Browsing by Subject "Biomedical Engineering"

Now showing 1 - 6 of 6
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    Advancing cognitive engineering methods to support user interface design for electronic health records
    (Elsevier, 2014-04) Thyvalikakath, Thankam P.; Dziabiak, Michael P.; Johnson, Raymond; Torres-Urquidy, Miguel Humberto; Acharya, Amit; Yabes, Jonathan; Schleyer, Titus K.; Department of Cariology, Operative Dentistry and Dental Public Health, IU School of Dentistry
    Background Despite many decades of research on the effective development of clinical systems in medicine, the adoption of health information technology to improve patient care continues to be slow, especially in ambulatory settings. This applies to dentistry as well, a primary care discipline with approximately 137,000 practitioners in the United States. A critical reason for slow adoption is the poor usability of clinical systems, which makes it difficult for providers to navigate through the information and obtain an integrated view of patient data. Objective In this study, we documented the cognitive processes and information management strategies used by dentists during a typical patient examination. The results will inform the design of a novel electronic dental record interface. Methods We conducted a cognitive task analysis (CTA) study to observe ten general dentists (five general dentists and five general dental faculty members, each with more than two years of clinical experience) examining three simulated patient cases using a think-aloud protocol. Results Dentists first reviewed the patient’s demographics, chief complaint, medical history and dental history to determine the general status of the patient. Subsequently, they proceeded to examine the patient’s intraoral status using radiographs, intraoral images, hard tissue and periodontal tissue information. The results also identified dentists’ patterns of navigation through patient’s information and additional information needs during a typical clinician-patient encounter. Conclusion This study reinforced the significance of applying cognitive engineering methods to inform the design of a clinical system. Second, applying CTA to a scenario closely simulating an actual patient encounter helped with capturing participants’ knowledge states and decision-making when diagnosing and treating a patient. The resultant knowledge of dentists’ patterns of information retrieval and review will significantly contribute to designing flexible and task-appropriate information presentation in electronic dental records.
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    Creating Virtual Spaces to Build Community Among Students Entering an Undergraduate Biomedical Engineering Program
    (Springer Nature, 2020-08-20) Higbee, Steven; Miller, Sharon; Waterfill, Abigail; Maxey, Kayla; Stella, Julie; Wallace, Joseph; Biomedical Engineering, School of Engineering and Technology
    After the transition to online instruction in response to the COVID-19 pandemic, students in our program lamented the loss of connection to their peers, more so than diminished access to faculty, teaching assistants, or other resources. Fortunately, given that the semester was well underway when the transition occurred and few students in our courses were new to our BME program, we feel that students missed out on relatively few formative community-building experiences. This would not be the case for a fall semester of online instruction, however, so we must take action for the sake of our incoming class of undergraduate students. Our experience from spring 2020 and our review of the relevant literature suggest that we can be successful at building community among our new cohort of BME students, regardless of the mode of instruction.
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    Developing Novel Antibacterial Dental Filling Composite Restoratives
    (2020-05) Caneli, Gulsah; Xie, Dong; Anderson, Gregory; Na, Sungsoo
    A novel antimicrobial dental composite system has been developed and evaluated. Both alumina and zirconia filler particles were covalently coated with an antibacterial resin and blended into a composite formulation, respectively. Surface hardness and bacterial viability were used to evaluate the coated alumina fi ller-modif ed composite. Compressive strength and bacterial viability were used to evaluate the coated zirconia ller-modi ed composite. Commercial composite Kerr was used as control. The specimens were conditioned in distilled water at 37 °C for 24 h prior to testing. Four bacterial species Streptococcus mutans, Staphylococcus aureus, Pseudomonas aeruginosa, and Escherichia coli were used to assess the bacterial viability. Effects of antibacterial moiety content, modif ed particle size and loading, and total fi ller content was investigated. Chapter 2 describes how we studied and evaluated the composite modi fed with antibacterial resin-coated alumina llers. The results showed that almost all the modi ed composites exhibited higher antibacterial activity along with improved surface hardness, as compared to unmodi fed one. Increasing antibacterial moiety content, particle size and loading, and total fi ller content generally increased surface hardness. Increasing antibacterial moiety, fi ller loading, and total fi ller content increased antibacterial activity. On the other hand, increasing particle size showed a negative impact on antibacterial activity. The leaching tests indicate that the modiChapter 3 describes how we studied and evaluated the composite modif ed with antibacterial resin-coated zirconia fi ller. The results showed that almost all the modif ed composites exhibited higher antibacterial activity along with decreased compressive strength, as compared to the unmodif ed control. It was found that with increasing antibacterial moiety content and modi fedfi ller loading, yield strength, modulus and compressive strength of the composite were decreased. In addition, the strengths of the composite were increased with increasing powder/liquid ratio. On the other hand, with increasing antibacterial moiety content, fi ller loading and powder/liquid ratio, antibacterial activity was enhanced. In summary, we have developed a novel antibacterial dental composite system for improved dental restoratives. Both composites modif ed with the antibacterial resin-coated alumina and zirconia fi ller have demonstrated signi cant antibacterial activities. The composite modi fed with the alumina fi ller showed improved hardness values, but the composite modif ed with the zirconia fi ller showed decreased compressive strength values. It appears that the developed system is a non-leaching antibacterial dental composite. ed experimental composite showed no leachable antibacterial component to bacteria.
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    Effect of Shear Stress on RhoA Activities and Cytoskeletal Organization in Chondrocytes
    (2013-09-05) Wan, Qiaoqiao; Na, Sungsoo; Li, Jiliang; Yokota, Hiroki
    Mechanical force environment is a major factor that influences cellular homeostasis and remodeling. The prevailing wisdom in this field demonstrated that a threshold of mechanical forces or deformation was required to affect cell signaling. However, by using a fluorescence resonance energy transfer (FRET)-based approach, we found that C28/I2 chondrocytes exhibited an increase in RhoA activities in response to high shear stress (10 or 20 dyn/cm2), while they showed a decrease in their RhoA activities to intermediate shear stress at 5 dyn/cm2. No changes were observed under low shear stress (2 dyn/ cm2). The observed two-level switch of RhoA activities was closely linked to the shear stress-induced alterations in actin cytoskeleton and traction forces. In the presence of constitutively active RhoA (RhoA-V14), intermediate shear stress suppressed RhoA activities, while high shear stress failed to activate them. Collectively, these results herein suggest that intensities of shear stress are critical in differential activation and inhibition of RhoA activities in chondrocytes.
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    Exploring Chondrocyte Integrin Regulation of Growth Factor IGF-I Expression from a Transient pAAV Vector
    (2013-08-20) Ratley, Samantha Kay; Trippel, Stephen B.; Lin, Chien-Chi; Stocum, David L.
    Insulin-like Growth Factor I (IGF-I) is a growth factor that stimulates both mitogenic and anabolic responses in articular chondrocytes. While it has been shown that exogenous IGF-I can regulate chondrocyte integrins, little is known regarding regulatory effects of IGF-I produced from a transiently expressed plasmid based adeno-associated virus (pAAV) vector. Because chondrocytes are using cellular machinery to overexpress IGF-I, it is of interest to see whether or not pAAV IGF-I will significantly upregulate or downregulate chondrocyte integrins. Additionally, it is of interest to know whether chondrocyte adhesion through integrins will have any regulatory effects on the production of IGF-I from the transgene. Therefore, this study will ascertain if pAAV IGF-I will have similar effects that exogenous IGF-I has on integrin regulation and if integrin silencing mechanisms will affect the production of IGF-I from the transgene. To test these hypotheses, adult articular chondrocytes were doubly transfected with the pAAV vector for IGF-I and short interference ribonucleic acid (siRNA) for integrins beta 1 and alpha V. Gene products were monitored at the transcriptional levels using quantitative real time polymerase chain reactions (qPCR) and IGF-I protein production was monitored at the translational level using enzyme linked immunoabsorbant assays (ELISAs). Adult articular chondrocytes doubly transfected were encapsulated in a three dimensional hydrogel system to simulate an in vivo environment. Samples were collected for analysis at days 2, 4, and 6 post encapsulation. Results show that IGF-I treatment with the pAAV vector does not cause significant changes in the transcriptional regulation of the beta 1 integrin in a three dimensional hydrogel system. The pAAV IGF-I vector did not cause significant regulatory changes on integrin alpha V at any time point during the experiment. Additionally, by knocking down the expression levels of integrins by using siRNA, it was shown that integrin knockdown does not have a significant regulatory effect on transcriptional or translational expression levels of IGF-I from the pAAV vector.
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    Systems Modeling of Gut Microbiome Regulation of Estrogen Receptor Beta Signaling in Ulcerative Colitis
    (2023-04-28) Trinh, Alan; Munoz, Javier; Cross, Tzu-Wen; Brubaker, Doug
    Introduction: The pathogenesis of ulcerative colitis (UC), a chronic inflammatory disorder, involves interactions between gut microbiome dysbiosis, epithelial cell barrier disruption, and immune hyperactivity. Men are 20% more likely to develop UC and 60% more likely to progress to colitis-associated cancer than women. A possible explanation for this may be the anti-inflammatory and epithelial-protective role of estrogen via estrogen receptor beta (ESR2) in the gut. However, extracting insights into how microbiomes regulate host cell signaling is challenged by high-dimensional data integrations across kingdoms and the need to extract interpretable biological information from complex models. To address these challenges and understand microbiome regulation of ESR2 signaling, we developed a partial least squares path modeling (PLS-PM)-inspired microbiome multi-omic modeling framework. Materials and Methods: Gut metabolomic, colorectal transcriptomic, and stool 16S rRNA-seq data from unique UC or non-IBD controls subjects (n=35) were obtained from the Inflammatory Bowel Disease Multi-Omics Database. Single sample gene set enrichment analysis was used to calculate pathway scores for genes up or down-regulated by ESR2 (ESR2UP/ESR2DN respectively).Latent variables (LV) obtained via regularized sparse partial least square regression (sPLSR) mdoels were extracted and used as predictors in two linear regression meta-models with dependent variables of ESR2UP or ESR2DN scores, and independent variables in each model consisting of patient LV scores on metabolites and 16S LVs along with sex and UC status. Significance testing on regression coefficients identified LV interactions synergistically predictive of ER Beta pathway activity. Results and Discussion: The first two LVs from each single-omic sPLSR models were extracted to create terms in the multi-omic meta-model accounting for sex and disease status. The meta-model was predictive of ESR2UP pathway score, implicating UC status (p=0.046), microbiota LV1 (p=0.0006), metabolites LV2 (p=0.045), and interactions of metabolite LV1:microbiota LV1 (p=0.003), microbiota LV1:UC (p=0.0008), and microbiota LV2:sex (p=0.019) in predicting ESR2UP pathway status. For ESR2DN, the 16S model clustered by ESR2DN activity while the metabolomic model clustering was best illustrated by disease status. The ESR2DN meta-model was predictive of ESR2DN pathway activity, implicating main effects of microbiota LV1 (p =0.004), metabolites LV2 (p=0.004), and diagnosis and the interaction effects of metabolites LV1:microbiota LV1 (p=0.005), microbiota LV1:UC (p=0.014), microbiota LV2:sex (p=0.017), and metabolites LV2:UC (p=0.035) in predicting ESR2DN pathway status. Acesulfame, an artificial sweetener, and oxymetazoline, a nasal decongestant, were some of the metabolites predicted by our model to have a differential effect on ESR2 activity based on patient sex. The metabolites predicted in our models are tested in cancer cell lines to understand estrogen regulatory effects on inflammation observed in UC. Method developed in this study can be applied to gain insight regarding regulation of signaling pathways in pathologies not limited to UC. Conclusions: We demonstrate the effectiveness of a PLS-PM based method for modeling relationships between host signaling and microbiome multi-omics data via this investigation of ER Beta activity in UC patients. We quantified significant multi-omic microbiome interactions with disease status and sex that impact ER Beta signaling which may aid in identifying new microbiome-targeted UC therapeutics stratified by sex-specific disease characteristics.