Juvenile idiopathic arthritis (JIA) is one of the most common chronic diseases in children. While... more Juvenile idiopathic arthritis (JIA) is one of the most common chronic diseases in children. While clinical outcomes for patients with juvenile JIA have improved, the underlying biology of the disease and mechanisms underlying therapeutic response/non-response are poorly understood. We have shown that active JIA is associated with distinct transcriptional abnormalities, and that the attainment of remission is associated with reorganization of transcriptional networks. In this study, we used a multi-omics approach to identify mechanisms driving the transcriptional abnormalities in peripheral blood CD4+ T cells of children with active JIA. We demonstrate that active JIA is associated with alterations in CD4+ T cell chromatin, as assessed by ATACseq studies. However, 3D chromatin architecture, assessed by HiChIP and simultaneous mapping of CTCF anchors of chromatin loops, reveals that normal 3D chromatin architecture is largely preserved. Overlapping CTCF binding, ATACseq, and RNAseq da...
A b s t r a c t Apparently in the beginning non-fired bricks were used for the shelter over the h... more A b s t r a c t Apparently in the beginning non-fired bricks were used for the shelter over the head. As the world progressed fired clay bricks found acceptability for construction. In Pakistan fired clay bricks are used in-plenty for erecting the houses. However, the technology is quite old and the practice is being repeated for several years. More commonly the bricks are porous; water absorbability is quite high and consequently the compressive strength and other properties are much lower than they should have been. In order to get an idea about quality of bricks, a comparative study of the properties of fired clay bricks of Hoofmann kiln versus Sada Bhatta (manually operated kiln) is done. A systematic study was carried out to determine var-ious properties such as water absorption, efflorescence, crushing strength, specific weight, specific gravity of common bricks and specific weight of baked clay. This was particularly deemed imperative because of the fact that the process of b...
ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. Howe... more ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without taking into account the transposase digested DNA fragments that contain additional nucleosome positioning information. We present the first dedicated ATAC-seq analysis tool, a semi-supervised machine learning approach named HMMRATAC. HMMRATAC splits a single ATAC-seq dataset into nucleosome-free and nucleosome-enriched signals, learns the unique chromatin structure around accessible regions, and then predicts accessible regions across the entire genome. We show that HMMRATAC outperforms the popular peak-calling algorithms on published human and mouse ATAC-seq datasets.
Construction projects are very complex in nature. Each activity involves multiple varying tasks. ... more Construction projects are very complex in nature. Each activity involves multiple varying tasks. Construction industry is the main source of economic growth. When change order occur performance of projects momentously affected. Change orders often have a serious impact on the quality, time and cost. Eventually it results in disputes, delays, and dissatisfactions among stakeholders and ultimately results in failures of projects. In past several studies have been done to evaluate the causes of change order and its effects. Attempts have been made to quantify these impacts by many researchers, but the aim of this study is to identify the causes of change order in two different phases i.e. preconstruction and construction stage. Views were taken from relevant experts over included factors after in-depth literature review from past researches. A questionnaire was made and floated with different construction players from clients, consultants and contractors side. The data was analyzed by...
Green Building rating tools are the essential need of this era, to cope up with the sustainable d... more Green Building rating tools are the essential need of this era, to cope up with the sustainable development goals, climate change, and natural resource degradation through buildings. Realization of green building incentives decently increased within past few decades with abrupt declination in real estate markets and economic depletion has decelerated the interest of investors towards the green building projects. This research calculates influence of costing elements in MyCREST (IS-design) using questionnaire survey distributed amongst qualified professionals (QP’S) of green buildings and expert practitioners. Firstly, factor score and then weightage factor was performed to produce the final result with weightage output for evaluating weighatge and ranking of the relevant criteria of MyCREST and life cycle cost elements respectively. It is found that the criteria of storm water management has weighatge of 0.236 as highest and criteria environmental management plan (EMP) as 0.061 as l...
Juvenile idiopathic arthritis (JIA) is one of the most common chronic diseases in children. While... more Juvenile idiopathic arthritis (JIA) is one of the most common chronic diseases in children. While clinical outcomes for patients with juvenile JIA have improved, the underlying biology of the disease and mechanisms underlying therapeutic response/non-response are poorly understood. We have shown that active JIA is associated with distinct transcriptional abnormalities, and that the attainment of remission is associated with reorganization of transcriptional networks. In this study, we used a multi-omics approach to identify mechanisms driving the transcriptional abnormalities in peripheral blood CD4+ T cells of children with active JIA. We demonstrate that active JIA is associated with alterations in CD4+ T cell chromatin, as assessed by ATACseq studies. However, 3D chromatin architecture, assessed by HiChIP and simultaneous mapping of CTCF anchors of chromatin loops, reveals that normal 3D chromatin architecture is largely preserved. Overlapping CTCF binding, ATACseq, and RNAseq da...
A b s t r a c t Apparently in the beginning non-fired bricks were used for the shelter over the h... more A b s t r a c t Apparently in the beginning non-fired bricks were used for the shelter over the head. As the world progressed fired clay bricks found acceptability for construction. In Pakistan fired clay bricks are used in-plenty for erecting the houses. However, the technology is quite old and the practice is being repeated for several years. More commonly the bricks are porous; water absorbability is quite high and consequently the compressive strength and other properties are much lower than they should have been. In order to get an idea about quality of bricks, a comparative study of the properties of fired clay bricks of Hoofmann kiln versus Sada Bhatta (manually operated kiln) is done. A systematic study was carried out to determine var-ious properties such as water absorption, efflorescence, crushing strength, specific weight, specific gravity of common bricks and specific weight of baked clay. This was particularly deemed imperative because of the fact that the process of b...
ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. Howe... more ATAC-seq has been widely adopted to identify accessible chromatin regions across the genome. However, current data analysis still utilizes approaches initially designed for ChIP-seq or DNase-seq, without taking into account the transposase digested DNA fragments that contain additional nucleosome positioning information. We present the first dedicated ATAC-seq analysis tool, a semi-supervised machine learning approach named HMMRATAC. HMMRATAC splits a single ATAC-seq dataset into nucleosome-free and nucleosome-enriched signals, learns the unique chromatin structure around accessible regions, and then predicts accessible regions across the entire genome. We show that HMMRATAC outperforms the popular peak-calling algorithms on published human and mouse ATAC-seq datasets.
Construction projects are very complex in nature. Each activity involves multiple varying tasks. ... more Construction projects are very complex in nature. Each activity involves multiple varying tasks. Construction industry is the main source of economic growth. When change order occur performance of projects momentously affected. Change orders often have a serious impact on the quality, time and cost. Eventually it results in disputes, delays, and dissatisfactions among stakeholders and ultimately results in failures of projects. In past several studies have been done to evaluate the causes of change order and its effects. Attempts have been made to quantify these impacts by many researchers, but the aim of this study is to identify the causes of change order in two different phases i.e. preconstruction and construction stage. Views were taken from relevant experts over included factors after in-depth literature review from past researches. A questionnaire was made and floated with different construction players from clients, consultants and contractors side. The data was analyzed by...
Green Building rating tools are the essential need of this era, to cope up with the sustainable d... more Green Building rating tools are the essential need of this era, to cope up with the sustainable development goals, climate change, and natural resource degradation through buildings. Realization of green building incentives decently increased within past few decades with abrupt declination in real estate markets and economic depletion has decelerated the interest of investors towards the green building projects. This research calculates influence of costing elements in MyCREST (IS-design) using questionnaire survey distributed amongst qualified professionals (QP’S) of green buildings and expert practitioners. Firstly, factor score and then weightage factor was performed to produce the final result with weightage output for evaluating weighatge and ranking of the relevant criteria of MyCREST and life cycle cost elements respectively. It is found that the criteria of storm water management has weighatge of 0.236 as highest and criteria environmental management plan (EMP) as 0.061 as l...
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Papers by Shahzaib Khan