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Clinical Application of a Modular Genomics Technique in Systemic Lupus Erythematosus: Progress towards Precision Medicine.

International journal of genomics

Zollars E, Courtney SM, Wolf BJ, Allaire N, Ranger A, Hardiman G, Petri M.
PMID: 27656648
Int J Genomics. 2016;2016:7862962. doi: 10.1155/2016/7862962. Epub 2016 Aug 30.

Monitoring disease activity in a complex, heterogeneous disease such as lupus is difficult. Both over- and undertreatment lead to damage. Current standard of care serologies are unreliable. Better measures of disease activity are necessary as we move into the...

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Zollars E, Courtney SM, Wolf BJ, et al. Clinical Application of a Modular Genomics Technique in Systemic Lupus Erythematosus: Progress towards Precision Medicine. Int J Genomics. 2016;2016:7862962doi: 10.1155/2016/7862962.
Zollars, E., Courtney, S. M., Wolf, B. J., Allaire, N., Ranger, A., Hardiman, G., & Petri, M. (2016). Clinical Application of a Modular Genomics Technique in Systemic Lupus Erythematosus: Progress towards Precision Medicine. International journal of genomics, 20167862962. https://doi.org/10.1155/2016/7862962
Zollars, Eric, et al. "Clinical Application of a Modular Genomics Technique in Systemic Lupus Erythematosus: Progress towards Precision Medicine." International journal of genomics vol. 2016 (2016): 7862962. doi: https://doi.org/10.1155/2016/7862962
Zollars E, Courtney SM, Wolf BJ, Allaire N, Ranger A, Hardiman G, Petri M. Clinical Application of a Modular Genomics Technique in Systemic Lupus Erythematosus: Progress towards Precision Medicine. Int J Genomics. 2016;2016:7862962. doi: 10.1155/2016/7862962. Epub 2016 Aug 30. PMID: 27656648; PMCID: PMC5021495.
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Rapid perceptual processing in two- and three-dimensional prostate images.

Journal of medical imaging (Bellingham, Wash.)

Treviño M, Turkbey B, Wood BJ, Pinto PA, Czarniecki M, Choyke PL, Horowitz TS.
PMID: 31930156
J Med Imaging (Bellingham). 2020 Mar;7(2):022406. doi: 10.1117/1.JMI.7.2.022406. Epub 2020 Jan 03.

Radiologists can identify whether a radiograph is abnormal or normal at above chance levels in breast and lung images presented for half a second or less. This early perceptual processing has only been demonstrated in static two-dimensional images (e.g.,...

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Treviño M, Turkbey B, Wood BJ, et al. Rapid perceptual processing in two- and three-dimensional prostate images. J Med Imaging (Bellingham). 2020;7(2):022406doi: 10.1117/1.JMI.7.2.022406.
Treviño, M., Turkbey, B., Wood, B. J., Pinto, P. A., Czarniecki, M., Choyke, P. L., & Horowitz, T. S. (2020). Rapid perceptual processing in two- and three-dimensional prostate images. Journal of medical imaging (Bellingham, Wash.), 7(2), 022406. https://doi.org/10.1117/1.JMI.7.2.022406
Treviño, Melissa, et al. "Rapid perceptual processing in two- and three-dimensional prostate images." Journal of medical imaging (Bellingham, Wash.) vol. 7,2 (2020): 022406. doi: https://doi.org/10.1117/1.JMI.7.2.022406
Treviño M, Turkbey B, Wood BJ, Pinto PA, Czarniecki M, Choyke PL, Horowitz TS. Rapid perceptual processing in two- and three-dimensional prostate images. J Med Imaging (Bellingham). 2020 Mar;7(2):022406. doi: 10.1117/1.JMI.7.2.022406. Epub 2020 Jan 03. PMID: 31930156; PMCID: PMC6941639.
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Biogenic silver nanoparticles reduce adherence, infection, and proliferation of toxoplasma gondii RH strain in HeLa cells without inflammatory mediators induction.

Experimental parasitology

Machado LF, Sanfelice RA, Bosqui LR, Assolini JP, Scandorieiro S, Navarro IT, Depieri Cataneo AH, Wowk PF, Nakazato G, Bordignon J, Pavanelli WR, Conchon-Costa I, Costa IN.
PMID: 32061628
Exp Parasitol. 2020 Feb 17;211:107853. doi: 10.1016/j.exppara.2020.107853. Epub 2020 Feb 17.

The highlights of biogenic silver nanoparticles (AgNp-Bio) include low toxicity - depending on size and concentration - and efficient antiparasitic activity. Therefore, the objective of this study was to assess the action of the AgNp-Bio on HeLa cells in...

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Machado LF, Sanfelice RA, Bosqui LR, et al. Biogenic silver nanoparticles reduce adherence, infection, and proliferation of toxoplasma gondii RH strain in HeLa cells without inflammatory mediators induction. Exp Parasitol. 2020;211:107853doi: 10.1016/j.exppara.2020.107853.
Machado, L. F., Sanfelice, R. A., Bosqui, L. R., Assolini, J. P., Scandorieiro, S., Navarro, I. T., Depieri Cataneo, A. H., Wowk, P. F., Nakazato, G., Bordignon, J., Pavanelli, W. R., Conchon-Costa, I., & Costa, I. N. (2020). Biogenic silver nanoparticles reduce adherence, infection, and proliferation of toxoplasma gondii RH strain in HeLa cells without inflammatory mediators induction. Experimental parasitology, 211107853. https://doi.org/10.1016/j.exppara.2020.107853
Machado, Laís Fernanda, et al. "Biogenic silver nanoparticles reduce adherence, infection, and proliferation of toxoplasma gondii RH strain in HeLa cells without inflammatory mediators induction." Experimental parasitology vol. 211 (2020): 107853. doi: https://doi.org/10.1016/j.exppara.2020.107853
Machado LF, Sanfelice RA, Bosqui LR, Assolini JP, Scandorieiro S, Navarro IT, Depieri Cataneo AH, Wowk PF, Nakazato G, Bordignon J, Pavanelli WR, Conchon-Costa I, Costa IN. Biogenic silver nanoparticles reduce adherence, infection, and proliferation of toxoplasma gondii RH strain in HeLa cells without inflammatory mediators induction. Exp Parasitol. 2020 Feb 17;211:107853. doi: 10.1016/j.exppara.2020.107853. Epub 2020 Feb 17. PMID: 32061628.
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Combined MRI-targeted Plus Systematic Confirmatory Biopsy Improves Risk Stratification for Patients Enrolling on Active Surveillance for Prostate Cancer.

Urology

O'Connor LP, Wang AZ, Yerram NK, Lebastchi AH, Ahdoot M, Gurram S, Zeng J, Mehralivand S, Harmon S, Merino MJ, Parnes HL, Choyke PL, Turkbey B, Wood BJ, Pinto PA.
PMID: 32679272
Urology. 2020 Oct;144:164-170. doi: 10.1016/j.urology.2020.06.061. Epub 2020 Jul 15.

OBJECTIVE: To evaluate the efficacy of combined MRI-targeted plus systematic 12-core biopsy (Cbx) to aid in the selection of patients for active surveillance (AS).METHODS: From July 2007 to January 2020, patients with Gleason Grade Group (GG) 1 or GG...

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O'Connor LP, Wang AZ, Yerram NK, et al. Combined MRI-targeted Plus Systematic Confirmatory Biopsy Improves Risk Stratification for Patients Enrolling on Active Surveillance for Prostate Cancer. Urology. 2020;144:164-170doi: 10.1016/j.urology.2020.06.061.
O'Connor, L. P., Wang, A. Z., Yerram, N. K., Lebastchi, A. H., Ahdoot, M., Gurram, S., Zeng, J., Mehralivand, S., Harmon, S., Merino, M. J., Parnes, H. L., Choyke, P. L., Turkbey, B., Wood, B. J., & Pinto, P. A. (2020). Combined MRI-targeted Plus Systematic Confirmatory Biopsy Improves Risk Stratification for Patients Enrolling on Active Surveillance for Prostate Cancer. Urology, 144164-170. https://doi.org/10.1016/j.urology.2020.06.061
O'Connor, Luke P, et al. "Combined MRI-targeted Plus Systematic Confirmatory Biopsy Improves Risk Stratification for Patients Enrolling on Active Surveillance for Prostate Cancer." Urology vol. 144 (2020): 164-170. doi: https://doi.org/10.1016/j.urology.2020.06.061
O'Connor LP, Wang AZ, Yerram NK, Lebastchi AH, Ahdoot M, Gurram S, Zeng J, Mehralivand S, Harmon S, Merino MJ, Parnes HL, Choyke PL, Turkbey B, Wood BJ, Pinto PA. Combined MRI-targeted Plus Systematic Confirmatory Biopsy Improves Risk Stratification for Patients Enrolling on Active Surveillance for Prostate Cancer. Urology. 2020 Oct;144:164-170. doi: 10.1016/j.urology.2020.06.061. Epub 2020 Jul 15. PMID: 32679272.
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An evaluation of common methods for dichotomization of continuous variables to discriminate disease status.

Communications in statistics: theory and methods

Prince Nelson SL, Ramakrishnan V, Nietert PJ, Kamen DL, Ramos PS, Wolf BJ.
PMID: 29962658
Commun Stat Theory Methods. 2017;46(21):10823-10834. doi: 10.1080/03610926.2016.1248783. Epub 2017 Aug 02.

Dichotomization of continuous variables to discriminate a dichotomous outcome is often useful in statistical applications. If a true threshold for a continuous variable exists, the challenge is identifying it. This paper examines common methods for dichotomization to identify which...

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Prince Nelson SL, Ramakrishnan V, Nietert PJ, et al. An evaluation of common methods for dichotomization of continuous variables to discriminate disease status. Commun Stat Theory Methods. 2017;46(21):10823-10834doi: 10.1080/03610926.2016.1248783.
Prince Nelson, S. L., Ramakrishnan, V., Nietert, P. J., Kamen, D. L., Ramos, P. S., & Wolf, B. J. (2017). An evaluation of common methods for dichotomization of continuous variables to discriminate disease status. Communications in statistics: theory and methods, 46(21), 10823-10834. https://doi.org/10.1080/03610926.2016.1248783
Prince Nelson, Sybil L, et al. "An evaluation of common methods for dichotomization of continuous variables to discriminate disease status." Communications in statistics: theory and methods vol. 46,21 (2017): 10823-10834. doi: https://doi.org/10.1080/03610926.2016.1248783
Prince Nelson SL, Ramakrishnan V, Nietert PJ, Kamen DL, Ramos PS, Wolf BJ. An evaluation of common methods for dichotomization of continuous variables to discriminate disease status. Commun Stat Theory Methods. 2017;46(21):10823-10834. doi: 10.1080/03610926.2016.1248783. Epub 2017 Aug 02. PMID: 29962658; PMCID: PMC6020169.
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A multiparametric magnetic resonance imaging-based virtual reality surgical navigation tool for robotic-assisted radical prostatectomy.

Turkish journal of urology

Mehralivand S, Kolagunda A, Hammerich K, Sabarwal V, Harmon S, Sanford T, Gold S, Hale G, Romero VV, Bloom J, Merino MJ, Wood BJ, Kambhamettu C, Choyke PL, Pinto PA, Türkbey B.
PMID: 31509508
Turk J Urol. 2019 Sep 01;45(5):357-365. doi: 10.5152/tud.2019.19133. Print 2019 Sep.

OBJECTIVE: Increased computational power and improved visualization hardware have generated more opportunities for virtual reality (VR) applications in healthcare. In this study, we test the feasibility of a VR-assisted surgical navigation system for robotic-assisted radical prostatectomy.MATERIAL AND METHODS: The...

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Mehralivand S, Kolagunda A, Hammerich K, et al. A multiparametric magnetic resonance imaging-based virtual reality surgical navigation tool for robotic-assisted radical prostatectomy. Turk J Urol. 2019;45(5):357-365doi: 10.5152/tud.2019.19133.
Mehralivand, S., Kolagunda, A., Hammerich, K., Sabarwal, V., Harmon, S., Sanford, T., Gold, S., Hale, G., Romero, V. V., Bloom, J., Merino, M. J., Wood, B. J., Kambhamettu, C., Choyke, P. L., Pinto, P. A., & Türkbey, B. (2019). A multiparametric magnetic resonance imaging-based virtual reality surgical navigation tool for robotic-assisted radical prostatectomy. Turkish journal of urology, 45(5), 357-365. https://doi.org/10.5152/tud.2019.19133
Mehralivand, Sherif, et al. "A multiparametric magnetic resonance imaging-based virtual reality surgical navigation tool for robotic-assisted radical prostatectomy." Turkish journal of urology vol. 45,5 (2019): 357-365. doi: https://doi.org/10.5152/tud.2019.19133
Mehralivand S, Kolagunda A, Hammerich K, Sabarwal V, Harmon S, Sanford T, Gold S, Hale G, Romero VV, Bloom J, Merino MJ, Wood BJ, Kambhamettu C, Choyke PL, Pinto PA, Türkbey B. A multiparametric magnetic resonance imaging-based virtual reality surgical navigation tool for robotic-assisted radical prostatectomy. Turk J Urol. 2019 Sep 01;45(5):357-365. doi: 10.5152/tud.2019.19133. Print 2019 Sep. PMID: 31509508; PMCID: PMC6739087.
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Shadow-consistent Semi-supervised Learning for Prostate Ultrasound Segmentation.

IEEE transactions on medical imaging

Xu X, Sanford T, Turkbey B, Xu S, Wood BJ, Yan P.
PMID: 34971530
IEEE Trans Med Imaging. 2021 Dec 31; doi: 10.1109/TMI.2021.3139999. Epub 2021 Dec 31.

Prostate segmentation in transrectal ultrasound (TRUS) image is an essential prerequisite for many prostate-related clinical procedures, which, however, is also a long-standing problem due to the challenges caused by the low image quality and shadow artifacts. In this paper,...

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Xu X, Sanford T, Turkbey B, et al. Shadow-consistent Semi-supervised Learning for Prostate Ultrasound Segmentation. IEEE Trans Med Imaging. 2021;doi: 10.1109/TMI.2021.3139999.
Xu, X., Sanford, T., Turkbey, B., Xu, S., Wood, B. J., & Yan, P. (2021). Shadow-consistent Semi-supervised Learning for Prostate Ultrasound Segmentation. IEEE transactions on medical imaging, . https://doi.org/10.1109/TMI.2021.3139999
Xu, Xuanang, et al. "Shadow-consistent Semi-supervised Learning for Prostate Ultrasound Segmentation." IEEE transactions on medical imaging vol. (2021). doi: https://doi.org/10.1109/TMI.2021.3139999
Xu X, Sanford T, Turkbey B, Xu S, Wood BJ, Yan P. Shadow-consistent Semi-supervised Learning for Prostate Ultrasound Segmentation. IEEE Trans Med Imaging. 2021 Dec 31; doi: 10.1109/TMI.2021.3139999. Epub 2021 Dec 31. PMID: 34971530.
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Prognostic significance of ethnicity and age in advanced stage epithelial ovarian cancer: An NRG oncology/gynecologic oncology group study.

Gynecologic oncology

duPont NC, Enserro D, Brady MF, Moxley K, Walker JL, Cosgrove C, Bixel K, Tewari KS, Thaker P, Wahner Hendrickson AE, Rubin S, Fujiwara K, Casey AC, Soper J, Burger RA, Monk BJ.
PMID: 34857397
Gynecol Oncol. 2021 Nov 29; doi: 10.1016/j.ygyno.2021.11.013. Epub 2021 Nov 29.

BACKGROUND: Age and ethnicity are among several factors that influence overall survival (OS) in ovarian cancer. The study objective was to determine whether ethnicity and age were of prognostic significance in women enrolled in a clinical trial evaluating the...

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duPont NC, Enserro D, Brady MF, et al. Prognostic significance of ethnicity and age in advanced stage epithelial ovarian cancer: An NRG oncology/gynecologic oncology group study. Gynecol Oncol. 2021;doi: 10.1016/j.ygyno.2021.11.013.
duPont, N. C., Enserro, D., Brady, M. F., Moxley, K., Walker, J. L., Cosgrove, C., Bixel, K., Tewari, K. S., Thaker, P., Wahner Hendrickson, A. E., Rubin, S., Fujiwara, K., Casey, A. C., Soper, J., Burger, R. A., & Monk, B. J. (2021). Prognostic significance of ethnicity and age in advanced stage epithelial ovarian cancer: An NRG oncology/gynecologic oncology group study. Gynecologic oncology, . https://doi.org/10.1016/j.ygyno.2021.11.013
duPont, Nefertiti C, et al. "Prognostic significance of ethnicity and age in advanced stage epithelial ovarian cancer: An NRG oncology/gynecologic oncology group study." Gynecologic oncology vol. (2021). doi: https://doi.org/10.1016/j.ygyno.2021.11.013
duPont NC, Enserro D, Brady MF, Moxley K, Walker JL, Cosgrove C, Bixel K, Tewari KS, Thaker P, Wahner Hendrickson AE, Rubin S, Fujiwara K, Casey AC, Soper J, Burger RA, Monk BJ. Prognostic significance of ethnicity and age in advanced stage epithelial ovarian cancer: An NRG oncology/gynecologic oncology group study. Gynecol Oncol. 2021 Nov 29; doi: 10.1016/j.ygyno.2021.11.013. Epub 2021 Nov 29. PMID: 34857397.
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Point-of-Care Ultrasound to Assess Gastric Content in Pediatric Emergency Department Procedural Sedation Patients.

Pediatric emergency care

Moake MM, Presley BC, Hill JG, Wolf BJ, Kane ID, Busch CE, Jackson BF.
PMID: 32769837
Pediatr Emerg Care. 2022 Jan 01;38(1):e178-e186. doi: 10.1097/PEC.0000000000002198.

OBJECTIVES: There is debate regarding the timing of procedural sedation and analgesia (PSA) in relation to fasting status. Point-of-care ultrasound (POCUS) provides the ability to measure gastric content and is being used as a surrogate for aspiration risk in...

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Moake MM, Presley BC, Hill JG, et al. Point-of-Care Ultrasound to Assess Gastric Content in Pediatric Emergency Department Procedural Sedation Patients. Pediatr Emerg Care. 2022;38(1):e178-e186doi: 10.1097/PEC.0000000000002198.
Moake, M. M., Presley, B. C., Hill, J. G., Wolf, B. J., Kane, I. D., Busch, C. E., & Jackson, B. F. (2022). Point-of-Care Ultrasound to Assess Gastric Content in Pediatric Emergency Department Procedural Sedation Patients. Pediatric emergency care, 38(1), e178-e186. https://doi.org/10.1097/PEC.0000000000002198
Moake, Matthew M, et al. "Point-of-Care Ultrasound to Assess Gastric Content in Pediatric Emergency Department Procedural Sedation Patients." Pediatric emergency care vol. 38,1 (2022): e178-e186. doi: https://doi.org/10.1097/PEC.0000000000002198
Moake MM, Presley BC, Hill JG, Wolf BJ, Kane ID, Busch CE, Jackson BF. Point-of-Care Ultrasound to Assess Gastric Content in Pediatric Emergency Department Procedural Sedation Patients. Pediatr Emerg Care. 2022 Jan 01;38(1):e178-e186. doi: 10.1097/PEC.0000000000002198. PMID: 32769837; PMCID: PMC7854775.
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Prediction Models of Treatment Response in Lupus Nephritis.

Kidney international

Ayoub I, Wolf BJ, Geng L, Song H, Khatiwada A, Tsao BP, Oates JC, Rovin BH.
PMID: 34871620
Kidney Int. 2021 Dec 03; doi: 10.1016/j.kint.2021.11.014. Epub 2021 Dec 03.

In order to develop prediction models of one-year treatment response in lupus nephritis, an approach using machine learning to combine traditional clinical data and novel urine biomarkers was undertaken. Contemporary lupus nephritis biomarkers were identified through an unbiased PubMed...

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Ayoub I, Wolf BJ, Geng L, et al. Prediction Models of Treatment Response in Lupus Nephritis. Kidney Int. 2021;doi: 10.1016/j.kint.2021.11.014.
Ayoub, I., Wolf, B. J., Geng, L., Song, H., Khatiwada, A., Tsao, B. P., Oates, J. C., & Rovin, B. H. (2021). Prediction Models of Treatment Response in Lupus Nephritis. Kidney international, . https://doi.org/10.1016/j.kint.2021.11.014
Ayoub, Isabelle, et al. "Prediction Models of Treatment Response in Lupus Nephritis." Kidney international vol. (2021). doi: https://doi.org/10.1016/j.kint.2021.11.014
Ayoub I, Wolf BJ, Geng L, Song H, Khatiwada A, Tsao BP, Oates JC, Rovin BH. Prediction Models of Treatment Response in Lupus Nephritis. Kidney Int. 2021 Dec 03; doi: 10.1016/j.kint.2021.11.014. Epub 2021 Dec 03. PMID: 34871620.
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Accuracy of genomic selection for reducing susceptibility to pendulous crop in turkey (Meleagris gallopavo).

Poultry science

Abdalla EA, Makanjuola BO, van Staaveren N, Wood BJ, Baes CF.
PMID: 34954445
Poult Sci. 2021 Nov 20;101(2):101601. doi: 10.1016/j.psj.2021.101601. Epub 2021 Nov 20.

Pendulous crop (PC) in the turkey occurs when the crop distends from its normal position, thereby preventing the movement of feed and water from the crop down into the digestive system. This condition negatively impacts the turkey industry at...

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Abdalla EA, Makanjuola BO, van Staaveren N, et al. Accuracy of genomic selection for reducing susceptibility to pendulous crop in turkey (Meleagris gallopavo). Poult Sci. 2021;101(2):101601doi: 10.1016/j.psj.2021.101601.
Abdalla, E. A., Makanjuola, B. O., van Staaveren, N., Wood, B. J., & Baes, C. F. (2021). Accuracy of genomic selection for reducing susceptibility to pendulous crop in turkey (Meleagris gallopavo). Poultry science, 101(2), 101601. https://doi.org/10.1016/j.psj.2021.101601
Abdalla, E A, et al. "Accuracy of genomic selection for reducing susceptibility to pendulous crop in turkey (Meleagris gallopavo)." Poultry science vol. 101,2 (2021): 101601. doi: https://doi.org/10.1016/j.psj.2021.101601
Abdalla EA, Makanjuola BO, van Staaveren N, Wood BJ, Baes CF. Accuracy of genomic selection for reducing susceptibility to pendulous crop in turkey (Meleagris gallopavo). Poult Sci. 2021 Nov 20;101(2):101601. doi: 10.1016/j.psj.2021.101601. Epub 2021 Nov 20. PMID: 34954445; PMCID: PMC8715376.
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Deep Learning Based Staging of Bone Lesions From Computed Tomography Scans.

IEEE access : practical innovations, open solutions

Masoudi S, Mehralivand S, Harmon SA, Lay N, Lindenberg L, Mena E, Pinto PA, Citrin DE, Gulley JL, Wood BJ, Dahut WL, Madan RA, Bagci U, Choyke PL, Turkbey B.
PMID: 34733603
IEEE Access. 2021;9:87531-87542. doi: 10.1109/access.2021.3074051. Epub 2021 Apr 20.

In this study, we formulated an efficient deep learning-based classification strategy for characterizing metastatic bone lesions using computed tomography scans (CTs) of prostate cancer patients. For this purpose, 2,880 annotated bone lesions from CT scans of 114 patients diagnosed...

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Masoudi S, Mehralivand S, Harmon SA, et al. Deep Learning Based Staging of Bone Lesions From Computed Tomography Scans. IEEE Access. 2021;9:87531-87542doi: 10.1109/access.2021.3074051.
Masoudi, S., Mehralivand, S., Harmon, S. A., Lay, N., Lindenberg, L., Mena, E., Pinto, P. A., Citrin, D. E., Gulley, J. L., Wood, B. J., Dahut, W. L., Madan, R. A., Bagci, U., Choyke, P. L., & Turkbey, B. (2021). Deep Learning Based Staging of Bone Lesions From Computed Tomography Scans. IEEE access : practical innovations, open solutions, 987531-87542. https://doi.org/10.1109/access.2021.3074051
Masoudi, Samira, et al. "Deep Learning Based Staging of Bone Lesions From Computed Tomography Scans." IEEE access : practical innovations, open solutions vol. 9 (2021): 87531-87542. doi: https://doi.org/10.1109/access.2021.3074051
Masoudi S, Mehralivand S, Harmon SA, Lay N, Lindenberg L, Mena E, Pinto PA, Citrin DE, Gulley JL, Wood BJ, Dahut WL, Madan RA, Bagci U, Choyke PL, Turkbey B. Deep Learning Based Staging of Bone Lesions From Computed Tomography Scans. IEEE Access. 2021;9:87531-87542. doi: 10.1109/access.2021.3074051. Epub 2021 Apr 20. PMID: 34733603; PMCID: PMC8562651.
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