Cancer Health Disparities Drivers with BERTopic Modelling and Pycaret Evaluation

The complex interplay of social, behavioural, lifestyle, environmental, health system, and natural health variables contribute to disparities in cancer treatment across racial and ethnic groups. Consequently, it is necessary to identify the variables contributing to cancer health inequalities and develop strategies to achieve health equality. Pubmed abstract on Cancer health disparities was scraped with a bio.Entrez python package. Preprocessed data with regex and Natural tool kit(NLTK), topic modelling with BERTopic embeddings, and c-TF-IDF to construct dense clusters and analyse top topics linked with Cancer health disparities. Model evaluation with Pycaret coherence score and web app deployment with Streamlit. The results showed that Topic 32 with terms obese, female, male, school, survey, student, post, and discrepancy had the best coherence score of 0.3687. In contrast, topic 8 with terms prevalence, adult, income, high, usage, diabetes, education, elderly, change and low, received the least coherence score of 0.3255. The model classifies each Subject Word score based on the scores, the granular topic concerns and trends related to cancer health disparities, investigates the connection between drivers of cancer health disparities, and evaluates the model with their coherence score values

Identification of genomic regions associated with cereal cyst nematode (Heterodera avenae Woll.) resistance in spring and winter wheat

Cereal cyst nematode (CCN) is a major threat to cereal crop production globally including wheat (Triticum aestivum L.). In the present study, single-locus and multi-locus models of Genome-Wide Association Study (GWAS) were used to find marker trait associations (MTAs) against CCN (Heterodera avenae) in wheat. In total, 180 wheat accessions (100 spring and 80 winter types) were screened against H. avenae in two independent years (2018/2019 "Environment 1" and 2019/2020 "Environment 2") under controlled conditions. A set of 12,908 SNP markers were used to perform the GWAS. Altogether, 11 significant MTAs, with threshold value of -log10 (p-values) >/= 3.0, were detected using 180 wheat accessions under combined environment (CE). A novel MTA (wsnp_Ex_c53387_56641291) was detected under all environments (E1, E2 and CE) and considered to be stable MTA. Among the identified 11 MTAs, eight were novel and three were co-localized with previously known genes/QTLs/MTAs. In total, 13 putative candidate genes showing differential expression in roots, and known to be involved in plant defense mechanisms were reported. These MTAs could help us to identify resistance alleles from new sources, which could be used to identify wheat varieties with enhanced CCN resistance

QTL mapping for resistance against cereal cyst nematode (Heterodera avenae Woll.) in wheat (Triticum aestivum L.)

The resistance to cereal cyst nematode (Heterodera avenae Woll.) in wheat (Triticum aestivum L.) was studied using 114 doubled haploid lines from a novel ITMI mapping population. These lines were screened for nematode infestation in a controlled environment for two years. QTL-mapping analyses were performed across two years (Y1 and Y2) as well as combining two years (CY) data. On the 114 lines that were screened, a total of 2,736 data points (genotype, batch or years, and replication combinations) were acquired. For QTL analysis, 12,093 markers (11,678 SNPs and 415 SSRs markers) were used, after filtering the genotypic data, for the QTL mapping. Composite interval mapping, using Haley-Knott regression (hk) method in R/QTL, was used for QTL analysis. In total, 19 QTLs were detected out of which 13 were novel and six were found to be colocalized or nearby to previously reported Cre genes, QTLs or MTAs for H. avenae or H. filipjevi. Nine QTLs were detected across all three groups (Y1, Y2 and CY) including a significant QTL "QCcn.ha-2D" on chromosome 2D that explains 23% of the variance. This QTL colocalized with a previously identified Cre3 locus. Novel QTL, QCcn.ha-2A, detected in the present study could be the possible unreported homeoloci to QCcn.ha-2D, QCcn.ha-2B.1 and QCcn.ha-2B.2. Six significant digenic epistatic interactions were also observed. In addition, 26 candidate genes were also identified including genes known for their involvement in PPNs (plant parasitic nematodes) resistance in different plant species. In-silico expression of putative candidate genes showed differential expression in roots during specific developmental stages. Results obtained in the present study are useful for wheat breeding to generate resistant genetic resources against H. avenae

The United States COVID-19 Forecast Hub dataset

Academic researchers, government agencies, industry groups, and individuals have produced forecasts at an unprecedented scale during the COVID-19 pandemic. To leverage these forecasts, the United States Centers for Disease Control and Prevention (CDC) partnered with an academic research lab at the University of Massachusetts Amherst to create the US COVID-19 Forecast Hub. Launched in April 2020, the Forecast Hub is a dataset with point and probabilistic forecasts of incident cases, incident hospitalizations, incident deaths, and cumulative deaths due to COVID-19 at county, state, and national, levels in the United States. Included forecasts represent a variety of modeling approaches, data sources, and assumptions regarding the spread of COVID-19. The goal of this dataset is to establish a standardized and comparable set of short-term forecasts from modeling teams. These data can be used to develop ensemble models, communicate forecasts to the public, create visualizations, compare models, and inform policies regarding COVID-19 mitigation. These open-source data are available via download from GitHub, through an online API, and through R packages

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals <1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data

Enhancing Computer-Aided Cervical Cancer Detection Using a Novel Fuzzy Rank-Based Fusion

Cervical cancer is a severe and pervasive disease that poses a significant health threat to women globally. The Pap smear test is an efficient and effective method for detecting cervical cancer in its early stages. However, manual screening is labor-intensive and requires expert cytologists, leading to potential delays and inconsistencies in diagnosis. Deep Learning-based Computer-Aided Diagnosis (CAD) has shown significant results and can ease the problem of manual screening. However, one single model is sometimes insufficient to capture the complex data pattern for accurate disease prediction. In this work, we develop an end-to-end architecture utilizing three pre-trained models for the initial cervical cancer prediction. To aggregate the outcomes of these models, we propose a novel fuzzy rank-based ensemble considering two non-linear functions for the final level prediction. Unlike simple fusion techniques, the proposed architecture provides the final predictions on the test samples by considering the base classifier’s confidence in the predictions. To further enhance the classification capabilities of these models, we integrate advanced augmentation techniques such as CutOut, MixUp, and CutMix. The proposed model is evaluated on two benchmark datasets, SIPaKMeD and Mendeley LBC, using a 5-fold cross-validation approach. On the SIPaKMeD dataset, the proposed ensemble architecture achieves a classification accuracy of 97.18% and an F1 score of 97.16%. On the Mendeley LBC dataset, the accuracy reaches 99.22% with an F1 score of 99.19%. Experimental results demonstrate the proposed architecture’s effectiveness and potential in cervical Pap smear image classification. This could aid medical professionals in making more informed treatment decisions, improving overall effectiveness in the testing process

Mapping of QTLs and meta-QTLs for Heterodera avenae Woll. resistance in common wheat (Triticum aestivum L.)

Abstract Background In hexaploid wheat, quantitative trait loci (QTL) and meta-QTL (MQTL) analyses were conducted to identify genomic regions controlling resistance to cereal cyst nematode (CCN), Heterodera avenae. A mapping population comprising 149 RILs derived from the cross HUW 468 × C 306 was used for composite interval mapping (CIM) and inclusive composite interval mapping (ICIM). Results Eight main effect QTLs on three chromosomes (1B, 2A and 3A) were identified using two repeat experiments. One of these QTLs was co-localized with a previously reported wheat gene Cre5 for resistance to CCN. Seven important digenic epistatic interactions (PVE = 5% or more) were also identified, each involving one main effect QTL and another novel E-QTL. Using QTLs earlier reported in literature, two meta-QTLs were also identified, which were also used for identification of 57 candidate genes (CGs). Out of these, 29 CGs have high expression in roots and encoded the following proteins having a role in resistance to plant parasitic nematodes (PPNs): (i) NB-ARC,P-loop containing NTP hydrolase, (ii) Protein Kinase, (iii) serine-threonine/tyrosine-PK, (iv) protein with leucine-rich repeat, (v) virus X resistance protein-like, (vi) zinc finger protein, (vii) RING/FYVE/PHD-type, (viii) glycosyl transferase, family 8 (GT8), (ix) rubisco protein with small subunit domain, (x) protein with SANT/Myb domain and (xi) a protein with a homeobox. Conclusion Identification and selection of resistance loci with additive and epistatic effect along with two MQTL and associated CGs, identified in the present study may prove useful for understanding the molecular basis of resistance against H. avenae in wheat and for marker-assisted selection (MAS) for breeding CCN resistant wheat cultivars

Segmentation of Spectral Plant Images Using Generative Adversary Network Techniques

The spectral image analysis of complex analytic systems is usually performed in analytical chemistry. Signals associated with the key analytics present in an image scene are extracted during spectral image analysis. Accordingly, the first step in spectral image analysis is to segment the image in order to extract the applicable signals for analysis. In contrast, using traditional methods of image segmentation in chronometry makes it difficult to extract the relevant signals. None of the approaches incorporate contextual information present in an image scene; therefore, the classification is limited to thresholds or pixels only. An image translation pixel-to-pixel (p2p) method for segmenting spectral images using a generative adversary network (GAN) is presented in this paper. The p2p GAN forms two neuronal models. During the production and detection processes, the representation learns how to segment ethereal images precisely. For the evaluation of the results, a partial discriminate analysis of the least-squares method was used to classify the images based on thresholds and pixels. From the experimental results, it was determined that the GAN-based p2p segmentation performs the best segmentation with an overall accuracy of 0.98 ± 0.06. This result shows that image processing techniques using deep learning contribute to enhanced spectral image processing. The outcomes of this research demonstrated the effectiveness of image-processing techniques that use deep learning to enhance spectral-image processing