Exploring Machine Learning Approaches to Precipitation Prediction: Post Processing of Daily Accumulated North American forecasts

This thesis presents recent work on exploring machine learning (ML) and deep learning (DL) models to improve the accuracy of 24 hour precipitation forecasts. Leveraging a comprehensive North American dataset of precipitation values from Numerical Weather Prediction (NWP) models and secondary meteorological features, the research showcases the need of ML techniques in post-processing NWP precipitation predictions. The evaluation reveals remarkable performance improvements over baseline model, with certain ML models achieving a 15% reduction in Mean Absolute Error (MAE), a 5% decrease in Root Mean Squared Error (RMSE), a 45% reduction in Median Absolute Error (MdAE), and a 50% decrease in Relative Bias (RB). Convolutional Neural Networks (CNN) and Gradient Boosting Regressor (GBR) emerged as top performers, demonstrating their proficiency in accurately predicting daily precipitation.Natural Sciences and Engineering Research Council of Canada Alliance Grant with Weatherlogics Inc.Master of Science in Applied Computer Scienc

Analysis of heat shock proteins and cytokines expressed during early stages of osteoarthritis in a mouse model

SummaryObjective:Osteoarthritis (OA) is a debilitating disease of the joints. The joints of affected individuals are characterized by a progressive degeneration of articular cartilage leading to inflammation and pain. The expression of heat shock proteins (HSPs) is a ubiquitous self-protective mechanism of all cells under stress, furthermore, the synovium of osteoarthritic individuals contains high levels of cytokines. This study seeks to establish the role of HSPs and cytokines in OA.Methods:We have investigated the presence of HSPs and cytokines in articular cartilage during early stages of OA in a mouse that is known to develop spontaneous OA lesions (C57 black mouse). The articular cartilage from closely related mice (C57BL/6) was used as control. Messenger RNAs (mRNAs) for HSPs (HSP32, HSP47, HSP60, HSP70, HSP84 and HSP86) and cytokines [interleukin-1β (IL-1β), interleukin-6 (IL-6), tumor necrosis factor-α (TNF-α) and interferon-γ (IFN-γ)] were detected by reverse transcription-polymerase chain reaction (RT-PCR).Results:The mRNA levels of HSP47, HSP70, HSP86, IL-6, and IFN-γ were up-regulated in the cartilage of C57 black mice, whereas, the level of expression of HSP32, HSP60, HSP84 and IL-1β remained unchanged. Furthermore, the expression of IL-1β, IL-6, TNF-α and IFN-γ mRNA was associated with expression of HSP60, HSP47, HSP70 and HSP70/HSP86 mRNA, respectively.Conclusions:The findings in this study suggest that chondrocytes are conditioned under non-physiological stress during early stages of OA, In addition, among HSPs, HSP70 was associated with two different highly expressed cytokines in C57 black mice, indicating the possible role of HSP70 as a characteristic indicator of early stage of OA

Hepatocyte Nuclear Factor 4 Provokes Expression of Epithelial Marker Genes, Acting As a Morphogen in Dedifferentiated Hepatoma Cells

Abstract. We have recently shown that stable expression of an epitope-tagged cDNA of the hepatocyte- enriched transcription factor, hepatocyte nuclear factor (HNF)4, in dedifferentiated rat hepatoma H5 cells is sufficient to provoke reexpression of a set of hepatocyte marker genes. Here, we demonstrate that the effects of HNF4 expression extend to the reestablishment of differentiated epithelial cell morphology and simple epithelial polarity. The acquisition of epithelial morphology occurs in two steps. First, expression of HNF4 results in reexpression of cytokeratin proteins and partial reestablishment of E-cadherin production. Only the transfectants are competent to respond to the synthetic glucocorticoid dexamethasone, which induces the second step of morphogenesis, including formation of the junctional complex and expression of a polarized cell phenotype. Cell fusion experiments revealed that the transfectant cells, which show only partial restoration of E-cadherin expression, produce an extinguisher that is capable of acting in trans to downregulate the E-cadherin gene of well-differentiated hepatoma cells. Bypass of this repression by stable expression of E-cadherin in H5 cells is sufficient to establish some epithelial cell characteristics, implying that the morphogenic potential of HNF4 in hepatic cells acts via activation of the E-cadherin gene. Thus, HNF4 seems to integrate the genetic programs of liver-specific gene expression and epithelial morphogenesis

Essential genes for astroglial development and axon pathfinding during zebrafish embryogenesis

The formation of the central nervous system depends on the coordinated development of neural and glial cell types that arise from a common precursor. Using an existing group of zebrafish mutants generated by viral insertion, we performed a “shelf-screen” to identify genes necessary for astroglial development and axon scaffold formation. We screened 274 of 315 viral insertion lines using antibodies that label axons (anti-Acetylated Tubulin) and astroglia (anti-Gfap) and identified 25 mutants with defects in gliogenesis, glial patterning, neurogenesis, and axon guidance. We also identified a novel class of mutants affecting radial glial cell numbers. Defects in astroglial patterning were always associated with axon defects, supporting an important role for axon-glial interactions during axon scaffold development. The genes disrupted in these viral lines have all been identified, providing a powerful new resource for the study of axon guidance, glio- and neurogenesis, and neuron-glial interactions during development of the vertebrate CNS.National Institutes of Health (U.S.) (Grant T32MH020051)National Institutes of Health (U.S.) (Grant F32NS043872

Characterization of the role of the proximal sequence element (PSE) and the TATA box in the human U6 small nuclear RNA (snRNA) gene transcription

Vita.Transcription of vertebrate U6 snRNA genes by RNA polymerase III requires two sequence elements in the proximal promoter region: the PSE (proximal sequence element, found in snRNA promoters transcribed by RNA polymerase II) and the TATA element (found in many mRNA promoters). The locations of the PSE and the TATA box are important determinants for transcriptional start site selection in their respective RNA polymerase II promoters. In vertebrate U6 genes the PSE and the TATA elements are located in approximately the same positions as in the polymerase II transcribed genes. However, their respective roles in initiation site selection, transcriptional efficiency and polymerase specificity are not known. I have analyzed the effects of spacing changes between the PSE and the TATA element, and between the two elements and the normal U6 start site on human U6 gene transcription in vitro and in transfected cells. My results discount the possibility that the location of either the PSE or the TATA element, by itself, dictates efficient selection of a transcriptional start site. Instead, I suggest that the two elements form a compound promoter element whose location dictates the start site of transcription from the hum an U6 gene promoter. Spacing changes between the PSE and the TATA element result in greatly reduced levels of transcription. These observations suggest the possibility that the factors that bind these two elements interact with each other. To test this hypothesis, I further investigated the possible interaction of the PSE and TATA binding proteins (PBP and TBP) when bound to normal or mutant U6 proximal promoters using a gel mobility shift assay. I detect a complex containing both PBP and TBP bound to the wild-type U6 promoter. Efficient formation of the triple complex is dependent on the presence of the PSE and the TATA box on the template DNA. Furthermore, U6 mutant promoters containing an increased spacing between the PSE and TATA box of 5 or 10 bp are impaired in the ability to form a complex that includes TBP. I infer from these results that PBP and TBP interact when their binding sites are properly positioned in a U6 gene promoter

Understanding extrusion technology for cereal–pulse blends: A review

AbstractIn recent times, extrusion cooking is being used to develop nutrient-dense products with an aim to benefit humans and to cater their nutritional requirements. The present paper discusses various aspects of twin-screw extrusion cooking and behaviour of its process parameters in relation to cereal–pulse blend. Profiling of raw material, i.e. moisture, protein, lipid, and starch, along with the assessment of product parameters including expansion ratio, bulk density, water absorption index, and water solubility index has been extensively reviewed to develop a desirable product. Therefore, in the present review paper, extrusion cooking has been highlighted and discussed in detail as a suitable technology for the development of cereal–pulse-based snacks/products

Characterization of the role of the proximal sequence element (PSE) and the TATA box in the human U6 small nuclear RNA (snRNA) gene transcription

Vita.Transcription of vertebrate U6 snRNA genes by RNA polymerase III requires two sequence elements in the proximal promoter region: the PSE (proximal sequence element, found in snRNA promoters transcribed by RNA polymerase II) and the TATA element (found in many mRNA promoters). The locations of the PSE and the TATA box are important determinants for transcriptional start site selection in their respective RNA polymerase II promoters. In vertebrate U6 genes the PSE and the TATA elements are located in approximately the same positions as in the polymerase II transcribed genes. However, their respective roles in initiation site selection, transcriptional efficiency and polymerase specificity are not known. I have analyzed the effects of spacing changes between the PSE and the TATA element, and between the two elements and the normal U6 start site on human U6 gene transcription in vitro and in transfected cells. My results discount the possibility that the location of either the PSE or the TATA element, by itself, dictates efficient selection of a transcriptional start site. Instead, I suggest that the two elements form a compound promoter element whose location dictates the start site of transcription from the hum an U6 gene promoter. Spacing changes between the PSE and the TATA element result in greatly reduced levels of transcription. These observations suggest the possibility that the factors that bind these two elements interact with each other. To test this hypothesis, I further investigated the possible interaction of the PSE and TATA binding proteins (PBP and TBP) when bound to normal or mutant U6 proximal promoters using a gel mobility shift assay. I detect a complex containing both PBP and TBP bound to the wild-type U6 promoter. Efficient formation of the triple complex is dependent on the presence of the PSE and the TATA box on the template DNA. Furthermore, U6 mutant promoters containing an increased spacing between the PSE and TATA box of 5 or 10 bp are impaired in the ability to form a complex that includes TBP. I infer from these results that PBP and TBP interact when their binding sites are properly positioned in a U6 gene promoter

Re-Engineering of Traditional Indian Wadi into Ready-to-Use High Protein Quality and Fibre Rich Chunk

In the present study an attempt has been made to re-engineer traditional wadi into wholesome ready-to-use cereal-pulse-based chunks rich in protein quality and fibre content. Chunks were made using extrusion-dehydration combination. Two formulations i.e., whole green gram dhal with instant oats and washed green gram dhal with whole oats were formulated. These chunks are versatile in nature as they can be easily incorporated in day-to-day home-made preparations such as pulao, potato curry and kadhi. Cereal-pulse ratio was calculated using NDpCal%. Limiting amino acids such as lysine, tryptophan, methionine, cysteine and threonine were calculated for maximum amino acid profile in cereal-pulse combination. Time-temperature combination for extrusion at 130oC and dehydration at 65oC for 7 hours and 15 minutes were standardized to obtain maximum protein and fibre content. Proximate analysis such as moisture, fat and ash content were analyzed. Protein content of formulation was 62.10% and 68.50% respectively. Fibre content of formulations was 2.99% and 2.45%, respectively. Using a 5-point hedonic scale, consumer preference trials of 102 consumers were conducted and analyzed. Evaluation of chunks prepared in potato curry, kadi and pulao showed preferences for colour 82%, 87%, 86%, texture and consistency 80%, 81%, 88%, flavour and aroma 74%, 82%, 86%, after taste 70%, 75%, 86% and overall acceptability 77%, 75%, 88% respectively. High temperature inactivates antinutritional compounds such as trypsin inhibitors, lectins, saponins etc. Hence, availability of protein content was increased. Developed products were palatable and easy to prepare