Immune Cell Expression Signatures in B cell Lymphoma

Intro: B-cell lymphomas are a group of diseases that originate from the B cell compartment of your white blood cells. B-cell lymphoma and High-Grade Lymphoma are difficult to distinguish by pathologists based on morphology but have been shown to have very different expression profiles by suggesting these lymphomas come from different stages of B-cell development. M&M: xCell is an analytical tool to impute gene expression profiles and provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Results: A program called xCell was utilized to see that High-Grade Lymphoma cases were enhanced for memory B-cell marks while Burkitt Lymphoma cases were improved for plasma cell signatures suggesting a potential difference in the normal cell counterpart. For immune-cell signatures in the microenvironment, I observed that High Grade Lymphoma samples had a statistically significant increase in T-regulatory cell signatures Conclusions: I observed that High Grade Lymphoma samples had a statistically significant increase in T-regulatory cell signatures while Burkitt Lymphoma samples had a statistically significant increase in T-helper 1 signatures. Taken together, these results suggest differential microenvironments in these malignancies which could be exploited in therapeutic strategies as T-regulatory and T-helper 1 subsets can influence anti-tumor responses.https://digitalcommons.unmc.edu/surp2020/1026/thumbnail.jp

Virtual CGH: an integrative approach to predict genetic abnormalities from gene expression microarray data applied in lymphoma

Background: Comparative Genomic Hybridization (CGH) is a molecular approach for detecting DNA Copy Number Alterations (CNAs) in tumor, which are among the key causes of tumorigenesis. However in the post-genomic era, most studies in cancer biology have been focusing on Gene Expression Profiling (GEP) but not CGH, and as a result, an enormous amount of GEP data had been accumulated in public databases for a wide variety of tumor types. We exploited this resource of GEP data to define possible recurrent CNAs in tumor. In addition, the CNAs identified by GEP would be more functionally relevant CNAs in the disease pathogenesis since the functional effects of CNAs can be reflected by altered gene expression. Methods: We proposed a novel computational approach, coined virtual CGH (vCGH), which employs hidden Markov models (HMMs) to predict DNA CNAs from their corresponding GEP data. vCGH was first trained on the paired GEP and CGH data generated from a sufficient number of tumor samples, and then applied to the GEP data of a new tumor sample to predict its CNAs. Results: Using cross-validation on 190 Diffuse Large B-Cell Lymphomas (DLBCL), vCGH achieved 80% sensitivity, 90% specificity and 90% accuracy for CNA prediction. The majority of the recurrent regions defined by vCGH are concordant with the experimental CGH, including gains of 1q, 2p16-p14, 3q27-q29, 6p25-p21, 7, 11q, 12 and 18q21, and losses of 6q, 8p23-p21, 9p24-p21 and 17p13 in DLBCL. In addition, vCGH predicted some recurrent functional abnormalities which were not observed in CGH, including gains of 1p, 2q and 6q and losses of 1q, 6p and 8q. Among those novel loci, 1q, 6q and 8q were significantly associated with the clinical outcomes in the DLBCL patients (p \u3c 0.05). Conclusions: We developed a novel computational approach, vCGH, to predict genome-wide genetic abnormalities from GEP data in lymphomas. vCGH can be generally applied to other types of tumors and may significantly enhance the detection of functionally important genetic abnormalities in cancer research

A trend pattern assessment approach to microarray gene expression profiling data analysis

We study the problem of how to assess the reliability of a statistical measurement on data set containing unknown quantity of noises, inconsistencies, and outliers. A practical approach that analyzes the dynamical patterns (trends) of the statistical measurements through a sequential extreme-boundary-points (EBP) weed-out process is explored. We categorize the weed-out trend patterns (WOTP) and examine their relation to the reliability of the measurement. The approach is applied to the processes of extracting genes that are predictive to BCL2 translocations and to clinical survival outcomes of diffuse large B-cell lymphoma (DLBCL) from DNA Microarray gene expression profiling data sets. Fisher’s Discriminate Criterion (FDC) is used as a statistical measurement in the processes. It is found that the weed-out trend analysis (WOTA) approach is effective for qualitatively assessing the statistics-based measurements in the experimentations conducted

HEALTH AND PHYSICAL EDUCATION (HPE) AS AN EDUCATIONAL DISCIPLINE IN PAKISTAN: CONTEMPORARY ISSUES AND PROSPECTS

Purpose of the study: This article reviews the importance of Health and Physical education (HPE) as an educational discipline in Pakistan: contemporary issues and prospects involved in the negligence of this important sphere of education which range from lack of interest of stakeholders in Pakistan. Methodology: Peer-reviewed and scholarly journals were searched for articles related to Health & Physical education program. Keywords included curriculum, physical activities, instruction, health and nutrition, carrier opportunities, guidance, teacher training because the review aimed to highlight the importance of HPE as an educational discipline in Pakistan and to address the prevailing issues and prospective improvement. Findings: The status of Health and Physical education as an academic discipline was discussed in the article. Among the comparison of the program in Pakistan with that of the others countries, a lack of awareness about the benefits and career opportunities for graduates of HPE is there. Applications of this study: Like other programs and projects, the HPE program aimed at the production of skillful youth who have comprehensive knowledge of the subject and also the practice. This study focused on only Health and physical education program but will help to bring positive change in the other discipline too and will facilitate the production of skilled youth in other academic programs. Novelty/Originality of this study: This review highlights the importance of the Health and Physical education program both at inter, BS ( Bachelor of Studies ), MS, & Ph.D. level and practical outcomes in the shape of physically, mentally, and emotionally fit graduates

Virtual CGH: an integrative approach to predict genetic abnormalities from gene expression microarray data applied in lymphoma

<p>Abstract</p> <p>Background</p> <p>Comparative Genomic Hybridization (CGH) is a molecular approach for detecting DNA Copy Number Alterations (CNAs) in tumor, which are among the key causes of tumorigenesis. However in the post-genomic era, most studies in cancer biology have been focusing on Gene Expression Profiling (GEP) but not CGH, and as a result, an enormous amount of GEP data had been accumulated in public databases for a wide variety of tumor types. We exploited this resource of GEP data to define possible recurrent CNAs in tumor. In addition, the CNAs identified by GEP would be more functionally relevant CNAs in the disease pathogenesis since the functional effects of CNAs can be reflected by altered gene expression.</p> <p>Methods</p> <p>We proposed a novel computational approach, coined virtual CGH (vCGH), which employs hidden Markov models (HMMs) to predict DNA CNAs from their corresponding GEP data. vCGH was first trained on the paired GEP and CGH data generated from a sufficient number of tumor samples, and then applied to the GEP data of a new tumor sample to predict its CNAs.</p> <p>Results</p> <p>Using cross-validation on 190 Diffuse Large B-Cell Lymphomas (DLBCL), vCGH achieved 80% sensitivity, 90% specificity and 90% accuracy for CNA prediction. The majority of the recurrent regions defined by vCGH are concordant with the experimental CGH, including gains of 1q, 2p16-p14, 3q27-q29, 6p25-p21, 7, 11q, 12 and 18q21, and losses of 6q, 8p23-p21, 9p24-p21 and 17p13 in DLBCL. In addition, vCGH predicted some recurrent functional abnormalities which were not observed in CGH, including gains of 1p, 2q and 6q and losses of 1q, 6p and 8q. Among those novel loci, 1q, 6q and 8q were significantly associated with the clinical outcomes in the DLBCL patients (p < 0.05).</p> <p>Conclusions</p> <p>We developed a novel computational approach, vCGH, to predict genome-wide genetic abnormalities from GEP data in lymphomas. vCGH can be generally applied to other types of tumors and may significantly enhance the detection of functionally important genetic abnormalities in cancer research.</p

An investigation of Students’ Organizational Problems of Cohesion and Coherence in English Essay Writing at Higher Secondary Levels of Sindh, Pakistan

Academic writing is a form of testing; moreover, most of the writing tasks and assignments across the country school curriculum, the designers of the writing assignments is also the audience and the evaluator, and that designer-evaluator expects student-writers to demonstrate particular knowledge and skills. Hence, like all the tests designers, developers of writing assignments should carefully consider different purposes, the parameters and constraints, and the evaluation criteria for each writing assignment. In this paper, we discussed organizational problems in essay writing such as, topic sentences, thesis statements, cohesion, coherence, completeness and unity. We applied a qualitative method for data collection.&nbsp; For this, we selected one hundred students to write essays on different topics. Among them, we chose twenty written essays for data analysis. The findings suggested that students have organizational problems in English essay writing. It was found in their writings that most of the students have difficulties in organization their essay. Students get difficulties in introduction, topic sentence, thesis statement, transition of ideas, and use of cohesive devices, sequence and writing conclusion. There are certain reasons. Firstly, the effects of background information of particular topic and general information. Secondly, the low language proficiency, the students get it difficulty to create coherence and unity in their writings. It is because they give more importance to language and meanings

EFFECT OF VERTICAL TRAILING ON VEGETATIVE, REPRODUCTIVE AND YIELD OF LUFFA AS INTERCROP IN COCONUT FIELD

Abstract Intercropping trial in coconut (Cocos nucifera L), was carried out for generating more income/yield. The experiment was conducted at Coastal Agricultural Research Station (CARS) Farm, PARC, Karachi. The Tori varieties planted ridge gourd (Luffa acutangulla Roxb.) and sponge gourd (Luffa cylindrica L.) under the trail staked and unstaked Tori were grown satisfactory under coconut plot. The results showed that the staked method compared to unstaked had 30-35% increase in yield and also insect pest protection. The yield data recorded showed that staked gave maximum yield. It was also found that the intercropping did not affect the agronomic trails and yield of the coconut, but increase the yield compared to palms alone