Browsing by Subject "methods"
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Item Adaptive-optics Optical Coherence Tomography Processing Using a Graphics Processing Unit(Institute of Electrical and Electronics Engineers, 2014) Shafer, Brandon A.; Kriske, Jeffery E.; Kocaoglu, Omer P.; Turner, Timothy L.; Liu, Zhuolin; Lee, John J.; Miller, Donald T.; Department of Engineering Technology, School of Engineering and TechnologyGraphics processing units are increasingly being used for scientific computing for their powerful parallel processing abilities, and moderate price compared to super computers and computing grids. In this paper we have used a general purpose graphics processing unit to process adaptive-optics optical coherence tomography (AOOCT) images in real time. Increasing the processing speed of AOOCT is an essential step in moving the super high resolution technology closer to clinical viability.Item Advances in translational bioinformatics facilitate revealing the landscape of complex disease mechanisms(Springer (Biomed Central Ltd.), 2014) Yang, Jack Y.; Dunker, A. Keith; Liu, Jun S.; Qin, Xiang; Arabnia, Hamid R.; Yang, William; Niemierko, Andrzej; Chen, Zhongxue; Luo, Zuojie; Wang, Liangjiang; Liu, Yunlong; Xu, Dong; Deng, Youping; Tong, Weida; Yang, Mary Qu; Department of Biochemistry and Molecular Biology, IU School of MedicineAdvances of high-throughput technologies have rapidly produced more and more data from DNAs and RNAs to proteins, especially large volumes of genome-scale data. However, connection of the genomic information to cellular functions and biological behaviours relies on the development of effective approaches at higher systems level. In particular, advances in RNA-Seq technology has helped the studies of transcriptome, RNA expressed from the genome, while systems biology on the other hand provides more comprehensive pictures, from which genes and proteins actively interact to lead to cellular behaviours and physiological phenotypes. As biological interactions mediate many biological processes that are essential for cellular function or disease development, it is important to systematically identify genomic information including genetic mutations from GWAS (genome-wide association study), differentially expressed genes, bidirectional promoters, intrinsic disordered proteins (IDP) and protein interactions to gain deep insights into the underlying mechanisms of gene regulations and networks. Furthermore, bidirectional promoters can co-regulate many biological pathways, where the roles of bidirectional promoters can be studied systematically for identifying co-regulating genes at interactive network level. Combining information from different but related studies can ultimately help revealing the landscape of molecular mechanisms underlying complex diseases such as cancer.Item 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 DentistryBackground 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.Item The American Heart Association Life's Simple 7 and incident cognitive impairment: The REasons for Geographic And Racial Differences in Stroke (REGARDS) study(Ovid Technologies Wolters Kluwer -American Heart Association, 2014-06) Thacker, Evan L.; Gillett, Sarah R.; Wadley, Virginia G.; Unverzagt, Frederick W.; Judd, Suzanne E.; McClure, Leslie A.; Howard, Virginia J.; Cushman, Mary; Department of Psychiatry, IU School of MedicineBACKGROUND: Life's Simple 7 is a new metric based on modifiable health behaviors and factors that the American Heart Association uses to promote improvements to cardiovascular health (CVH). We hypothesized that better Life's Simple 7 scores are associated with lower incidence of cognitive impairment. METHODS AND RESULTS: For this prospective cohort study, we included REasons for Geographic And Racial Differences in Stroke (REGARDS) participants aged 45+ who had normal global cognitive status at baseline and no history of stroke (N=17 761). We calculated baseline Life's Simple 7 score (range, 0 to 14) based on smoking, diet, physical activity, body mass index, blood pressure, total cholesterol, and fasting glucose. We identified incident cognitive impairment using a 3-test measure of verbal learning, memory, and fluency obtained a mean of 4 years after baseline. Relative to the lowest tertile of Life's Simple 7 score (0 to 6 points), odds ratios of incident cognitive impairment were 0.65 (0.52, 0.81) in the middle tertile (7 to 8 points) and 0.63 (0.51, 0.79) in the highest tertile (9 to 14 points). The association was similar in blacks and whites, as well as outside and within the Southeastern stroke belt region of the United States. CONCLUSIONS: Compared with low CVH, intermediate and high CVH were both associated with substantially lower incidence of cognitive impairment. We did not observe a dose-response pattern; people with intermediate and high levels of CVH had similar incidence of cognitive impairment. This suggests that even when high CVH is not achieved, intermediate levels of CVH are preferable to low CVH.Item An analytical approach to 3D orthodontic load systems(The Angle Orthodontist, 2014-09) Katona, Thomas R.; Isikbay, Serkis C.; Chen, Jie; Department of Orthodontics and Oral Facial Genetics, IU School of DentistryOBJECTIVE: To present and demonstrate a pseudo three-dimensional (3D) analytical approach for the characterization of orthodontic load (force and moment) systems. MATERIALS AND METHODS: Previously measured 3D load systems were evaluated and compared using the traditional two-dimensional (2D) plane approach and the newly proposed vector method. RESULTS: Although both methods demonstrated that the loop designs were not ideal for translatory space closure, they did so for entirely different and conflicting reasons. CONCLUSIONS: The traditional 2D approach to the analysis of 3D load systems is flawed, but the established 2D orthodontic concepts can be substantially preserved and adapted to 3D with the use of a modified coordinate system that is aligned with the desired tooth translation.Item Assessment of white matter loss using bond-selective photoacoustic imaging in a rat model of contusive spinal cord injury(Mary Ann Liebert, 2014-12-15) Wu, Wei; Wang, Pu; Cheng, Ji-Xin; Xu, Xiao-Ming; Department of Neurological Surgery, IU School of MedicineWhite matter (WM) loss is a critical event after spinal cord injury (SCI). Conventionally, such loss has been measured with histological and histochemical approaches, although the procedures are complex and may cause artifact. Recently, coherent Raman microscopy has been proven to be an emerging technology to study de- and remyelination of the injured spinal cord; however, limited penetration depth and small imaging field prevent it from comprehensive assessments of large areas of damaged tissues. Here, we report the use of bond-selective photoacoustic (PA) imaging with 1730-nm excitation, where the first overtone vibration of CH2 bond is located, to assess WM loss after a contusive SCI in adult rats. By employing the first overtone vibration of CH2 bond as the contrast, the mapping of the WM in an intact spinal cord was achieved in a label-free three-dimensional manner, and the physiological change of the spinal cord before and after injury was observed. Moreover, the recovery of the spinal cord from contusive injury with the treatment of a neuroprotective nanomedicine ferulic-acid-conjugated glycol chitosan (FA-GC) was also observed. Our study suggests that bond-selective PA imaging is a valuable tool to assess the progression of WM pathology after SCI as well as neuroprotective therapeutics in a label-free manner.Item Clinical Islet Xenotransplantation: A Step Forward(Elsevier, 2016-10) Ekser, Burcin; Bottino, Rita; Cooper, David K. C.; Department of Surgery, IU School of MedicineItem Comparative Responsiveness of Pain Measures in Cancer Patients(Elsevier, 2012-08) Kroenke, Kurt; Theobald, Dale; Wu, Jingwei; Tu, Wanzhu; Krebs, Erin E.; Department of Medicine, IU School of MedicineBrief measures to assess and monitor pain in cancer patients are available, but few head-to-head psychometric comparisons of different measures have been reported. Baseline and 3-month data were analyzed from 274 patients enrolled in the Indiana Cancer Pain and Depression (INCPAD) trial. Participants completed the Brief Pain Inventory (BPI), the PEG (a 3-item abbreviated version of the BPI), the short form (SF)-36 pain scale, and a pain global rating of change measure. The global rating was used as the criterion for standardized response mean and receiver operating characteristic curve analyses. To assess responsiveness to the trial intervention, we evaluated standardized effect size statistics stratified by trial arm. All measures were responsive to global improvement, discriminated between participants with and without improvement, and detected a significant intervention treatment effect. Short and longer measures were similarly responsive. Also, composite measures that combined pain severity and interference into a single score (BPI total, PEG, SF-36 pain) performed comparably to separate measures of each domain (BPI severity and BPI interference).Item Cost-effectiveness of first-line antiretroviral therapy for HIV-infected African children less than 3 years of age(Ovid Technologies (Wolters Kluwer) - Lippincott Williams & Wilkins, 2015-06-19) Ciaranello, Andrea L.; Doherty, Kathleen; Penazzato, Martina; Lindsey, Jane C.; Harrison, Linda; Kelly, Kathleen; Walensky, Rochelle P.; Essajee, Shaffiq; Losina, Elena; Muhe, Lulu; Wools-Kaloustian, Kara; Ayaya, Samuel; Weinstein, Milton C.; Palumbo, Paul; Freedberg, Kenneth A.; Department of Medicine, IU School of MedicineBACKGROUND: The International Maternal, Pediatric, and Adolescent Clinical Trials P1060 trial demonstrated superior outcomes for HIV-infected children less than 3 years old initiating antiretroviral therapy (ART) with lopinavir/ritonavir compared to nevirapine, but lopinavir/ritonavir is four-fold costlier. DESIGN/METHODS: We used the Cost-Effectiveness of Preventing AIDS Complications (CEPAC)-Pediatric model, with published and P1060 data, to project outcomes under three strategies: no ART; first-line nevirapine (with second-line lopinavir/ritonavir); and first-line lopinavir/ritonavir (second-line nevirapine). The base-case examined South African children initiating ART at age 12 months; sensitivity analyses varied all key model parameters. Outcomes included life expectancy, lifetime costs, and incremental cost-effectiveness ratios [ICERs; dollars/year of life saved ($/YLS)]. We considered interventions with ICERs less than 1× per-capita gross domestic product (South Africa: $7500)/YLS as 'very cost-effective,' interventions with ICERs below 3× gross domestic product/YLS as 'cost-effective,' and interventions leading to longer life expectancy and lower lifetime costs as 'cost-saving'. RESULTS: Projected life expectancy was 2.8 years with no ART. Both ART regimens markedly improved life expectancy and were very cost-effective, compared to no ART. First-line lopinavir/ritonavir led to longer life expectancy (28.8 years) and lower lifetime costs ($41 350/person, from lower second-line costs) than first-line nevirapine (27.6 years, $44 030). First-line lopinavir/ritonavir remained cost-saving or very cost-effective compared to first-line nevirapine unless: liquid lopinavir/ritonavir led to two-fold higher virologic failure rates or 15-fold greater costs than in the base-case, or second-line ART following first-line lopinavir/ritonavir was very ineffective. CONCLUSIONS: On the basis of P1060 data, first-line lopinavir/ritonavir leads to longer life expectancy and is cost-saving or very cost-effective compared to first-line nevirapine. This supports WHO guidelines, but increasing access to pediatric ART is critical regardless of the regimen used.Item Coupling Interval Variability Differentiates Ventricular Ectopic Complexes Arising in the Aortic Sinus of Valsalva and Great Cardiac Vein From Other Sources(Elsevier, 2014-05-27) Bradfield, Jason S.; Homsi, Mohamed; Shivkumar, Kalyanam; Miller, John M.; Department of Medicine, IU School of MedicineObjectives The objective of this study was to determine whether premature ventricular contractions (PVCs) arising from the aortic sinuses of Valsalva (SOV) and great cardiac vein (GCV) have coupling interval (CI) characteristics that differentiate them from other ectopic foci. Background PVCs occur at relatively fixed CI from the preceding normal QRS complex in most patients. However, we observed patients with PVCs originating in unusual areas (SOV and GCV) in whom the PVC CI was highly variable. We hypothesized that PVCs from these areas occur seemingly randomly because of the lack of electrotonic effects of the surrounding myocardium. Methods Seventy-three consecutive patients referred for PVC ablation were assessed. Twelve consecutive PVC CIs were recorded. The ΔCI (maximum – minimum CI) was measured. Results We studied 73 patients (age 50 ± 16 years, 47% male). The PVC origin was right ventricular (RV) in 29 (40%), left ventricular (LV) in 17 (23%), SOV in 21 (29%), and GCV in 6 (8%). There was a significant difference between the mean ΔCI of RV/LV PVCs compared with SOV/GCV PVCs (33 ± 15 ms vs. 116 ± 52 ms, p < 0.0001). A ΔCI of >60 ms demonstrated a sensitivity of 89%, specificity of 100%, positive predictive value of 100%, and negative predictive value of 94%. Cardiac events were more common in the SOV/GCV group versus the RV/LV group (7 of 27 [26%] vs. 2 of 46 [4%], p < 0.02). Conclusions ΔCI is more pronounced in PVCs originating from the SOV or GCV. A ΔCI of 60 ms helps discriminate the origin of PVCs before diagnostic electrophysiological study and may be associated with increased frequency of cardiac events.