptual framework focusing on stakeholder theories, communication and management strategies to be implied on the engagement of stakeholders of new technology developments of fertilizer industry in Malaysia. Framework espoused in this paper will provide insights into the various stakeholder theories and engagement strategies from different principal necessary for a successful introduction of new technology development in the above stated industry. The proposed framework has theoretical significance in filling the gap of the body of knowledge in the implementation of communication strategies in Malaysian fertilizer industry.
Abstract: Heat transfer from two cam shape cylinder in tandem
arrangement had been studied numerically.
The distance between the centers of cylinders (L) is allowed to
vary to change the longitudinal pitch ratio (L/Deq). The equivalent
diameter of the cylinder (Deq) is 27.6 mm and longitudinal pitch ratio
varies in range 2
Abstract: In this paper flow around two cam shaped cylinders had been studied numerically. The equivalent diameter of cylinders is 27.6 mm. The space between center to center of two cam shaped cylinders is define as longitudinal pitch ratio and it varies in range of
2 varies in range of 50
Abstract: Multi-residue analysis method for penicillins was
developed and validated in bovine muscle, chicken, milk, and flatfish.
Detection was based on liquid chromatography tandem mass
spectrometry (LC/MS/MS). The developed method was validated for
specificity, precision, recovery, and linearity. The analytes were
extracted with 80% acetonitrile and clean-up by a single
reversed-phase solid-phase extraction step. Six penicillins presented
recoveries higher than 76% with the exception of Amoxicillin
(59.7%). Relative standard deviations (RSDs) were not more than
10%. LOQs values ranged from 0.1 and to 4.5 ug/kg. The method was
applied to 128 real samples. Benzylpenicillin was detected in 15
samples and Cloxacillin was detected in 7 samples. Oxacillin was
detected in 2 samples. But the detected levels were under the MRL
levels for penicillins in samples.
Abstract: The literature reports a large number of approaches for
measuring the similarity between protein sequences. Most of these
approaches estimate this similarity using alignment-based techniques
that do not necessarily yield biologically plausible results, for two
reasons.
First, for the case of non-alignable (i.e., not yet definitively aligned
and biologically approved) sequences such as multi-domain, circular
permutation and tandem repeat protein sequences, alignment-based
approaches do not succeed in producing biologically plausible results.
This is due to the nature of the alignment, which is based on the
matching of subsequences in equivalent positions, while non-alignable
proteins often have similar and conserved domains in non-equivalent
positions.
Second, the alignment-based approaches lead to similarity measures
that depend heavily on the parameters set by the user for the alignment
(e.g., gap penalties and substitution matrices). For easily alignable
protein sequences, it's possible to supply a suitable combination of
input parameters that allows such an approach to yield biologically
plausible results. However, for difficult-to-align protein sequences,
supplying different combinations of input parameters yields different
results. Such variable results create ambiguities and complicate the
similarity measurement task.
To overcome these drawbacks, this paper describes a novel and
effective approach for measuring the similarity between protein
sequences, called SAF for Substitution and Alignment Free. Without
resorting either to the alignment of protein sequences or to substitution
relations between amino acids, SAF is able to efficiently detect the
significant subsequences that best represent the intrinsic properties of
protein sequences, those underlying the chronological dependencies of
structural features and biochemical activities of protein sequences.
Moreover, by using a new efficient subsequence matching scheme,
SAF more efficiently handles protein sequences that contain similar
structural features with significant meaning in chronologically
non-equivalent positions. To show the effectiveness of SAF, extensive
experiments were performed on protein datasets from different
databases, and the results were compared with those obtained by
several mainstream algorithms.
Abstract: Approximate tandem repeats in a genomic sequence are
two or more contiguous, similar copies of a pattern of nucleotides.
They are used in DNA mapping, studying molecular evolution
mechanisms, forensic analysis and research in diagnosis of inherited
diseases. All their functions are still investigated and not well
defined, but increasing biological databases together with tools for
identification of these repeats may lead to discovery of their specific
role or correlation with particular features. This paper presents a new
approach for finding approximate tandem repeats in a given sequence,
where the similarity between consecutive repeats is measured using
the Hamming distance. It is an enhancement of a method for finding
exact tandem repeats in DNA sequences based on the Burrows-
Wheeler transform.
Abstract: The introduction of haptic elements in a graphic user interfaces are becoming more widespread. Since haptics are being introduced rapidly into computational tools, investigating how these models affect Human-Computer Interaction would help define how to integrate and model new modes of interaction. The interest of this paper is to discuss and investigate the issues surrounding Haptic and Graphic User Interface designs (GUI) as separate systems, as well as understand how these work in tandem. The development of these systems is explored from a psychological perspective, based on how usability is addressed through learning and affordances, defined by J.J. Gibson. Haptic design can be a powerful tool, aiding in intuitive learning. The problems discussed within the text is how can haptic interfaces be integrated within a GUI without the sense of frivolity. Juxtaposing haptics and Graphic user interfaces has issues of motivation; GUI tends to have a performatory process, while Haptic Interfaces use affordances to learn tool use. In a deeper view, it is noted that two modes of perception, foveal and ambient, dictate perception. These two modes were once thought to work in tandem, however it has been discovered that these processes work independently from each other. Foveal modes interpret orientation is space which provide for posture, locomotion, and motor skills with variations of the sensory information, which instructs perceptions of object-task performance. It is contended, here, that object-task performance is a key element in the use of Haptic Interfaces because exploratory learning uses affordances in order to use an object, without meditating an experience cognitively. It is a direct experience that, through iteration, can lead to skill-sets. It is also indicated that object-task performance will not work as efficiently without the use of exploratory or kinesthetic learning practices. Therefore, object-task performance is not as congruently explored in GUI than it is practiced in Haptic interfaces.