Reaz Uddin - Academia.edu (original) (raw)

Papers by Reaz Uddin

Proceedings of the 25th ACM SIGSPATIAL International Conference on Advances in Geographic Information Systems, 2017

Consider objects moving in a road network (e.g., groups of people or delivery vehicles), who may ... more Consider objects moving in a road network (e.g., groups of people or delivery vehicles), who may be free to choose routes, yet be required to arrive at certain locations at certain times. Such objects may need to assemble in groups within the network (friends meet while visiting a city, vehicles need to exchange items or information) without violating arrival constraints. Planning for such assemblies is hard when the network or the number of objects is large. Conversely, discovering actual or potential assemblies of such objects is important in many surveillance, security, and law-enforcement applications. This can be hard when object arrival observations are sparse due to inadequate sensor coverage or object countermeasures. We propose the novel class of assembly queries to model these scenarios, and present a unified scheme that addresses both of these complementary challenges. Given a set of objects and arrival constraints, we show how to first obtain the set of all possible loca...

Letters in Drug Design & Discovery

Background: Clostridioides difficile (CD) is a multi-drug resistant, enteric pathogenic bacterium... more Background: Clostridioides difficile (CD) is a multi-drug resistant, enteric pathogenic bacterium. The CD associated infections are the leading cause of nosocomial diarrhea that can further lead to pseudomembranous colitis up to a toxic mega-colon or sepsis with greater mortality and morbidity risks. The CD infection possess higher rates of recurrence due to its greater resistance against antibiotics. Considering its higher rates of recurrence, it has become a major burden on the healthcare facilities. Therefore, there is a dire need to identify novel drug targets to combat with the antibiotic resistance of Clostridioides difficile. Objective: To identify and propose new and novel drug targets against the Clostridioides difficile. Methods: In the current study, a computational subtractive genomics approach was applied to obtain a set of potential drug targets that exists in the multi-drug resistant strain of Clostridioides difficile. Here, the uncharacterized proteins were studied a...

Computational Biology and Chemistry

Journal of Biomolecular Structure and Dynamics

This study is about proposing a vaccine for all four strains of dengue virus (DENV) that could be... more This study is about proposing a vaccine for all four strains of dengue virus (DENV) that could be an important approach for reaching the WHO goal of reducing dengue morbidity and mortality. The significance of the DENV envelope proteins III lies in the fact that it elicits an immune response and hence can be a potential vaccine design candidate. This domain appears to play a key role in the host cell receptor binding for viral entry and in inducing long lasting protective immunity against the infection. We used long molecular dynamic simulation and mutagenesis scanning methods to provide the dynamic environment and propose the potential mutation that may result in enhancing the binding specificity and affinity of the antigen-antibody (Ag-Ab) complex. The binding free energetics were also estimated using free energy perturbation method. One charged mutation that is theorinine 93L to arginine interacting with epitopic glutamic acid 368 strongly contributing in increasing the binding affinity as well as specificity, predicted as -9.6 kcal/mol gain in 2H12-Fab with dengue envelope domain III binding free energy relative to the wild-type. In conclusion, the one charged residue that showed theoretically enhances the binding affinity of Ag-Ab complex by making couple of interactions i.e. by substituting theorinine to arginine in the antibody chains and can be considered as potential dengue vaccine candidate. Communicated by Ramaswamy H. Sarma.

Pathogens

Mycobacterium avium complex (MAC) is a major cause of non-tuberculous pulmonary and disseminated ... more Mycobacterium avium complex (MAC) is a major cause of non-tuberculous pulmonary and disseminated diseases worldwide, inducing bronchiectasis, and affects HIV and immunocompromised patients. In MAC, Mycobacterium avium subsp. hominissuis is a pathogen that infects humans and mammals, and that is why it is a focus of this study. It is crucial to find essential drug targets to eradicate the infections caused by these virulent microorganisms. The application of bioinformatics and proteomics has made a significant impact on discovering unique drug targets against the deadly pathogens. One successful bioinformatics methodology is the use of in silico subtractive genomics. In this study, the aim was to identify the unique, non-host and essential protein-based drug targets of Mycobacterium avium subsp. hominissuis via in silico a subtractive genomics approach. Therefore, an in silico subtractive genomics approach was applied in which complete proteome is subtracted systematically to shortli...

Journal of Risk and Financial Management

This paper introduces Quasi-Maximum Likelihood Estimation for Long Memory Stock Transaction Data ... more This paper introduces Quasi-Maximum Likelihood Estimation for Long Memory Stock Transaction Data of unknown underlying distribution. The moments with conditional heteroscedasticity have been discussed. In a Monte Carlo experiment, it was found that the QML estimator performs as well as CLS and FGLS in terms of eliminating serial correlations, but the estimator can be sensitive to start value. Hence, two-stage QML has been suggested. In empirical estimation on two stock transaction data for Ericsson and AstraZeneca, the 2SQML turns out relatively more efficient than CLS and FGLS. The empirical results suggest that both of the series have long memory properties that imply that the impact of macroeconomic news or rumors in one point of time has a persistence impact on future transactions.

Frontiers in Cellular and Infection Microbiology

Pathogenic microorganisms exploit host metabolism for sustained survival by rewiring its metaboli... more Pathogenic microorganisms exploit host metabolism for sustained survival by rewiring its metabolic interactions. Therefore, several metabolic changes are induced in both pathogen and host cells in the course of infection. A systems-based approach to elucidate those changes includes the integrative use of genome-scale metabolic networks and molecular omics data, with the overall goal of better characterizing infection mechanisms for novel treatment strategies. This review focuses on novel aspects of metabolism-oriented systems-based investigation of pathogen-human interactions. The reviewed approaches are the generation of dual-omics data for the characterization of metabolic signatures of pathogen-host interactions, the reconstruction of pathogen-host integrated genome-scale metabolic networks, which has a high potential to be applied to pathogen-gut microbiota interactions, and the structure-based analysis of enzymes playing role in those interactions. The integrative use of those approaches will pave the way for the identification of novel biomarkers and drug targets for the prediction and prevention of infectious diseases.

Khulna University Business Review

Purpose: This study has put a great effort to measure the empowerment status of women who are bot... more Purpose: This study has put a great effort to measure the empowerment status of women who are both higher educated and employed. Sampling and data collection: Data were collected form women employed in various organization like banks, educational institutions, NGOs and others for this study. Empowerment was measured based on economic freedom, household decision making, social…

Computational biology and chemistry, 2018

Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acq... more Pseudomonas aeruginosa is an opportunistic gram-negative bacterium that has the capability to acquire resistance under hostile conditions and become a threat worldwide. It is involved in nosocomial infections. In the current study, potential novel drug targets against P. aeruginosa have been identified using core proteomic analysis and Protein-Protein Interactions (PPIs) studies. The non-redundant reference proteome of 68 strains having complete genome and latest assembly version of P. aeruginosa were downloaded from ftp NCBI RefSeq server in October 2016. The standalone CD-HIT tool was used to cluster ortholog proteins (having >=80% amino acid identity) present in all strains. The pan-proteome was clustered in 12,380 Clusters of Orthologous Proteins (COPs). By using in-house shell scripts, 3252 common COPs were extracted out and designated as clusters of core proteome. The core proteome of PAO1 strain was selected by fetching PAO1's proteome from common COPs. As a result, 12...

Chemical biology & drug design, 2018

The molecular basis for the inhibitory action of a benzimidazole inhibitor compound to hepatitis ... more The molecular basis for the inhibitory action of a benzimidazole inhibitor compound to hepatitis C virus E1 envelope protein was examined computationally. Structures for the wild-type E1 protein and seven mutants were modelled using an ab initio protein structure prediction algorithm, and these models were docked with the benzimidazole inhibitor. Top-ranked conformers for each docked structure were examined in the context of the putative function of the inhibitor that blocks fusion of the envelope protein to the host cells. The results for the wild-type protein and that for a series of mutants containing reported single, double and triple resistance mutations demonstrate that the inhibitor binds in the vicinity of residue Phe99 (at position 291 in the encoded polyprotein) at the C-terminal end of a putative fusion domain. In so doing, the compound inhibits the virus from fusing to host cells and blocks viral replication in accord with the results from cell-based infection studies.

Journal of molecular graphics & modelling, Jan 21, 2018

Multidrug-resistant Acinetobacter baumannii is indeed to be the most successful nosocomial pathog... more Multidrug-resistant Acinetobacter baumannii is indeed to be the most successful nosocomial pathogen responsible for myriad infections in modern health care system. Computational methodologies based on genomics and proteomics proved to be powerful tools for providing substantial information about different aspects of A. baumannii biology that made it possible to design new approaches for treating multi, extensive and total drug resistant isolates of A. baumannii. In this current approach, 35 completely annotated proteomes of A. bauamnnii were filtered through a comprehensive subtractive proteomics pipeline for broad-spectrum drug candidates. In total, 10 proteins (KdsA, KdsB, LpxA, LpxC, LpxD, GpsE, PhoB, UvrY, KdpE and OmpR) could serve as ideal candidates for designing novel antibiotics. The work was extended with KdsA enzyme for structure information, prediction of intrinsic disorders, active site details, and structure based virtual screening of library containing natural product...

Microbial pathogenesis, Jan 24, 2017

Streptococcus pneumoniae (pneumococcus) is a Gram-positive bacterium. Humans are the major target... more Streptococcus pneumoniae (pneumococcus) is a Gram-positive bacterium. Humans are the major target for the pneumococcus. The pneumococcus is a common etiological agent of many different diseases such as bacterial meningitis, pneumonia, otitis media (OM), sinusitis, and conjunctivitis. According to the WHO, the pneumococcus is responsible for causing 1 million deaths each year. In 2000, over 14 million children worldwide under the age of 5 years were diagnosed with a pneumococcal disease, with the highest incidence seen in Africa. The human population most susceptible to pneumococcal infections is that of children due to their immature immune system. A sensational increase in antibiotic resistance among S. pneumoniae has been witnessed in different parts of the world since 1980s. The increase of resistance of S. pneumoniae to antibiotics is of major concern throughout the world. Worldwide, there are concerns about rising levels of antibiotic resistance and fears that the efficacy of a...

International journal of biological macromolecules, Jan 2, 2018

In the recent decades, the interest on glycosidases has dramatically increased, mainly because th... more In the recent decades, the interest on glycosidases has dramatically increased, mainly because these enzymes play a vital role in many biological processes. Based on the biological potential associated to these enzymes, several glycosidase inhibitors have been developed. In this review, the most important inhibitors targeting these enzymes, including the disaccharides, iminosugars, monocyclic iminosugars, bicyclic iminosugars, thiosugars and carbasugars will be discussed and special attention will be given to the ones that are currently used clinically. This review summarizes and characterizes the current knowledge regarding the classes of glycosidase inhibitors that have therapeutic potential in a wide range of diseases. It highlights the patents, relevant research and patent applications filed in the past years in the field. Since the glycosidase inhibitors are involved in several chronic diseases and possibly pandemic, the pharmaceutical research towards developing new generation...

Journal of Molecular Graphics and Modelling

MurF ligase catalyzes the final cytoplasmic step of bacterial peptidoglycan biosynthesis and, as ... more MurF ligase catalyzes the final cytoplasmic step of bacterial peptidoglycan biosynthesis and, as such, is a validated target for therapeutic intervention. Herein, we performed molecular docking to identify putative inhibitors of Acinetobacter baumannii MurF (AbMurF). Based on comparative docking analysis, compound 114 (ethyl pyridine substituted 3-cyanothiophene) was predicted to potentially be the most active ligand. Computational pharmacokinetic characterization of drug-likeness of the compound showed it to fulfil all the parameters of Muegge and the MDDR rule. A molecular dynamic simulation of 114 indicated the complex to be stable on the basis of an average root mean square deviation (RMSD) value of 2.09Å for the ligand. The stability of the complex was further supported by root mean square fluctuation (RMSF), beta factor and radius of gyration values. Analyzing the complex using radial distribution function (RDF) and a novel analytical tool termed the axial frequency distribution (AFD) illustrated that after simulation the ligand is positioned in close vicinity of the protein active site where Thr42 and Asp43 participate in hydrogen bonding and stabilization of the complex. Binding free energy calculations based on the Poisson-Boltzmann or Generalized-Born Surface Area Continuum Solvation (MM(PB/GB)SA) method indicated the van der Waals contribution to the overall binding energy of the complex to be dominant along with electrostatic contributions involving the hot spot amino acids from the protein active site. The present results indicate that the screened compound 114 may act as a parent structure for designing potent derivatives against AbMurF in specific and MurF of other bacterial pathogens in general.

European journal of pharmaceutical sciences : official journal of the European Federation for Pharmaceutical Sciences, Jan 4, 2017

Patently, Protein-Protein Interactions (PPIs) lie at the core of significant biological functions... more Patently, Protein-Protein Interactions (PPIs) lie at the core of significant biological functions and make the foundation of host-pathogen relationships. Hence, the current study is aimed to use computational biology techniques to predict host-pathogen Protein-Protein Interactions (HP-PPIs) between MRSA and Humans as potential drug targets ultimately proposing new possible inhibitors against them. As a matter of fact this study is based on the Interolog method which implies that homologous proteins retain their ability to interact. A distant homolog approach based on Interolog method was employed to speculate MRSA protein homologs in Humans using PSI-BLAST. In addition the protein interaction partners of these homologs as listed in Database of Interacting Proteins (DIP) were predicted to interact with MRSA as well. Moreover, a direct approach using BLAST was also applied so as to attain further confidence in the strategy. Consequently, the common HP-PPIs predicted by both approaches...

Understanding moving object behaviors, also known as trajectory semantics, is an important proble... more Understanding moving object behaviors, also known as trajectory semantics, is an important problem that affects many decision making applications. Previous works typically identify such behaviors by using known landmarks, also termed as Regions of Interest (ROIs) (parks, museums, malls, etc.) that are geographically collocated with the trajectory. The main objective of this thesis is to identify trajectory semantics, by looking only at the trajectory data, i.e., without assuming pre-knowledge of ROIs. We first present a new trajectory behavior, by defining the notion of dwell regions. A region R is a dwell region for a moving object O if, given a threshold distance d and duration t, every point of R remains within distance d of O for at least time t. Clearly, points within R are likely to be of interest to O. We present methods for determining dwell regions for both streaming and archived data. Next, we introduce a novel query that can be used to track conclaves (i.e., secret meetings) of a group of moving object. In this environment we assume only partial observations of the individual object movements, within the context of a local transportation network. This is a realistic assumption due vi to sparsely-distributed surveillance cameras or lack of observations in general. Given such limited observations we seek to infer the set of all possible conclaves. The third chapter of the thesis addresses ROI identification. An ROI is typically defined as a region where a large number of moving objects remain for at least a given time interval. Previous methods require sequential scanning of the entire dataset to find ROIs when the semantics (number of objects, time duration) change. Here, we propose a novel method based on object density, to efficiently identify ROIs with arbitrary semantics; this method scans the dataset only once. We also revisit indexing of trajectories using Hilbert curves. Instead of using minimum bounding rectangles we present methods to use Hilbert curves to index trajectory polylines. Our method outperforms the state of the art methods for spatial range queries by two to fifteen times. Even though such transformation does not preserve the Euclidean distance, we show, that our approach can also be used to efficiently answer kNN queries.

PLOS ONE, 2016

Background Infections caused by Salmonella enterica, a Gram-negative facultative anaerobic bacter... more Background Infections caused by Salmonella enterica, a Gram-negative facultative anaerobic bacteria belonging to the family of Enterobacteriaceae, are major threats to the health of humans and animals. The recent availability of complete genome data of pathogenic strains of the S. enterica gives new avenues for the identification of drug targets and drug candidates. We have used the genomic and metabolic pathway data to identify pathways and proteins essential to the pathogen and absent from the host. Methods We took the whole proteome sequence data of 42 strains of S. enterica and Homo sapiens along with KEGG-annotated metabolic pathway data, clustered proteins sequences using CD-HIT, identified essential genes using DEG database and discarded S. enterica homologs of human proteins in unique metabolic pathways (UMPs) and characterized hypothetical proteins with SVM-prot and InterProScan. Through this core proteomic analysis we have identified enzymes essential to the pathogen.

Medicinal Chemistry Research, 2016

Leprosy is caused by Mycobacterium leprae a major health concern in several countries of the worl... more Leprosy is caused by Mycobacterium leprae a major health concern in several countries of the world particularly in Asia and Africa. The preventive measurement has been adopted by the combined efforts of the leprosy burden countries and WHO. However, the situation is getting worse due to the emergence of the resistant strains of the M. leprae. The continuous efforts are underway to discover new chemical agent as a therapeutic to cure the diseases caused by the resistant pathogens of bacterial origins. The resistant pathogens are still growing on alarming rate. In order to overcome the resistant pathogens, a relatively newer approach has been applied since last decade. One of them involves the computational subtractive genomics, in which the complete proteome of the bacterial pathogen is step-wise reduced to few potential drug targets. The steps include the finding of non-host proteins, essentiality of the proteins to the pathogens and involvement of the shortlisted proteins in essential metabolic pathways of the pathogen, which are necessary for the bacterial survival. In the current study, we applied computational subtractive genomics on complete proteome of the M. leprae and ended up with 16 hypothetical proteins as potential drug targets against which new active molecules can be proposed to ameliorate the activity to cure the disease associated with them. The study is innovative and has a potential to improve the research directions in unraveling the novel cure of leprosy.