Article Search Tool and Topic Classifier

This thesis focuses on 3 main tasks related to Document Recommendations. The first approach deals with applying existing techniques on Document Recommendations using Doc2Vec. A robust representation of the same is presented to understand how noise induced in the embedding space affects predictions of the recommendations. The next phase focuses on improving the above recommendations using a Topic Classifier. A Hierarchical Attention Network is employed for this purpose. In order to increase the accuracy of prediction, this work establishes a relation to embedding size of the words in the article. In the last phase, model-agnostic Explainable AI (XAI) techniques are implemented to prove the findings in this thesis. XAI techniques are also employed to show how we can fine tune model hyper-parameters for a black-box model

The Gut Commensal Bacteroides thetaiotaomicron Exacerbates Enteric Infection through Modification of the Metabolic Landscape

SummaryThe enteric pathogen enterohemorrhagic Escherichia coli (EHEC) causes severe diarrhea, but the influence of the gut microbiota on EHEC infection is largely unknown. A predominant member of the microbiota, Bacteroides thetaiotaomicron (Bt), is resident at EHEC attachment sites. We show that Bt enhances EHEC virulence gene expression through the transcription factor Cra, which is functionally sensitive to sugar concentrations. This enhanced virulence accompanies increased formation of attaching and effacing (AE) lesions requisite for EHEC colonization. Infection with Citrobacter rodentium, a natural mouse pathogen homologous to EHEC, in Bt-reconstituted mice results in increased gut permeability along with exacerbated host pathology and mortality compared to mice deplete of microflora. Bt modifies the metabolite environment at infection sites, increasing metabolites involved in gluconeogenesis, with stark increases in succinate, which can be sensed by Cra. Our findings suggest that microbiota composition affects disease outcome and may explain links between microbiota composition and disease susceptibility

Characterization of Fusobacterium isolates from the respiratory tract of white-tailed deer (Odocoileus virginianus)

A total of 23 clinical isolates of Fusobacterium spp. were recovered at necropsy over a 2-year period from the respiratory tract of white-tailed deer (Odocoileus virginianus). Isolates were identified as Fusobacterium varium (18/23), Fusobacterium necrophorum subsp. funduliforme (3/23), and Fusobacterium necrophorum subsp. necrophorum (2/23). Using polymerase chain reaction–based detection of virulence genes, all F. necrophorum isolates were positive for the promoter region of the leukotoxin operon and the hemagglutinin-related protein gene, while all F. varium isolates were negative. The presence of the leukotoxin gene in F. necrophorum isolates and the absence of this gene in F. varium isolates were confirmed by Southern hybridization using 2 separate probes. Toxicity to bovine polymorphonuclear leukocytes was observed with all F. necrophorum isolates, but was not observed in any F. varium isolates. Susceptibility to antimicrobials was markedly different for F. varium as compared to F. necrophorum. In summary, no evidence of leukotoxin production was detected in any of the 23 F. varium isolates used in the current study. The data suggests that F. varium, the most common species isolated, may be a significant pathogen in deer with a different virulence mechanism than F. necrophorum

Cell Based Drug Delivery: Micrococcus luteus Loaded Neutrophils as Chlorhexidine Delivery Vehicles in a Mouse Model of Liver Abscesses in Cattle

Citation: Wendel, S. O., Menon, S., Alshetaiwi, H., Shrestha, T. B., Chlebanowski, L., Hsu, W. W., . . . Troyer, D. L. (2015). Cell Based Drug Delivery: Micrococcus luteus Loaded Neutrophils as Chlorhexidine Delivery Vehicles in a Mouse Model of Liver Abscesses in Cattle. Plos One, 10(5), 13. doi:10.1371/journal.pone.0128144The recent WHO report on antibiotic resistances shows a dramatic increase of microbial resistance against antibiotics. With only a few new antibiotics in the pipeline, a different drug delivery approach is urgently needed. We have obtained evidence demonstrating the effectiveness of a cell based drug delivery system that utilizes the innate immune system as targeting carrier for antibacterial drugs. In this study we show the efficient loading of neutrophil granulocytes with chlorhexidine and the complete killing of E. coli as well as Fusobacterium necrophorum in in-vitro studies. Fusobacterium necrophorum causes hepatic abscesses in cattle fed high grain diets. We also show in a mouse model that this delivery system targets infections of F. necrophorum in the liver and reduces the bacterial burden by an order of magnitude from approximately 2.10(6) to 1.10(5)

Dementia and Diabetes Mellitus: Association with Apolipoprotein E4 Polymorphism from a Hospital in Southern India

Objective. To evaluate the association of Apolipoprotein E4 (ApoE4) in Alzheimer's dementia (AD) with comorbid diabetes mellitus (DM). Methods. The study included subjects with Alzheimer's dementia (AD) (n = 209), individuals with non-Alzheimer's dementia (nAD) (n = 122), individuals with parental history of AD (f/hAD) (n = 70), and control individuals who had normal cognitive functions and no parental history of dementia (NC) (n = 193). Dementia was diagnosed using International Classification of Diseases-10 revision (ICD-10) criteria. DM was assessed on the basis of self-report and/or use of antidiabetic medications. ApoE genotyping was done using sequence-specific primer polymerase chain reaction. Results. ApoE4 allele frequencies were highest among AD with comorbid DM (0.35) followed by AD without DM (0.25), nAD with DM (0.13), nAD without comorbid DM (0.12), and NC (0.08). Frequency of ApoE4 in persons with f/hAD was 0.13. The association of AD with co-morbid DM in ApoE4 carriers was more in comparison to NC with DM (OR = 5.68, P = 0.04). Conclusion. There is a significant association between AD with co-morbid DM and ApoE4 genotype

Clinical and histopathological correlation of oral malignancy and potentially malignant disorders based on a screening program at high-risk population in Tamil Nadu, India

BackgroundThere is a high incidence of oral cancer and oral potential malignant disorder observed in southeast Asian countries such as India. Our study aimed to assess the correlation between screening and histopathological diagnosis and to predict the specificity and sensitivity of chair-side/field-based assessment of the oral lesion.Materials and methodsA total of 40,852 subjects aged between 20 and 60 years were screened in the 1st phase of the study, suspected lesions were stained with toluidine blue (Manufactured by Otto Chemicals private limited, India) at two time points, those who stained positively during the two points were taken up for biopsy. Provisional diagnosis was later correlated with histopathological diagnosis.ResultsSubjects who underwent biopsy had a mean age of (49.01 ± 9.8 years), Leukoplakia (1.5%) was the most common lesion observed among tobacco users, interestingly it had the least correlation (39.6%) in diagnosis, Overall sensitivity (88%) and a positive predictive value (80%) was high for clinical diagnosis of OPMD in our study.ConclusionCorrelation of clinical and histopathological diagnosis observed in our study confirms higher yield of true positives while screening in remote and vulnerable populations, which would assure a better quality of life for these subjects

An appraisal of rainfall estimation over India using remote sensing and in situ measurements

167-177The most important meteorological parameter Rainfall, shows high variability in space and time, particularly over Tropics / Monsoon region. Many new observational and analysis methods to observe / analyse them by remote sensing techniques (Satellites, Doppler Weather Radars) have emerged over the decades, besides the dense network of in situ rain gauges, Automatic Weather Stations (AWS) etc on ground. The scales of observations being vastly different for in situ and remote sensing methods, large discrepancies between different techniques are inherent. These problems have been brought out through various validation studies by many groups in the country. Even on the daily all India spatial scale, basically only the peaks and troughs from satellite estimates match reasonably well with in situ data. Results of a case study during an intense and long-lasting rain event over Chennai, from DWR, with different satellite products and ground truth are presented. The importance of DWR rainfall data in significantly improving the integrated products is emphasised. A simple two-way approach to establish Z – R relationship for the DWRs in the country is also suggested. A well-coordinated integrated programme to study the inter comparability of precipitation at various spatio- temporal scales in the context of our water resources, model validation, extreme rainfall events, Climate change, etc., is called for. The desired accuracies from satellite data vis a vis IMD gridded data for different applications have been summarised

Multiple novel prostate cancer susceptibility signals identified by fine-mapping of known risk loci among Europeans

Genome-wide association studies (GWAS) have identified numerous common prostate cancer (PrCa) susceptibility loci. We have fine-mapped 64 GWAS regions known at the conclusion of the iCOGS study using large-scale genotyping and imputation in 25 723 PrCa cases and 26 274 controls of European ancestry. We detected evidence for multiple independent signals at 16 regions, 12 of which contained additional newly identified significant associations. A single signal comprising a spectrum of correlated variation was observed at 39 regions; 35 of which are now described by a novel more significantly associated lead SNP, while the originally reported variant remained as the lead SNP only in 4 regions. We also confirmed two association signals in Europeans that had been previously reported only in East-Asian GWAS. Based on statistical evidence and linkage disequilibrium (LD) structure, we have curated and narrowed down the list of the most likely candidate causal variants for each region. Functional annotation using data from ENCODE filtered for PrCa cell lines and eQTL analysis demonstrated significant enrichment for overlap with bio-features within this set. By incorporating the novel risk variants identified here alongside the refined data for existing association signals, we estimate that these loci now explain ∼38.9% of the familial relative risk of PrCa, an 8.9% improvement over the previously reported GWAS tag SNPs. This suggests that a significant fraction of the heritability of PrCa may have been hidden during the discovery phase of GWAS, in particular due to the presence of multiple independent signals within the same regio

Optimasi Portofolio Resiko Menggunakan Model Markowitz MVO Dikaitkan dengan Keterbatasan Manusia dalam Memprediksi Masa Depan dalam Perspektif Al-Qur`an

Risk portfolio on modern finance has become increasingly technical, requiring the use of sophisticated mathematical tools in both research and practice. Since companies cannot insure themselves completely against risk, as human incompetence in predicting the future precisely that written in Al-Quran surah Luqman verse 34, they have to manage it to yield an optimal portfolio. The objective here is to minimize the variance among all portfolios, or alternatively, to maximize expected return among all portfolios that has at least a certain expected return. Furthermore, this study focuses on optimizing risk portfolio so called Markowitz MVO (Mean-Variance Optimization). Some theoretical frameworks for analysis are arithmetic mean, geometric mean, variance, covariance, linear programming, and quadratic programming. Moreover, finding a minimum variance portfolio produces a convex quadratic programming, that is minimizing the objective function ðð¥with constraintsð ð 𥠥 ðandð´ð¥ = ð. The outcome of this research is the solution of optimal risk portofolio in some investments that could be finished smoothly using MATLAB R2007b software together with its graphic analysis