Abugida Normalizer and Parser for Unicode texts

This paper proposes two libraries to address common and uncommon issues with Unicode-based writing schemes for Indic languages. The first is a normalizer that corrects inconsistencies caused by the encoding scheme https://pypi.org/project/bnunicodenormalizer/ . The second is a grapheme parser for Abugida text https://pypi.org/project/indicparser/ . Both tools are more efficient and effective than previously used tools. We report 400% increase in speed and ensure significantly better performance for different language model based downstream tasks.Comment: 3 pages, 1 figur

Novel CNGA3 and CNGB3 mutations in two Pakistani families with achromatopsia

PURPOSE: To identify the genetic defect in two Pakistani families with autosomal recessive achromatopsia. METHODS: Two families (RP26 and RP44) were originally diagnosed with retinal dystrophy based upon their medical history. To localize the causative genes in these families, homozygosity mapping was performed using Affymetrix 10K single nucleotide polymorphism (SNP) arrays. Sequence analysis was used to find the mutations in candidate genes cyclic nucleotide-gated channel alpha-3 (CNGA3; family RP26) and cyclic nucleotide-gated channel beta-3 (CNGB3; family RP44). Control individuals were analyzed by allele-specific PCR for the CNGA3 mutation and BstXI restriction analysis for the CNGB3 mutation. After genetic analysis, clinical diagnosis was re-evaluated by electroretinography and color vision testing. During the course of this study, selected affected members of family RP26 were given pink glasses as supportive therapy. RESULTS: Sequence analysis of the positional candidate genes identified a novel missense mutation in CNGA3 (c.822G>T; p.R274S) in family RP26, and a novel CNGB3 frameshift mutation (c.1825delG; p.V609WfsX9) in family RP44. Clinical re-evaluation after genetic analysis revealed that both families have segregating autosomal recessive achromatopsia. CONCLUSIONS: Genetic analysis of two Pakistani families with retinal disease enabled the establishment of the correct diagnosis of achromatopsia. Two novel mutations were identified in CNGA3 and CNGB3 that are both specifically expressed in cone photoreceptors. Re-evaluation of the clinical status revealed that both families had achromatopsia. The use of pink glasses in patients was helpful in reducing photophobia and enabled rod-mediated vision

BaDLAD: A Large Multi-Domain Bengali Document Layout Analysis Dataset

While strides have been made in deep learning based Bengali Optical Character Recognition (OCR) in the past decade, the absence of large Document Layout Analysis (DLA) datasets has hindered the application of OCR in document transcription, e.g., transcribing historical documents and newspapers. Moreover, rule-based DLA systems that are currently being employed in practice are not robust to domain variations and out-of-distribution layouts. To this end, we present the first multidomain large Bengali Document Layout Analysis Dataset: BaDLAD. This dataset contains 33,695 human annotated document samples from six domains - i) books and magazines, ii) public domain govt. documents, iii) liberation war documents, iv) newspapers, v) historical newspapers, and vi) property deeds, with 710K polygon annotations for four unit types: text-box, paragraph, image, and table. Through preliminary experiments benchmarking the performance of existing state-of-the-art deep learning architectures for English DLA, we demonstrate the efficacy of our dataset in training deep learning based Bengali document digitization models

A homozygous p.Glu150Lys mutation in the opsin gene of two Pakistani families with autosomal recessive retinitis pigmentosa

PURPOSE: To identify the gene mutations responsible for autosomal recessive retinitis pigmentosa (arRP) in Pakistani families. METHODS: A cohort of consanguineous families with typical RP phenotype in patients was screened by homozygosity mapping using microsatellite markers that mapped close to 21 known arRP genes and five arRP loci. Mutation analysis was performed by direct sequencing of the candidate gene. RESULTS: In two families, RP21 and RP53, homozygosity mapping suggested RHO, the gene encoding rhodopsin, as a candidate disease gene on chromosome 3q21. In six out of seven affected members from the two families, direct sequencing of RHO identified a homozygous c.448G>A mutation resulting in the p.Glu150Lys amino acid change. This variant was first reported in PMK197, an Indian arRP family. Single nucleotide polymorphism analysis in RP21, RP53, and PMK197 showed a common disease-associated haplotype in the three families. CONCLUSIONS: In two consanguineous Pakistani families with typical arRP phenotype in the patients, we identified a disease-causing mutation (p.Glu150Lys) in the RHO gene. Single nucleotide polymorphism analysis suggests that the previously reported Indian family (PMK197) and the two Pakistani families studied here share the RHO p.Glu150Lys mutation due to a common ancestry

Identification of alternative exon usage in cancer survival using hierarchical modeling

Background Alternative exon usage (AEU) is an important component of gene expression regulation. Exon expression platforms allow the detection of associations between AEU and phenotypes such as cancer. Numerous studies have identified associations between gene expression and the brain cancer glioblastoma multiforme (GBM). The few consistent gene expression biomarkers of GBM that have been reported may be due to the limited consideration of AEU and the analytical approaches used. The objectives of this study were to develop a model that accounts for the variations in expression present between the exons within a gene and to identify AEU biomarkers of GBM survival. Methods The expression of exons corresponding to 25,403 genes was related to the survival of 250 individuals diagnosed with GBM in a training data set. Genes exhibiting AEU in the training data set were confirmed in an independent validation data set of 78 patients. A hierarchical model allows the consideration of covariation between exons within a gene and of the effect of the epidemiological characteristics of the patients was developed to identify associations between exon expression and patient survival. The same model serves multi-exon models with and without AEU and single-exon models. Results AEU associated with GBM survival was identified on 2477 genes (P-value < 5.0E-04 (FDR adjusted P-value < 5.0E-04). G-protein coupled receptor 98 (Gpr98) and epidermal growth factor (Egf) were among the genes exhibiting AEU with 30 and 9 exons associated with GBM survival, respectively. Pathways enriched among the AEU genes included focal adhesion, ECM-receptor interaction, ABC transporters and pathways in cancer. In addition, 24 multi-exon genes without AEU and 8 single-exon genes were associated with GBM survival (P-value < 0.0005). Conclusions The inferred patterns of AEU were consistent with in silico AS models. The hierarchical model used offered a flexible and simple way to interpret and identify associations between survival that accommodates multi-exon genes with or without AEU and single exon genes

Understanding gender determination in dioecious Amaranthus weeds palmer amaranth (Amaranthus palmeri) and waterhemp (Amaranthus tuberculatus)

Over the last few decades, numerous examples of multiple herbicide resistance in weeds have been reported. Many studies have documented various mechanisms through which weeds evade herbicidal action. This evolution of resistance in weed populations has been fueled by the intensive and extensive use of herbicides. Thus, the tactics that helped us in weed management turned out to be short term and have put at risk the future of weed management. Various factors, such as reduced farming system diversity, extensive use of herbicide-resistant crops, and the recent lack of herbicide discovery by industry, have all contributed towards undermining the foundations of weed management. As of today, 217 weed species have been reported to have established resistance to the herbicides. Furthermore, resistance was reported to all major known herbicide modes of action. This rapid rise in herbicide resistance among key weed species requires immediate attention. Development of novel weed management strategies is necessary, as the last mode of action developed to act against weeds was in 1990. However, this will require a far better understanding of weed biology and ecology than we currently have. It is, therefore, pivotal to understand the biology beneath the sex determination of dioecious weeds. Common waterhemp (Amaranthus tuberculatus (Moq.) Sauer var. rudis (Sauer) Costea and Tardif) and Palmer amaranth (Amaranthus palmeri S. Watson) are troublesome weeds of row-crop production in the United States. Their dioecious reproductive systems ensure outcrossing, facilitating rapid evolution and distribution of resistances to multiple herbicides. Little is known, however, about the genetic basis of dioecy in Amaranthus species. Understanding dioecy in these weeds can help us in establishing a probable control strategy for both weeds. Thus, the major aim of this study is to identify the mechanism of sex-determination in both these weedy species. In this work, we use restriction-site associated DNA sequencing (RAD- Seq) to investigate the genetic basis of sex determination in A. tuberculatus and A. palmeri. For each species, approximately 200 plants of each sex were sampled and used to create RAD-Seq libraries. The resulting libraries were separately barcoded and then pooled for sequencing with the Illumina platform, yielding millions of 64-base-pair reads. These reads were analyzed to identify sex-specific and sex-biased sequences. We identified 345 male-specific sequences from the A. palmeri data set and 2754 male-specific sequences in A. tuberculatus. An unexpected 723 female-specific sequences were identified in a subset of the A. tuberculatus females. Markers were developed for a few of these female-specific sequences to test for the presence of female-specific sequences in waterhemp female plants. However, these markers were unable to be used successfully. Male-specific markers were developed for both species, and these were used successfully to identify males. In the near term, sex-specific markers will be useful to the A. tuberculatus and A. palmeri research communities (e.g., to predict sex for crossing experiments). In the long-term, this research will provide the foundational tools for detailed investigations into the molecular biology and evolution of dioecy in weedy amaranths.U of I OnlyAuthor requested U of Illinois access only (OA after 2yrs) in Vireo ETD syste

Response of the rhizobial-mycorrhizal-lentil symbiosis to arsenic

The thesis focused on the response of the rhizobial-mycorrhizal-lentil symbiosis to arsenic as an environmental contaminant.  This was instigated by the concern over the arsenic contaminated irrigation water problem in South East Asia, and in particularly, its impact on Bangladesh agriculture.  This led to a holistic approach to the study, by investigating the effect of inoculation with Rhizobium leguminosarum and the AM fungus Glomus mosseae, as well as application of superphosphate and rock phosphate, on lentil growth, nitrogenase activity and nutrient uptake (especially N and P) in the presence of arsenic contaminated irrigation water.  Positive effects of mycorrhizal inoculation on lentil (Lens culinaris L.) growth, nitrogen fixation and P nutrition were observed, along with reduced uptake of As in roots, shoots and pods.  Decreased plant growth, nitrogen fixation, nutrient uptake, mycorrhizal infection and increased uptake of arsenic in root, shoot and pods were observed due to application of arsenate contaminated irrigation water.  The use of a lux based bacterial biosensor test demonstrated that mycorrhizal inoculation reduced arsenic bioavailability in soil and that most of the toxicity was associated with the colloidal and fine particulate soil fraction.  When rock phosphate was applied, an increase of P uptake only was observed.  In contrast, superphosphate increased both P and As uptake and decreased mycorrhizal infection and activity. In summary, this thesis has shown that mycorrhizal inoculation appears to offer great potential as an effective tool contributing to crop management for technique in minimisation of the total intake of As by human and livestock.  The observed decreased in uptake of As into pods of mycorrhizal lentil has particularly important potential implications for human health.EThOS - Electronic Theses Online ServiceGBUnited Kingdo