Welcome to SOAR: Shocker Open Access Repository!
SOAR is the institutional repository of Wichita State University. The purpose of SOAR is to make the University's digital scholarship available to global audience and to serve as a reliable digital storage. SOAR has a dual function of a publication platform and a digital archive. University faculty and staff are invited to publish research works, data, or documents in SOAR. For information on SOAR services and collections, policies, submission, and workflows, visit SOAR libguide or contact: firstname.lastname@example.org.
ItemFeature engineering from meta-data for prediction of differentially expressed genes: An investigation of Mus musculus exposed to space-conditions(Elsevier Ltd, 2024-04)Transcription profiling is a key process that can reveal those biological mechanisms driving the response to various exposure conditions or gene perturbations. In this work, we investigate the prediction of differentially expressed genes (DEGs) when exposed to conditions in space from a set of diverse engineered features. To do this, we collected DEGs and non-differentially expressed genes (NDEGs) of Mus musculus-based experiments on the GeneLab database. We engineered a diverse set of features from factors reported in the literature to affect gene expression. An extreme gradient boosting (XGBoost) model was trained to predict if a given gene would be differentially expressed at various levels of differential expression. The test results on a separate holdout dataset showed an area under the receiver operating characteristics curves (AUCs) of 0.90±0.07, averaged across the five selected percentages of the most and least differentially expressed genes. Subsequently, we investigated the impact of selection of features, both individually with a correlation-based feature-selection procedure and in groups with a combination procedure, on the prediction performance. The feature selection confirmed some known drivers of adaptation to radiation and highlighted some new transcription factors and micro RNAs (miRNAs). Finally, gene ontology (GO) analysis revealed biological processes that tend to have expression patterns most suitable for this approach. This work highlights the potential of detection of differentially expressed genes using a machine learning (ML) approach, and provides some evidence of gene expression changes being captured by a diverse feature set not related to the condition under study. ItemSumoPred-PLM: human SUMOylation and SUMO2/3 sites Prediction using Pre-trained Protein Language Model(Oxford University Press, 2024-03)SUMOylation is an essential post-translational modification system with the ability to regulate nearly all aspects of cellular physiology. Three major paralogues SUMO1, SUMO2 and SUMO3 form a covalent bond between the small ubiquitin-like modifier with lysine residues at consensus sites in protein substrates. Biochemical studies continue to identify unique biological functions for protein targets conjugated to SUMO1 versus the highly homologous SUMO2 and SUMO3 paralogues. Yet, the field has failed to harness contemporary AI approaches including pre-trained protein language models to fully expand and/or recognize the SUMOylated proteome. Herein, we present a novel, deep learning-based approach called SumoPred-PLM for human SUMOylation prediction with sensitivity, specificity, Matthew's correlation coefficient, and accuracy of 74.64%, 73.36%, 0.48% and 74.00%, respectively, on the CPLM 4.0 independent test dataset. In addition, this novel platform uses contextualized embeddings obtained from a pre-trained protein language model, ProtT5-XL-UniRef50 to identify SUMO2/3-specific conjugation sites. The results demonstrate that SumoPred-PLM is a powerful and unique computational tool to predict SUMOylation sites in proteins and accelerate discovery. ItemMultiplatform High-Definition Ion Mobility Separations of the Largest Epimeric Peptides(American Chemical Society, 2024-02)Ion mobility spectrometry (IMS) coupled to mass spectrometry (MS) has become a versatile tool to fractionate complex mixtures, distinguish structural isomers, and elucidate molecular geometries. Along with the whole MS field, IMS/MS advances to ever larger species. A topical proteomic problem is the discovery and characterization of d-amino acid-containing peptides (DAACPs) that are critical to neurotransmission and toxicology. Both linear IMS and FAIMS previously disentangled D/L epimers with up to ~30 residues. In the first study using all three most powerful IMS methodologies--trapped IMS, cyclic IMS, and FAIMS--we demonstrate baseline resolution of the largest known D/L peptides (CHH from $Homarus americanus$ with 72 residues) with a dynamic range up to 100. This expands FAIMS analyses of isomeric modified peptides, especially using hydrogen-rich buffers, to the ~50-100 residue range of small proteins. The spectra for D and L are unprecedentedly strikingly similar except for a uniform shift of the separation parameter, indicating the conserved epimer-specific structural elements across multiple charge states and conformers. As the interepimer resolution tracks the average for smaller DAACPs, the IMS approaches could help search for yet larger DAACPs. The a priori method to calibrate cyclic (including multipass) IMS developed here may be broadly useful. ItemHip and Trunk Variables in University Students with and without Recurrent Low Back Pain(North American Sports Medicine Institute, 2024-02)Background Low back pain (LBP) is a leading cause of disability. Recurrent low back pain (rLBP) is defined as two or more episodes of LBP in a 12-month period, each lasting more than 24 hours and separated by at least one pain-free month. Many studies have shown that hip and trunk variables have an influence on LBP. However, most of these are studies of participants with acute or chronic LBP rather than rLBP. Purpose To examine the difference between hip and trunk variables of university students with and without rLBP. Study Design Cross-Sectional Methods Participants with and without rLBP between 18 and 35 years of age not currently undergoing clinical orthopedic care were recruited for this cross-sectional study. Bilateral hip range of motion (ROM) and trunk ROM were measured with a goniometer or measuring tape (hip motions in all planes along with trunk flexion, extension, and lateral flexion). Strength of the hip extensors, abductors, and external rotators was measured using a handheld dynamometer, and a single-leg bridge endurance test was performed to assess differences and correlations between outcomes. Results Twenty-six subjects aged 18 to 35 years with rLBP (n=10) and without rLBP (n=16) participated. Statistically significant differences between the two groups were found for right and left hip flexion (p = 0.029 and 0.039, respectively), right hip adduction (p = 0.043), and right hip extension (p = 0.021). No significant differences were found between groups for strength, endurance, or other ROM measures. Conclusion The findings of this study show statistically significant although clinically non-meaningful differences in hip flexion, extension, and adduction ROM in the rLBP group compared to the control group. This lack of clinically meaningful difference may be relevant to testing procedures and treatment of patients or athletes with rLBP. This study also suggests that hip strength and endurance may not play a major role in the development or treatment of rLBP. Level of Evidence: 3. ItemEffects of "Read to the Mountain" intervention on secondary students’ phonics skills and reading confidence(Wichita State University, 2023-12)Secondary students face seemingly insurmountable odds when endeavoring to learn to read, especially if the students have learning disabilities that impact reading. This study examines the effect on phonological-orthographic retention over the first two units, single letter consonants and vowels, of the Read to the Mountain phonics intervention program over eighteen sessions. Participants include nine secondary-grade students, five boys and four girls. The intervention program embeds synthetic phonics, historical linguistics, incremental rehearsal, phonics games, evidence-based, high-leverage practices, and common special education accommodations. The study utilized descriptive quantitative analysis with pre-post testing via the Quick Phonics Screener, full flashcard deck, and the reading confidence survey. Daily progress monitoring is through incremental rehearsal. The net effect for phonics retention for the participants using the Read to the Mountain phonics intervention is statistically significant increases across the data matrix among all four methods of phonemic awareness probes.
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