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Item Open Access 1,001 Ways to Share VIVO Data(2017-08-15) Trimmer, JK; Murry, DThis presentation shows a variety of ways to repurpose data from a research discovery system like Scholars@Duke.Item Open Access 2024 Advanced Scientific Computing Advisory Committee (ASCR) Facilities Subcommittee Recommendations(2024-05-01) Seidel, Ed; Randles, Amanda; Arthur, Rick; Bergman, Keren; Carlson, Bill; Deelman, Ewa; Grout, Ray; Hendrickson, Bruce; Reed, DanItem Open Access 3D TEE-Applications for Daily Practice (canceled)(2020-04-21) Cherry, AnneDiscussion of applications for 3D TEE in the Operating Room.Item Open Access A full house: Re-shuffling our transfer strategy to better manage capacity across Duke Hospitals(2016-03-01) Setji, Noppon; Gallagher, David; Rougeux, Matthew; Gerardo, Charles; Verma, Lalit; Sawyer, Suzanne; Odom, Nancia; Oliver, Joan; Demarco, Frank; Ross, AdiaSee uploaded pdf versionItem Open Access A Glimpse Into Duke Research: Where Are You Now?(2017-02-28) Yuan, A; Feng, L; Qin, X; Zhao, YDuke is one of the leading sites for research across the nation, throughout the world where professionals are defining the way to a better and healthier future. A thorough understanding of how Duke networks behave is crucial to their efficient operation. By visualizing data on networks, it is possible to greatly improve our knowledge of how Duke researchers collaborate and detect patterns that would not be evident in a database alone. Our focus is on mapping collaboration networks. Clusters of nodes in the maps show both the research communities that coalesce from different departments or affiliations and the relationship among those communities. The maps also show the collaborations that have not been made, which indicate opportunities for future research. The goal of this visualization was to examine the geographic spread of collaborations represented in the scholars@duke dataset. The goal of the Scholars@Duke Visualization Challenge was to create visualizations that capture the richness and dynamism of Duke research. The datasets were provided by Scholars@Duke (https://schoalrs.duke.edu/) and they describe publications, authorships, and scholarly collaborations from university researchers over the past 5 years.Item Open Access A mathematical framework to quantitatively balance clinical and radiation risk in Computed Tomography(2021-12-01) Ria, Francesco; Zhang, Anru; Lerebours, Reginald; Erkanli, Alaattin; Solomon, justin; Marin, Daniele; Samei, EhsanPurpose: Risk in medical imaging is a combination of radiation risk and clinical risk, which is largely driven by the effective diagnosis. While radiation risk has traditionally been the main focus of Computed Tomography (CT) optimization, such a goal cannot be achieved without considering clinical risk. The purpose of this study was to develop a comprehensive mathematical framework that considers both radiation and clinical risks based on the specific task, the investigated disease, and the interpretive performance (i.e., false positive and false negative rates), tested across a representative clinical CT population. Methods and Materials: The proposed mathematical framework defined the radiation risk to be a linear function of the radiation dose, the population prevalence of the disease, and the false positive rate. The clinical risk was defined to be a function of the population prevalence, the expected life-expectancy loss for an incorrect diagnosis, and the interpretative performance in terms of the AUC as a function of radiation dose. A Total Risk (TR) was defined as the sum of the radiation risk and the clinical risk. With IRB approval, the mathematical function was applied to a dataset of 80 adult CT studies investigating localized stage liver cancer (LLC) for a specific false positive rate of 5% reconstructed with both Filtered Back Projection (FBP) and Iterative Reconstruction (IR) algorithm. Linear mixed effects models were evaluated to determine the relationship between radiation dose and radiation risk and interpretative performance, respectively. Lastly, the analytical minimum of the TR curve was determined and reported. Results: TR is largely affected by clinical risk for low radiation dose whereas radiation risk is dominant at high radiation dose. Concerning the application to the LLC population, the median minimum risk in terms of mortality per 100 patients was 0.04 in FBP and 0.03 in IR images; the corresponding CTDIvol values were 38.5 mGy and 25.7 mGy, respectively. Conclusions: The proposed mathematical framework offers a complete quantitative description of risk in CT enabling a comprehensive risk-to-benefit assessment essential in the effective justification of radiological procedures and in the design of optimal clinical protocols. Clinical Relevance/Application: The quantification of both radiation and clinical risk using comparable units allows the calculation of the overall risk paving the road towards a comprehensive risk-to-benefit assessment in CT.Item Open Access A Monopoly on Marcan Priority? Fallacies at the Heart of Q(Society of Biblical Literature Seminar Papers 2000, 2000) Goodacre, MSItem Open Access A new look at an old disease: Is Pompe disease a neuromuscular disorder with CNS involvement?(Molecular Genetics and Metabolism, 2020-02) Korlimarla, Aditi; Chen, Steven; Austin, Stephanie L; Provenzale, James M; Kishnani, Priya SItem Open Access Item Open Access A Recommender System for Music Less Singing Voice Signals(2019 4th International Conference on Electrical Information and Communication Technology (EICT), 2019-12) Salehin, GM Nazmus; Shahjahan, MdItem Open Access A simple technique for augmentation of axonal ingrowth into chondroitinase-treated acellular nerve grafts using nerve growth factor.(Annals of plastic surgery, 2012-05) Ovalle, Fernando; Patel, Ashit; Pollins, Alonda; de la Torre, Jorge; Vasconez, Luis; Hunt, Thomas R; Bucy, R Pat; Shack, R Bruce; Thayer, Wesley PBackground and purpose
Improvement in axonal regeneration may lead to the development of longer nerve grafts and improved outcomes for patients with peripheral nerve injury. Although the use of acellular nerve grafts has been well documented (Groves et al, Exp Neurol. 2005;195:278-292; Krekoski et al, J Neurosci. 2001;21:6206-6213; Massey et al, Exp Neurol. 2008;209:426-445; Neubauer et al, Exp Neurol. 2007;207:163-170; Zuo et al, Exp Neurol. 2002;176:221-228), less is known about the ability of neurotrophic factors to enhance axonal regeneration. This study evaluates axonal ingrowth augmentation using acellular, chondroitinase-treated nerve grafts doped with nerve growth factor (NGF).Methods
Acellular chondroitinase-treated murine nerve grafts were placed in experimental (NGF-treated grafts) and control (carrier-only grafts) rats. Five days after implantation, axonal regeneration was assessed by immunocytochemistry along with digital image analysis.Results
Higher axon count was observed throughout the length of the nerve in the NGF group (P < 0.0001), peaking at 3 mm from proximal repair (P = 0.02). Although the NGF group displayed a higher axon count per slice, the mean diameter of individual NGF axons was smaller (P < 0.0001), potentially consistent with induction of sensory axons (Rich et al, J Neurocytol. 1987;16:261-268; Sofroniew et al, Annu Rev Neurosci. 2001;24:1217-1128; Yip et al, J Neurosci. 1984;4:2986-2992).Conclusion
The simple technique of doping acellular, chondroitinase-treated nerve grafts with NGF can augment axonal ingrowth and possibly preferentially induce sensory axons.Item Open Access A Spatio-temporal Coupling Method to Reduce the Time-to-Solution of Cardiovascular Simulations(http://ieeexplore.ieee.org/abstract/document/6877292/, 2017-01-28) Randles, A; Kaxiras, EKWe present a new parallel-in-time method designed to reduce the overall time-to-solution of a patient-specific cardiovascular flow simulation. Using a modified Para real algorithm, our approach extends strong scalability beyond spatial parallelism with fully controllable accuracy and no decrease in stability. We discuss the coupling of spatial and temporal domain decompositions used in our implementation, and showcase the use of the method on a study of blood flow through the aorta. We observe an additional 40% reduction in overall wall clock time with no significant loss of accuracy, in agreement with a predictive performance model.Item Open Access A Spectrum of Stakeholder Perspective Taking in Early-Stage Design(Proceedings of the Design Society, 2023-07-01) Rieken, Elizabeth; Bond, Kathleen; Best, Rachel Moore; Burleson, Grace; Brubaker, Eric ReynoldsStakeholder perspective taking is a critical skill in early-stage problem exploration and framing. We examined stakeholder perspective taking within an early-stage design team of engineers at NASA to begin to understand in what ways and under what conditions designers adopt stakeholder perspectives in the context of professional engineering organizations. Our findings identify a spectrum of perspective taking during problem framing deliberations that ranges from (1) fully taking the stakeholder's point of view (POV), (2) interpreting the stakeholder's POV using the designer's POV, (3) implanting the stakeholder's POV into the designer's POV, to (4) fully taking the designer's own POV. We also identify and describe conditions that appeared to encourage or hinder perspective taking in this setting. These findings are significant because they suggest ways to gauge and encourage the skill of stakeholder perspective taking among professional engineers working on real-world design challenges with societal implications.Item Open Access Accuracy of Noise Magnitude Measurements from Patient CT Images(https://aapm.onlinelibrary.wiley.com/doi/epdf/10.1002/mp.16525, 2023-07-23) Ria, Francesco; Setiawan, Hananiel; Abadi, Ehsan; Samei, EhsanPurpose Noise magnitude is a main CT image quality indicator. In vivo measurements emerged as a patient-specific methodology to assess and qualify CT noise, yet methods to do so vary. Current noise measurement methods in soft tissues and air surrounding the patient use distinct image segmentations, HU thresholds, and region-of-interests, resulting in noise estimation variations. In this study, we compared two noise magnitude calculation methods against the gold standard ensemble noise in two cohorts of virtually-generated patient images across 36 imaging conditions. Methods 1800 image datasets were generated using a virtual trial platform based on anthropomorphic phantoms (XCAT) and a validated, scanner-specific CT simulator (DukeSim). XCAT phantoms were repeatedly imaged 50 times using Chest and Abdominopelvic protocols, three dose levels, and three reconstruction kernels, using both FBP and IR algorithms. Noise magnitudes were calculated in the air surrounding the patient (An) and soft tissues (GNI) by applying HU<-900 and -300Item Open Access ACL Loading And Jump Performance Are Decreased With Increased Knee Flexion Landing And Soft Landing(MEDICINE AND SCIENCE IN SPORTS AND EXERCISE, 2013-05) Dai, Boyi; Garrett, William E; Gross, Michael T; Padua, Darin A; Queen, Robin M; Yu, BingItem Open Access Acute Effects Of Gait Change During Simulated Pregnancy Using The Empathy Belly (R)(MEDICINE AND SCIENCE IN SPORTS AND EXERCISE, 2010-05) Butler, Robert J; Elpers, Melissa; Queen, Robin MItem Open Access ACUTE PULMONARY EMBOLISM: Risk Of Venous Thromboembolism In Patients With Systemic Sclerosis: A Systematic Review And Meta-Analysis(American Journal of Respiratory and Critical Care Medicine) Srivali, Narat; Ungprasert, Patompong; Caples, Sean MBackground/Purpose: Deep venous thrombosis (DVT) and pulmonary embolism (PE), collectively known as venous thromboembolism (VTE), are common problems associated with significant morbidity and mortality. Chronic inflammation, though not generally regarded as traditional risk factor for VTE, is increasingly recognized as a potential predisposing factor. In fact, several chronic inflammatory disorders, such as rheumatoid arthritis and idiopathic inflammatory myopathy, have been shown to increase rates of VTE in large epidemiologic studies. However, the data on systemic sclerosis (SSc), a relatively uncommon chronic inflammatory disorder, remain unclear due to conflicting studies. To further investigate this possible association, we conducted a systematic review and meta-analysis of observational studies that compared the risk of VTE in patients with SSc versus those without it. Methods: Two investigators (N.S. and P.U.) independently searched published studies indexed in MEDLINE, EMBASE and the Cochrane database from inception to April 2014 using the terms for systemic sclerosis in conjunction with the terms “venous thromboembolism”, “pulmonary embolism” and “deep venous thrombosis”. A manual search of references of retrieved articles was also performed. The inclusion criteria were as follows: (1) observational studies published as original studies to evaluate the association between SSc and VTE and (2) odds ratios (OR’s), relative risk (RR’s) or hazard ratio (HR’s) or standardized incidence ratio (SIR’s) with 95% confidence intervals (CI’s) were provided. Study eligibility was independently determined by the two investigators noted above. Newcastle-Ottawa scale was used to assess the quality of included studies. RevMan 5.2 software was used for the data analysis. Point estimates and standard errors were extracted from individual studies and were combined by the generic inverse variance method of DerSimonian and Laird. Given the high likelihood of between study variance, we used a random-effect model rather than a fixed-effect model. Cochran’s Q test was used to determine the study’s statistical heterogeneity. Results: Out of 348 potentially relevant articles, four studies (three retrospective cohort studies and one case-control study) were identified that met the above criteria and were included in our analysis. The pooled risk ratio of VTE in patients with SSc is 1.89 (95% CI, 1.47 to 2.42). The statistical heterogeneity of this meta-analysis was high with an I2 of 78 %. Conclusion: Our study demonstrates an increased risk of VTE among patients with SSc. Clinicians should consider VTE when a patient with SSc presents with extremity and/or respiratory symptoms.Item Open Access Adaptability index: quantifying CT tube current modulation performance from dose and quality informatics(2017-03-17) Ria, F; Wilson, JM; Zhang, Y; Samei, EThe balance between risk and benefit in modern CT scanners is governed by the automatic adaptation mechanisms that adjust x-ray flux for accommodating patient size to achieve certain image noise values. The effectiveness of this adaptation is an important aspect of CT performance and should ideally be characterized in the context of real patient cases. Objective of this study was to characterize CT performance with an index that includes image-noise and radiation dose across a clinical patient population. The study included 1526 examinations performed by three scanners, from two vendors, used for two clinical protocols (abdominopelvic and chest). The dose-patient size and noise-patient size dependencies were linearized, and a 3D-fit was performed for each protocol and each scanner with a planar function. In the fit residual plots the Root Mean Square Error (RMSE) values were estimated as a metric of CT adaptability across the patient population. The RMSE values were between 0.0344 HU1/2 and 0.0215 HU1/2: different scanners offer varying degrees of reproducibility of noise and dose across the population. This analysis could be performed with phantoms, but phantom data would only provide information concerning specific exposure parameters for a scan: instead, a general population comparison is a way to obtain new information related to the relevant clinical adaptability of scanner models. A theoretical relationship between image noise, CTDIvol and patient size was determined based on real patient data. This relationship may provide a new index related to the scanners' adaptability concerning image quality and radiation dose across a patient population. © (2017) COPYRIGHT Society of Photo-Optical Instrumentation Engineers (SPIE). Downloading of the abstract is permitted for personal use only.Item Open Access Admission Serum Magnesium Levels Predict the Risk of Acute Respiratory Failure Requiring Mechanical Ventilation in Hospitalized Patients(Chest, 2015-10-01) Srivali, Narat; Thongprayoon, Charat; Thongprayoon, Charat; Erickson, StephenPURPOSE: The association between admission serum magnesium (Mg) levels and risk of acute respiratory failure (ARF) requiring mechanical ventilation in hospitalized patients is limited. The aim of this study was to assess the risk of developing ARF in all hospitalized patients with various admission Mg levels. METHODS: This is a single-center retrospective study conducted at a tertiary referral hospital. All hospitalized adult patients who had admission Mg available from January to December 2013 were analyzed in this study. Admission Mg was categorized based on its distribution into six groups (less than 1.5, 1.5 to 1.7, 1.7 to 1.9, 1.9 to 2.1, 2.1 to 2.3, and greater than 2.3 mg/dL). The primary outcome was in-hospital ARF requiring mechanical ventilation occurring after hospital admission. Logistic regression analysis was performed to obtain the odds ratio of ARF of various admission Mg levels using Mg of 1.7 to 1.9 mg/dL as the reference group. RESULTS: Of 9,780 patients enrolled, ARF occurred in 619 patients (6.3%). The lowest incidence of ARF was when serum Mg within 1.7-1.9 mg/dL. A U-shaped curve emerged demonstrating higher incidences of ARF associated with both hypoMg (<1.7) and hyperMg (>1.9). After adjusting for potential confounders, both hypoMg (<1.5 mg/dL) and hyperMg (>2.3 mg/dL) were associated with an increased risk of developing ARF requiring mechanical ventilation with odds ratios of 1.69 (95% CI 1.19-2.36) and 1.40 (95% CI 1.02-1.91), respectively. CONCLUSIONS: Both admission hypoMg and hyperMg were associated with an increased risk for in-hospital ARF requiring mechanical ventilation. CLINICAL IMPLICATIONS: Our study demonstrated that admission Mg level was correlated with the incidence of ARF requiring mechanical ventilation during hospitalization so physician should be awared and correct Mg level accordingly.Item Open Access Age-Related Adverse Inflammatory and Metabolic Changes Begin Early in Adulthood.(The journals of gerontology. Series A, Biological sciences and medical sciences, 2018-05-22) Parker, Daniel; Sloane, Richard; Pieper, Carl F; Hall, Katherine S; Kraus, Virginia B; Kraus, William E; Huebner, Janet L; Ilkayeva, Olga R; Bain, James R; Newby, L Kristin; Cohen, Harvey Jay; Morey, Miriam CAging is characterized by deleterious immune and metabolic changes, but the onset of these changes is unknown. We measured immune and metabolic biomarkers in adults beginning at age 30. To our knowledge, this is the first study to evaluate these biomarkers in adults aged 30 to over 80. Biomarkers were quantified in 961 adults. Tumor necrosis factor alpha (TNF-α), tumor necrosis factor receptor I (TNFR-I), tumor necrosis factor receptor II (TNFR-II), interleukin (IL)-2, IL-6, VCAM-I, D-Dimer, G-CSF, regulated on activation, normal T cell expressed and secreted (RANTES), matrix metalloproteinase-3 (MMP-3), adiponectin, and paraoxonase activity were measured by ELISA. Acylcarnitines and amino acids (AAs) were measured by mass spectrometry and reduced to a single factor using principal components analysis (PCA). Glycine was analyzed separately. The relationship between age and biomarkers was analyzed by linear regression with sex, race, and body mass index (BMI) as covariates. Age was positively correlated with TNF-α, TNFR-I, TNFR-II, IL-6, IL-2, VCAM-1, D-Dimer, MMP-3, adiponectin, acylcarnitines, and AAs. Age was negative correlated with G-CSF, RANTES, and paraoxonase activity. BMI was significant for all biomarkers except IL-2, VCAM-1, RANTES, paraoxonase activity, and the AA factor. Excluding MMP-3, greater BMI was associated with potentially adverse changes in biomarker concentrations. Age-related changes in immune and metabolic biomarkers, known to be associated with poor outcomes in older adults, begin as early as the thirties.