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Articles 1 - 7 of 7
Full-Text Articles in Physical Sciences and Mathematics
Sctiger: A Deep-Learning Method For Inferring Gene Regulatory Networks From Case Versus Control Scrna-Seq Datasets., Madison Dautle, Shaoqiang Zhang, Yong Chen
Sctiger: A Deep-Learning Method For Inferring Gene Regulatory Networks From Case Versus Control Scrna-Seq Datasets., Madison Dautle, Shaoqiang Zhang, Yong Chen
Faculty Scholarship for the College of Science & Mathematics
Inferring gene regulatory networks (GRNs) from single-cell RNA-seq (scRNA-seq) data is an important computational question to find regulatory mechanisms involved in fundamental cellular processes. Although many computational methods have been designed to predict GRNs from scRNA-seq data, they usually have high false positive rates and none infer GRNs by directly using the paired datasets of case-versus-control experiments. Here we present a novel deep-learning-based method, named scTIGER, for GRN detection by using the co-differential relationships of gene expression profiles in paired scRNA-seq datasets. scTIGER employs cell-type-based pseudotiming, an attention-based convolutional neural network method and permutation-based significance testing for inferring GRNs among …
Ultrasound-Assisted Air-Jet Spinning Of Silk Fibroin-Soy Protein Nanofiber Composite Biomaterials., Futian Yang, Fang Wang, Janine Mazahreh, Xiao Hu
Ultrasound-Assisted Air-Jet Spinning Of Silk Fibroin-Soy Protein Nanofiber Composite Biomaterials., Futian Yang, Fang Wang, Janine Mazahreh, Xiao Hu
Faculty Scholarship for the College of Science & Mathematics
Ultrasound utilizes a non-radiation technology that can meet modern standards to gain access to cheap, reliable and sustainable modern energy. Ultrasound technology can be implemented in the field of biomaterials for its exceptional potential in controlling the shape of nanomaterials. This study presents the first example of the production of soy and silk fibroin protein composite nanofibers in various ratios via combining ultrasonic technology with air-spray spinning. Characterization of ultrasonic spun nanofibers was performed by scanning electron microscopy (SEM), Fourier-transform infrared spectroscopy (FTIR), X-ray powder diffraction (XRD), differential scanning calorimetry (DSC), thermogravimetric (TG) analysis, water contact angle, water retention, enzymatic …
Kif6 Trp719arg Genetic Variant Increases Risk For Thoracic Aortic Dissection, Juan J Velasco, Yupeng Li, Bulat A Ziganshin, Mohammad A Zafar, John A Rizzo, Deqiong Ma, Hui Zang, Asanish Kalyanasundaram, John A Elefteriades
Kif6 Trp719arg Genetic Variant Increases Risk For Thoracic Aortic Dissection, Juan J Velasco, Yupeng Li, Bulat A Ziganshin, Mohammad A Zafar, John A Rizzo, Deqiong Ma, Hui Zang, Asanish Kalyanasundaram, John A Elefteriades
Faculty Scholarship for the College of Science & Mathematics
Background: KIF6 (kinesin family member 6), a protein coded by the KIF6 gene, serves an important intracellular function to transport organelles along microtubules. In a pilot study, we found that a common KIF6 Trp719Arg variant increased the propensity of thoracic aortic aneurysms (TAA) to suffer dissection (AD). The present study aims for a definite investigation of the predictive ability of KIF6 719Arg vis à vis AD. Confirmatory findings would enhance natural history prediction in TAA. Methods: 1108 subjects (899 aneurysm and 209 dissection patients) had KIF6 719Arg variant status determined. Results: The 719Arg variant in the KIF6 gene correlated strongly …
Recent Progress In Biopolymer-Based Hydrogel Materials For Biomedical Applications., Ayaz Mahmood, Dev Patel, Brandon Hickson, John Desrochers, Xiao Hu
Recent Progress In Biopolymer-Based Hydrogel Materials For Biomedical Applications., Ayaz Mahmood, Dev Patel, Brandon Hickson, John Desrochers, Xiao Hu
Faculty Scholarship for the College of Science & Mathematics
Hydrogels from biopolymers are readily synthesized, can possess various characteristics for different applications, and have been widely used in biomedicine to help with patient treatments and outcomes. Polysaccharides, polypeptides, and nucleic acids can be produced into hydrogels, each for unique purposes depending on their qualities. Examples of polypeptide hydrogels include collagen, gelatin, and elastin, and polysaccharide hydrogels include alginate, cellulose, and glycosaminoglycan. Many different theories have been formulated to research hydrogels, which include Flory-Rehner theory, Rubber Elasticity Theory, and the calculation of porosity and pore size. All these theories take into consideration enthalpy, entropy, and other thermodynamic variables so that …
Bruton's Tyrosine Kinase Targeting In Multiple Myeloma., Max Von Suskil, Kazi Nasrin Sultana, Weam Othman Elbezanti, Omar S Al-Odat, Robert Chitren, Amit K Tiwari, Kishore B Challagundla, Sandeep Kumar Srivastava, Subash C. Jonnalagadda, Tulin Budak-Alpdogan, Manoj K Pandey
Bruton's Tyrosine Kinase Targeting In Multiple Myeloma., Max Von Suskil, Kazi Nasrin Sultana, Weam Othman Elbezanti, Omar S Al-Odat, Robert Chitren, Amit K Tiwari, Kishore B Challagundla, Sandeep Kumar Srivastava, Subash C. Jonnalagadda, Tulin Budak-Alpdogan, Manoj K Pandey
Faculty Scholarship for the College of Science & Mathematics
Multiple myeloma (MM), a clonal plasma cell disorder, disrupts the bones' hematopoiesis and microenvironment homeostasis and ability to mediate an immune response against malignant clones. Despite prominent survival improvement with newer treatment modalities since the 2000s, MM is still considered a non-curable disease. Patients experience disease recurrence episodes with clonal evolution, and with each relapse disease comes back with a more aggressive phenotype. Bruton's Tyrosine Kinase (BTK) has been a major target for B cell clonal disorders and its role in clonal plasma cell disorders is under active investigation. BTK is a cytosolic kinase which plays a major role in …
Protein And Polysaccharide-Based Magnetic Composite Materials For Medical Applications., Elizabeth J Bealer, Kyril Kavetsky, Sierra Dutko, Samuel Lofland, Xiao Hu
Protein And Polysaccharide-Based Magnetic Composite Materials For Medical Applications., Elizabeth J Bealer, Kyril Kavetsky, Sierra Dutko, Samuel Lofland, Xiao Hu
Faculty Scholarship for the College of Science & Mathematics
The combination of protein and polysaccharides with magnetic materials has been implemented in biomedical applications for decades. Proteins such as silk, collagen, and elastin and polysaccharides such as chitosan, cellulose, and alginate have been heavily used in composite biomaterials. The wide diversity in the structure of the materials including their primary monomer/amino acid sequences allow for tunable properties. Various types of these composites are highly regarded due to their biocompatible, thermal, and mechanical properties while retaining their biological characteristics. This review provides information on protein and polysaccharide materials combined with magnetic elements in the biomedical space showcasing the materials used, …
Binding Of Braco19 To A Telomeric G-Quadruplex Dna Probed By All-Atom Molecular Dynamics Simulations With Explicit Solvent., Babitha Machireddy, Holli-Joi Sullivan, Chun Wu
Binding Of Braco19 To A Telomeric G-Quadruplex Dna Probed By All-Atom Molecular Dynamics Simulations With Explicit Solvent., Babitha Machireddy, Holli-Joi Sullivan, Chun Wu
Faculty Scholarship for the College of Science & Mathematics
Although BRACO19 is a potent G-quadruplex binder, its potential for clinical usage is hindered by its low selectivity towards DNA G-quadruplex over duplex. High-resolution structures of BRACO19 in complex with neither single-stranded telomeric DNA G-quadruplexes nor B-DNA duplex are available. In this study, the binding pathway of BRACO19 was probed by 27.5 µs molecular dynamics binding simulations with a free ligand (BRACO19) to a DNA duplex and three different topological folds of the human telomeric DNA G-quadruplex (parallel, anti-parallel and hybrid). The most stable binding modes were identified as end stacking and groove binding for the DNA G-quadruplexes and duplex, …