Search results for: Kjiana E. Schwab

Authors: Roxane A. Legaie, Kjiana E. Schwab, Caroline E. Gargett

Abstract:

Studies looking at the changes in gene expression from RNAseq data often make use of linear models. It is also common practice to focus on a subset of data for a comparison of interest, leaving aside the samples not involved in this particular comparison. This work shows the importance of including all observations in the modeling process to better estimate variance parameters, even when the samples included are not directly used in the comparison under test. The human endometrium is a dynamic tissue, which undergoes cycles of growth and regression with each menstrual cycle. The mesenchymal stem cells (MSCs) present in the endometrium are likely responsible for this remarkable regenerative capacity. However recent studies suggest that MSCs also plays a role in the pathogenesis of endometriosis, one of the most common medical conditions affecting the lower abdomen in women in which the endometrial tissue grows outside the womb. In this study we compared gene expression profiles between MSCs and non-stem cell counterparts (‘non-MSC’) obtained from women with (‘E’) or without (‘noE’) endometriosis from RNAseq. Raw read counts were used for differential expression analysis using a linear model with the limma-voom R package, including either all samples in the study or only the samples belonging to the subset of interest (e.g. for the comparison ‘E vs noE in MSC cells’, including only MSC samples from E and noE patients but not the non-MSC ones). Using the full dataset we identified about 100 differentially expressed (DE) genes between E and noE samples in MSC samples (adj.p-val < 0.05 and |logFC|>1) while only 9 DE genes were identified when using only the subset of data (MSC samples only). Important genes known to be involved in endometriosis such as KLF9 and RND3 were missed in the latter case. When looking at the MSC vs non-MSC cells comparison, the linear model including all samples identified 260 genes for noE samples (including the stem cell marker SUSD2) while the subset analysis did not identify any DE genes. When looking at E samples, 12 genes were identified with the first approach and only 1 with the subset approach. Although the stem cell marker RGS5 was found in both cases, the subset test missed important genes involved in stem cell differentiation such as NOTCH3 and other potentially related genes to be used for further investigation and pathway analysis.

Keywords: differential expression, endometriosis, linear model, RNAseq

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Authors: Cris Bravo

Abstract:

Social entrepreneurship is a new and exciting topic that holds a great promise in helping alleviate the social problems of the world. As a new subject, the meaning of the term is too broad and this is counterproductive in trying to build understanding around the concept. The purpose of this study is to identify and compare the elements of social entrepreneurship as defined by seven international organizations leading social entrepreneurship projects: Ashoka Foundation, Skoll Foundation, Schwab Foundation and Yunus Center; as well as from three other institutions fostering social entrepreneurship: Global Social Benefit Institute, BRAC University, and Socialab. The study used document analysis from Skoll Foundation, Schwab Foundation, Yunus Center and Ashoka Foundation; and open ended interview to experts from the Global Social Benefit Institute at Santa Clara University in United States, BRAC University from Bangladesh, and Socialab from Argentina. The study identified three clearly differentiated schools of thought, based on their views on revenue, scalability, replicability and geographic location. While this study is by no means exhaustive, it provides an indication of the patterns of ideas fostered by important players in the field. By clearly identifying the similarities and differences in the concept of social entrepreneurship, research and practitioners are better equipped to build on the subject, and to promote more adequate and accurate social policies to foster the development of social entrepreneurship.

Keywords: replicability, revenue, scalability, schools of thought, social entrepreneurship

Procedia PDF Downloads 341

Authors: Malgorzata Schwab, Ashis Kumer Biswas

Abstract:

In this concept paper, we explore the topic of Reversibility in Neural Networks leveraged for Network Integrity Verification and crafted the term ''Trusted Neural Network'' (TNN), paired with the API abstraction around it, to embrace the idea formally. This newly proposed high-level generalizable TNN model builds upon the Invertible Neural Network architecture, trained simultaneously in both forward and reverse directions. This allows for the original system inputs to be compared with the ones reconstructed from the outputs in the reversed flow to assess the integrity of the end-to-end inference flow. The outcome of that assessment is captured as an Integrity Score. Concrete implementation reflecting the needs of specific problem domains can be derived from this general approach and is demonstrated in the experiments. The model aspires to become a useful practice in drafting high-level systems architectures which incorporate AI capabilities.

Keywords: trusted, neural, invertible, API

Procedia PDF Downloads 108

Authors: Xiran Wang, Johanna Trinkl, Thomas Hoffmann, Wilfried Schwab

Abstract:

Malonyltransferases (MATs) are enzymes that play a key role in the biosynthesis of secondary metabolites in plants, such as flavonoids and anthocyanins. As a kind of flavonoid-rich fruit, strawberries are an ideal model to study MATs. From Goodberry metabolome data, in the hybrid generation of 2 strawberries various, Fragaria × ananassa cv. 'Senga Sengana' and 'Candonga', we found the malonylated flavonoid concentration is significantly higher in 'Senga Sengana' compared with 'Candonga'. Therefore, we aimed to identify and characterize the malonyltransferases responsible for the different malonylated flavonoid concentrations in two different strawberry cultivars. In this study, we have found 6 MATs via genome mapping, metabolome analysis, gene cloning, and enzyme assay from strawberries, which catalyzed the malonylation of flavonoid substrates: quercetin-3-glucoside, kaempferol-3-glucoside, pelargonidin-3-glucoside, and cyanidin-3-glucoside. All four compounds reacted with FaMATs to varying degrees. These MATs have important implication into strawberries’ flavonoid biosynthesis, and also provide insights into insights into flavonoid biosynthesis, potential applications in agriculture, plant science, and pharmacy, and information on the regulation of secondary metabolism in plants.

Keywords: malonyltransferase, strawberry, flavonoid biosynthesis, enzyme assay

Procedia PDF Downloads 90