shahid ullah - Academia.edu (original) (raw)

Papers by shahid ullah

Trials, Jan 16, 2018

Although China has a large number of older people living with diabetes and hypertension, the prim... more Although China has a large number of older people living with diabetes and hypertension, the primary care system is underdeveloped and so management of these conditions in community care settings is suboptimal. Studies have shown that the collaborative care model across care settings that address both pharmacology and nonpharmacology interventions can achieve hypertension control for older people with diabetes. Barriers to implementing and evaluating this model of care are widely recognized in low and middle-income countries including China. This study will therefore test the hypothesis that a hypertension management program built on collaboration between hospitals and community health service centers in China can improve blood pressure control in people aged 60 years and older with diabetes as compared to usual care. A cluster randomized controlled trial will randomly allocate 10 wards from four hospitals in Nanchang to either an intervention group (N = 5) or a usual care group (N ...

Nucleic acids research, Jan 26, 2016

We report a database of circadian genes in eukaryotes (CGDB, http://cgdb.biocuckoo.org), containi... more We report a database of circadian genes in eukaryotes (CGDB, http://cgdb.biocuckoo.org), containing ∼73 000 circadian-related genes in 68 animals, 39 plants and 41 fungi. Circadian rhythm is ∼24 h rhythm in behavioral and physiological processes that exists in almost all organisms on the earth. Defects in the circadian system are highly associated with a number of diseases such as cancers. Although several databases have been established for rhythmically expressed genes, a comprehensive database of cycling genes across phyla is still lacking. From the literature, we collected 1382 genes of which transcript level oscillations were validated using methods such as RT-PCR, northern blot and in situ hybridization. Given that many genes exhibit different oscillatory patterns in different tissues/cells within an organism, we have included information regarding the phase and amplitude of the oscillation, as well as the tissue/cells in which the oscillation was identified. Using these well c...

Briefings in bioinformatics, Jul 30, 2016

Protein methylation is an essential posttranslational modification (PTM) mostly occurs at lysine ... more Protein methylation is an essential posttranslational modification (PTM) mostly occurs at lysine and arginine residues, and regulates a variety of cellular processes. Owing to the rapid progresses in the large-scale identification of methylation sites, the available data set was dramatically expanded, and more attention has been paid on the identification of specific methylation types of modification residues. Here, we briefly summarized the current progresses in computational prediction of methylation sites, which provided an accurate, rapid and efficient approach in contrast with labor-intensive experiments. We collected 5421 methyllysines and methylarginines in 2592 proteins from the literature, and classified most of the sites into different types. Data analyses demonstrated that different types of methylated proteins were preferentially involved in different biological processes and pathways, whereas a unique sequence preference was observed for each type of methylation sites. ...

Geriatrics & Gerontology International, 2014

In addition, authors may also transmit, print and share copies with colleagues, provided that the... more In addition, authors may also transmit, print and share copies with colleagues, provided that there is no systematic distribution of the submitted version, e.g. posting on a listserve, network or automated delivery.

Australasian Journal on Ageing, 2013

Aging & Mental Health, 2014

Objectives: To investigate caregiver burden in dementia and explore factors associated with diffe... more Objectives: To investigate caregiver burden in dementia and explore factors associated with different types of burden in a country without formal caregiver support using a province in China as a case. Method: Cross-sectional questionnaire survey was used to collect data. One hundred and fifty-two family caregivers of people with dementia in community settings were recruited from 2012-2013 using convenience sampling. Objective burden was measured by caregiving hours and dementiarelated financial burden. Subjective burden was measured and analysed using the Caregiver Burden Inventory and the Neuropsychiatric Inventory-Questionnaire. Multivariate regression models were employed to analyse factors associated with each type of subjective burden. Results: Five types of subjective burden were measured by the Caregiver Burden Inventory namely: physical burden, emotional burden, time-dependence burden, developmental burden, and social burden. Caregiver distress, as a subjective burden was measured by the Neuropsychiatric Inventory-Questionnaire and reported by relating to the severity of care recipients' behavioural and psychological symptoms of dementia. This caregiver cohort showed a high level of physical, timedependence and developmental burdens, but a low level of emotional and social burdens. Factors 5 contributing to each type of subjective burden measured by the Caregiver Burden Inventory differed from each other. Conclusion: The high level of objective burden and subjective burden identified in this study suggests that government-funded formal caregiver support should be established and services should be designed to target different types of burdens and factors contributing to these burdens.

Scientific Reports, 2016

Protein phosphorylation is one of the most important post-translational modifications (PTMs) and ... more Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites, and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf. biocuckoo.org. As one of the most well-studied and ubiquitous post-translational modifications (PTMs) in proteins, phosphorylation is a conserved mechanism in both eukaryotes and prokaryotes, participates in almost all of biological processes, and reversibly determines the cellular dynamics and plasticity 1-5. In eukaryotes, phosphorylation mainly occurs on a subset of three types of amino acids, including serine, threonine and tyrosine residues. Phosphorylation events are dynamically but precisely regulated, and the core machinery of a phosphorylation system contains numerous protein kinases (PKs) for modifying proteins as "writers", phospho-binding proteins for recognizing and interacting with phosphorylation sites as "readers", and protein phosphatases (PPs) for demodifying substrates as "erasers" 2,3,6,7. The aberrant phosphorylation has been extensively reported to be highly associated with human diseases, such as cancers 8 , neurodegenerative diseases 9 and metabolic disorders 10. In this regard, the identification and functional analysis of phosphosites are fundamental for understanding the molecular mechanisms and regulatory roles of protein phosphorylation. Recently, rapid progresses in high-throughput liquid chromatography/mass spectrometry (LC-MS) techniques have greatly advanced the identification of phosphorylation sites 11-13. For example, using a mouse model of multistage skin carcinogenesis, Zanivan et al. identified and quantified 3,457 proteins with 5,249 phosphorylation sites 12. Also, using a label-free technology, Lundby et al. totally quantified 31,480 phosphorylation sites in 7,280 proteins across 14 rat organs and tissues 13. Recently, Humphrey et al. developed a new platform of EasyPhos, which can rapidly quantify over 10,000 phosphorylation sites from cell or tissue samples in a single run 11. Since a flood of sites have been generated, computational analysis of the phosphoproteomic data in a systematic level has also been boomed, such as the prediction of site-specific kinase-substrate relations (ssKSRs) 14-16 , the reconstruction and modeling of phosphorylation networks 1,17 , the molecular evolutionary analysis of

Computer Methods and Programs in Biomedicine Update

Background COVID-19 is a global outbreak of a disease from a new virus, occurred in Wuhan China i... more Background COVID-19 is a global outbreak of a disease from a new virus, occurred in Wuhan China in December 2019. Several databases have been published on this pandemic, but the research community still needs an easy way to get comprehensive information on COVID-19. Objectives COVID-19 pandemic database (CO-19 PDB) aims to provide wonderful insights for COVID-19 researchers with the well-gathered of all the COVID-19 data to one platform, which is a global challenge for the research community these days. Methods We gathered 59 updated databases since December-2019 until May 2021 and divided them into six categories: digital image database, genomic database, literature database, visualization tools database, chemical structure database, and social science database. These categories focus on taking number of functions from the images, information from gene sequences, updates from relevant papers, essays, reports, articles, and books, the data or information in the form of maps, graphs, and charts, information of bonds between atoms, and updates about events of the physical and social environment, respectively. Results Users can search the information of interest in two ways including typing the name of the database in the search bar or by clicking the right category directly. Computer languages such as CSS, PHP, HTML, Java, etc. are utilized to construct CO-19 PDB. Conclusion This article attempts to compile up-to-date appropriate COVID-19 datasets and resources that have not been compiled and given in such an accessible and user-friendly manner. As a result, the CO-19 PDB offers extensive open data sharing for both worldwide research communities and local people. Further, we have planned future development of new features, that will be awesome for future study.

Scientific Reports, 2014

Recent studies have indicated that different post-translational modifications (PTMs) synergistica... more Recent studies have indicated that different post-translational modifications (PTMs) synergistically orchestrate specific biological processes by crosstalks. However, the preference of the crosstalk among different PTMs and the evolutionary constraint on the PTM crosstalk need further dissections. In this study, the in situ crosstalk at the same positions among three tyrosine PTMs including sulfation, nitration and phosphorylation were systematically analyzed. The experimentally identified sulfation, nitration and phosphorylation sites were collected and integrated with reliable predictions to perform large-scale analyses of in situ crosstalks. From the results, we observed that the in situ crosstalk between sulfation and nitration is significantly under-represented, whereas both sulfation and nitration prefer to co-occupy with phosphorylation at same tyrosines. Further analyses suggested that sulfation and nitration preferentially co-occur with phosphorylation at specific positions in proteins, and participate in distinct biological processes and functions. More interestingly, the long-term evolutionary analysis indicated that multi-PTM targeting tyrosines didn't show any higher conservation than singly modified ones. Also, the analysis of human genetic variations demonstrated that there is no additional functional constraint on inherited disease, cancer or rare mutations of multiply modified tyrosines. Taken together, our systematic analyses provided a better understanding of the in situ crosstalk among PTMs. T hrough modification of proteins by covalent attachment of other functional groups or by proteolytic cleavage, post-translational modifications (PTMs) temporally and spatially affect protein activity, stability and trafficking, regulate most of biological and physiological functions, and determine the cellular dynamics and plasticity 1-3. In particular, one PTM can crosstalk with other PTMs to synergistically orchestrate specific processes through three distinct mechanisms 4-13. First, different PTMs can co-occur in the same proteins and crosstalk in a cis-regulatory manner 4,5. For example, the phosphorylation of the motif YKXEXXpSP (Y is a hydrophobic residue, X is any amino acid, pS is a phosphorylatable serine) at S303 of HSF1, a heat shock transcription factor, enhances the adjacent lysine sumoylation at K298 4 (Fig. 1a). Also, a recently computational analysis suggested that a considerable proportion of acetylated lysines might influence the PTMs such as phosphorylation, methylation and ubiquitination of adjacent sites 6. Second, one PTM can regulate another PTM by modifying its cognate enzymes and vice versa, in a trans-regulatory mode 7-9. For example, the E3 ubiquitin ligase complex of Rictor/Cullin-1/Rbx1 ubiquitinates an AGC kinase of SGK1 and promote its degradation, whereas the T1135 of Rictor can be phosphorylated by multiple AGC kinases including SGK1, and such a phosphorylation disrupts the interaction of Rictor and Cullin-1 to inhibit the ubiquitination of SGK1 8 (Fig. 1b). Third, multiple PTMs can ''in situ'' interplay with each other by competitively modifying same residues 10-13. For example, a circadian clock protein PER2 is competitively O-GlcNAcylated and phosphorylated at S662, while the in situ crosstalk precisely regulates the PER2 repressor activity 13 (Fig. 1c). In addition, different types of PTM crosstalks can simultaneously occur and regulate biological functions in a complicated manner. For example, PKCd phosphorylates Caspase-3 14 , which reciprocally cleaves PKC-d as a trans-crosstalk 15 (Fig. 1d). Also, p53 can be activated through the PKCd-mediated phosphorylation of S46 16 , and such a phosphorylation promotes its

Database : the journal of biological databases and curation, 2015

As one of the most important post-translational modifications, phosphorylation is highly involved... more As one of the most important post-translational modifications, phosphorylation is highly involved in almost all of biological processes through temporally and spatially modifying substrate proteins. Recently, phosphorylation in prokaryotes attracted much attention for its critical roles in various cellular processes such as signal transduction. Thus, an integrative data resource of the prokaryotic phosphorylation will be useful for further analysis. In this study, we presented a curated database of phosphorylation sites in prokaryotes (dbPSP, Database URL: http://dbpsp.biocuckoo.org) for 96 prokaryotic organisms, which belong to 11 phyla in two domains including bacteria and archaea. From the scientific literature, we manually collected experimentally identified phosphorylation sites on seven types of residues, including serine, threonine, tyrosine, aspartic acid, histidine, cysteine and arginine. In total, the dbPSP database contains 7391 phosphorylation sites in 3750 prokaryotic p...