Analysis of the Relationships among Longest Common Subsequences, Shortest Common Supersequences and Patterns and its application on Pattern Discovery in Biological Sequences

For a set of mulitple sequences, their patterns,Longest Common Subsequences (LCS) and Shortest Common Supersequences (SCS) represent different aspects of these sequences profile, and they can all be used for biological sequence comparisons and analysis. Revealing the relationship between the patterns and LCS,SCS might provide us with a deeper view of the patterns of biological sequences, in turn leading to better understanding of them. However, There is no careful examinaton about the relationship between patterns, LCS and SCS. In this paper, we have analyzed their relation, and given some lemmas. Based on their relations, a set of algorithms called the PALS (PAtterns by Lcs and Scs) algorithms are propsoed to discover patterns in a set of biological sequences. These algorithms first generate the results for LCS and SCS of sequences by heuristic, and consequently derive patterns from these results. Experiments show that the PALS algorithms perform well (both in efficiency and in accuracy) on a variety of sequences. The PALS approach also provides us with a solution for transforming between the heuristic results of SCS and LCS.Comment: Extended version of paper presented in IEEE BIBE 2006 submitted to journal for revie

Examination of the relationship between essential genes in PPI network and hub proteins in reverse nearest neighbor topology

Abstract Background In many protein-protein interaction (PPI) networks, densely connected hub proteins are more likely to be essential proteins. This is referred to as the "centrality-lethality rule", which indicates that the topological placement of a protein in PPI network is connected with its biological essentiality. Though such connections are observed in many PPI networks, the underlying topological properties for these connections are not yet clearly understood. Some suggested putative connections are the involvement of essential proteins in the maintenance of overall network connections, or that they play a role in essential protein clusters. In this work, we have attempted to examine the placement of essential proteins and the network topology from a different perspective by determining the correlation of protein essentiality and reverse nearest neighbor topology (RNN). Results The RNN topology is a weighted directed graph derived from PPI network, and it is a natural representation of the topological dependences between proteins within the PPI network. Similar to the original PPI network, we have observed that essential proteins tend to be hub proteins in RNN topology. Additionally, essential genes are enriched in clusters containing many hub proteins in RNN topology (RNN protein clusters). Based on these two properties of essential genes in RNN topology, we have proposed a new measure; the RNN cluster centrality. Results from a variety of PPI networks demonstrate that RNN cluster centrality outperforms other centrality measures with regard to the proportion of selected proteins that are essential proteins. We also investigated the biological importance of RNN clusters. Conclusions This study reveals that RNN cluster centrality provides the best correlation of protein essentiality and placement of proteins in PPI network. Additionally, merged RNN clusters were found to be topologically important in that essential proteins are significantly enriched in RNN clusters, and biologically important because they play an important role in many Gene Ontology (GO) processes.http://deepblue.lib.umich.edu/bitstream/2027.42/78257/1/1471-2105-11-505.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78257/2/1471-2105-11-505-S1.DOChttp://deepblue.lib.umich.edu/bitstream/2027.42/78257/3/1471-2105-11-505.pdfPeer Reviewe

Algorithms for multi-point range query and reverse nearest neighbour search

Ph.DDOCTOR OF PHILOSOPH

Characterisation of protein-truncating and missense variants in PALB2 in 15 768 women from Malaysia and Singapore

Funder: National University Cancer Institute, Singapore; FundRef: http://dx.doi.org/10.13039/501100011105Background: Rare protein-truncating variants (PTVs) in partner and localiser of BRCA2 (PALB2) confer increased risk to breast cancer, but relatively few studies have reported the prevalence in South-East Asian populations. Here, we describe the prevalence of rare variants in PALB2 in a population-based study of 7840 breast cancer cases and 7928 healthy Chinese, Malay and Indian women from Malaysia and Singapore, and describe the functional impact of germline missense variants identified in this population. Methods: Mutation testing was performed on germline DNA (n=15 768) using targeted sequencing panels. The functional impact of missense variants was tested in mouse embryonic stem cell based functional assays. Results: PTVs in PALB2 were found in 0.73% of breast cancer patients and 0.14% of healthy individuals (OR=5.44; 95% CI 2.85 to 10.39, p<0.0001). In contrast, rare missense variants in PALB2 were not associated with increased risk of breast cancer. Whereas PTVs were associated with later stage of presentation and higher-grade tumours, no significant association was observed with missense variants in PALB2. However, two novel rare missense variants (p.L1027R and p.G1043V) produced unstable proteins and resulted in a decrease in homologous recombination-mediated repair of DNA double-strand breaks. Conclusion: Despite genetic and lifestyle differences between Asian and other populations, the population prevalence of PALB2 PTVs and associated relative risk of breast cancer, are similar to those reported in European populations

Detecting hubs and quasi cliques in scale-free networks

Scale-free networks are believed to closely model most real-world networks. An interesting property of such networks is the existence of so-called hub and community structures. In this paper, we model hubs as high-degree nodes and communities as quasi cliques. We propose a new problem formulation called the ¿-list dominating set and show how this single problem is suited to model both the structures in real-world networks better than traditional problems like vertex cover and clique. Additionally, we provide a fixed-parameter tractable algorithm to this detect these structures and show experimental results on protein-protein interaction networks

Phototreatment of Palm Oil Mill Effluent (POME) over Cu/TiO2 Photocatalyst

The current work reported on the use of different formulations of Cu/TiO2 photocatalysts for the UV-irradiation of palm oil mills effluent (POME). Different copper loadings, viz. 2 wt%, 5 wt%, 10 wt%, 15 wt%, 20 wt% and 25 wt% were doped onto titania. XRD pattern confirmed the presence of anatase TiO2 as primary phase due to mild calcination temperature (573 K). Photo-decomposition of POME over 20 wt% Cu/TiO2 exhibited the highest conversion (27.0%) attributed to its large pore diameter (20.0 nm). In addition, optimum loading was 0.83 g/l. © 2014 BCREC UNDIP. All rights reservedReceived: 5th January 2014; Revised: 8th April 2014; Accepted: 8th April 2014[How to Cite: Hoong, N.K., Deraman, M.R., Ang, C.H., Chong, S.K., Kong, Z.Y., Khan, M.R., Cheng, C.K., (2014). Phototreatment of Palm Oil Mill Effluent (POME) over Cu/TiO2 Photocatalyst. Bulletin of Chemical Reaction Engineering &amp; Catalysis, 9 (2): 121-127. (doi:10.9767/bcrec.9.2.6011.121-127)][Permalink/DOI: http://dx.doi.org/10.9767/bcrec.9.2.6011.121-127 ]</p

Phototreatment of Palm Oil Mill Effluent (POME) over Cu/TiO2 Photocatalyst

The current work reported on the use of different formulations of Cu/TiO2 photocatalysts for the UV-irradiation of palm oil mills effluent (POME). Different copper loadings, viz. 2 wt%, 5 wt%, 10 wt%, 15 wt%, 20 wt% and 25 wt% were doped onto titania. XRD pattern confirmed the presence of anatase TiO2 as primary phase due to mild calcination temperature (573 K). Photo-decomposition of POME over 20 wt% Cu/TiO2 exhibited the highest conversion (27.0%) attributed to its large pore diameter (20.0 nm). In addition, optimum loading was 0.83 g/l

Assessing the effects of operating parameters on flocculation of

Harvesting of microalgae is one of the main challenges in the production of biodiesel due to the small cell size of microalgae cells. Chemical flocculants have been generally used in the harvesting of microalgae, but they are harmful to the environment and relatively costly. Therefore, the utilization of waste biomass in producing bioflocculants is the current research niche to introduce environmental-friendly harvesting method and to minimize the cost of biodiesel production. Thus, in the current work, flocculation Chlorella vulgaris using mild acid-extracted bioflocculants from miscellaneous waste biomass (cockle shell, peanut shell and banana peel) were conducted by varying the pH values, the dosage of bioflocculants and temperatures. Cockle shell bioflocculant demonstrated the best flocculation performance, with highest flocculation efficiency of 85.2% compared to the peanut shell bioflocculant with flocculation efficiency of 37% and banana peel bioflocculant with flocculation efficiency of 16.3%. The optimum flocculation conditions for cockle shell bioflocculant were determined as follow: pH 9, bioflocculant dosage of 140mg/L and temperature of 30oC. The findings herein presented practical applicability of bioflocculants extracted from cockle shell for safe, rapid and inexpensive microalgae harvesting

Small hiatal hernia and postprandial reflux after vertical sleeve gastrectomy: A multiethnic Asian cohort.

BackgroundLaparoscopic vertical sleeve gastrectomy (LSG) is a popular bariatric procedure performed in Asia, as obesity continues to be on the rise in our population. A major problem faced is the development of de novo gastroesophageal reflux disease (GERD) after LSG, which can be chronic and debilitating. In this study, we aim to assess the relationship between the presence of small hiatal hernia (HH) and the development of postoperative GERD, as well as to explore the correlation between GERD symptoms after LSG and timing of meals. In doing so, we hope to gain a better understanding about the type of reflux that occurs after LSG and take a step closer towards effectively managing this difficult to treat condition.MethodsWe retrospectively reviewed data collected from patients who underwent LSG in our hospital from Dec 2008 to Dec 2016. All patients underwent preoperative upper GI endoscopy, during which the identification of hiatal hernia takes place. Patients' information and reflux symptoms are recorded using standardized questionnaires, which are administered preoperatively, and again during postoperative follow up visits.ResultsOf the 255 patients, 125 patients (74%) developed de novo GERD within 6 months post-sleeve gastrectomy. The rate of de novo GERD was 57.1% in the group with HH, and 76.4% in the group without HH. Adjusted analysis showed no significant association between HH and GERD (RR = 0.682; 95% CI 0.419 to 1.111; P = 0.125). 88% of the patients who developed postoperative GERD reported postprandial symptoms occurring only after meals, and the remaining 12% of patients reported no correlation between the timing of GERD symptoms and meals.ConclusionThere is no direct correlation between the presence of small hiatal hernia and GERD symptoms after LSG. Hence, the presence of a small sliding hiatal hernia should not be exclusion for sleeve gastrectomy. Electing not to perform concomitant hiatal hernia repair also does not appear to result in higher rates of postoperative or de novo GERD