Publications by authors named "Scott Chapman"

100 Publications

Global Wheat Head Detection (GWHD) Dataset: A Large and Diverse Dataset of High-Resolution RGB-Labelled Images to Develop and Benchmark Wheat Head Detection Methods.

Plant Phenomics 2020 20;2020:3521852. Epub 2020 Aug 20.

Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Midori-cho, Nishitokyo City, Tokyo, Japan.

The detection of wheat heads in plant images is an important task for estimating pertinent wheat traits including head population density and head characteristics such as health, size, maturity stage, and the presence of awns. Several studies have developed methods for wheat head detection from high-resolution RGB imagery based on machine learning algorithms. However, these methods have generally been calibrated and validated on limited datasets. High variability in observational conditions, genotypic differences, development stages, and head orientation makes wheat head detection a challenge for computer vision. Further, possible blurring due to motion or wind and overlap between heads for dense populations make this task even more complex. Through a joint international collaborative effort, we have built a large, diverse, and well-labelled dataset of wheat images, called the Global Wheat Head Detection (GWHD) dataset. It contains 4700 high-resolution RGB images and 190000 labelled wheat heads collected from several countries around the world at different growth stages with a wide range of genotypes. Guidelines for image acquisition, associating minimum metadata to respect FAIR principles, and consistent head labelling methods are proposed when developing new head detection datasets. The GWHD dataset is publicly available at http://www.global-wheat.com/and aimed at developing and benchmarking methods for wheat head detection.
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http://dx.doi.org/10.34133/2020/3521852DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7706323PMC
August 2020

Endovascular approach to arterial branches mimicking a type II endoleak after popliteal artery aneurysm exclusion and bypass.

J Vasc Surg Cases Innov Tech 2020 Dec 6;6(4):659-663. Epub 2020 Sep 6.

Department of Vascular Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pa.

The management of popliteal artery aneurysms (PAAs) has continued to evolve. Open surgical treatment remains an excellent option. Aneurysm exclusion with saphenous vein bypass through a medial incision remains a preferred approach. After PAA exclusion, however, a possibility remains of sac expansion from geniculate arterial branches. This can mimic a type II endoleak occurring after endovascular aortic aneurysm repair. In the present report, we have described an endovascular technique used to treat an enlarging PAA after exclusion and bypass.
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http://dx.doi.org/10.1016/j.jvscit.2020.08.025DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7683216PMC
December 2020

Propensity score adjusted comparison of three-factor versus four-factor prothrombin complex concentrate for emergent warfarin reversal: a retrospective cohort study.

BMC Emerg Med 2020 11 26;20(1):93. Epub 2020 Nov 26.

Department of Experimental and Clinical Pharmacology, College of Pharmacy, University of Minnesota, 7-115E Weaver-Densford Hall, 308 Harvard St. SE, Minneapolis, MN, 55455, USA.

Background: Prothrombin Complex Concentrates (PCC) are prescribed for emergent warfarin reversal (EWR). The comparative effectiveness and safety among PCC products are not fully understood.

Methods: Patients in an academic level one trauma center who received PCC3 or PCC4 for EWR were identified. Patient characteristics, PCC dose and time of dose, pre- and post-INR and time of measurement, fresh frozen plasma and vitamin K doses, and patient outcomes were collected. Patients whose pre-PCC International Normalized Ratio (INR) was > 6 h before PCC dose or the pre-post PCC INR was > 12 h were excluded. The primary outcome was achieving an INR ≤ 1.5 post PCC. Secondary outcomes were the change in INR over time, post PCC INR, thromboembolic events (TE), and death during hospital stay. Logistic regression modelled the primary outcome with and without a propensity score adjustment accounting for age, sex, actual body weight, dose, initial INR value, and time between INR measurements. Data are reported as median (IQR) or n (%) with p < 0.05 considered significant.

Results: Eighty patients were included (PCC3 = 57, PCC4 = 23). More PCC4 patients achieved goal INR (87.0% vs. 31.6%, odds ratio (OR) = 14.4, 95% CI: 3.80-54.93, p < 0.001). This result remained true after adjusting for possible confounders (AOR = 10.7, 95% CI: 2.17-51.24, p < 0.001). The post-PCC INR was lower in the PCC4 group (1.3 (1.3-1.5) vs. 1.7 (1.5-2.0)). The INR change was greater for PCC4 (2.3 (1.3-3.3) vs. 1.1 (0.6-2.0), p = 0.003). Death during hospital stay (p = 0.52) and TE (p = 1.00) were not significantly different.

Conclusions: PCC4 was associated with a higher achievement of goal INR than PCC3. This relationship was observed in the unadjusted and propensity score adjusted results.
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http://dx.doi.org/10.1186/s12873-020-00386-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7691107PMC
November 2020

Guidance for Restarting Inflammatory Bowel Disease Therapy in Patients Who Withheld Immunosuppressant Medications During COVID-19.

J Crohns Colitis 2020 Oct;14(Supplement_3):S769-S773

Department of Gastroenterology, Evaggelismos-Ophthalmiatreion Athinon-Polykliniki GHA, Athens, Greece.

Patients with inflammatory bowel diseases [IBD] are frequently treated with immunosuppressant medications. During the coronavirus disease 2019 [COVID-19] pandemic, recommendations for IBD management have included that patients should stay on their immunosuppressant medications if they are not infected with the severe acute respiratory syndrome coronavirus 2 [SARS-CoV-2], but to temporarily hold these medications if symptomatic with COVID-19 or asymptomatic but have tested positive for SARS-CoV-2. As more IBD patients are infected globally, it is important to also understand how to manage IBD medications during convalescence while an individual with IBD is recovering from COVID-19. In this review, we address the differences between a test-based versus a symptoms-based strategy as related to COVID-19, and offer recommendations on when it is appropriate to consider restarting IBD therapy in patients testing positive for SARS-CoV-2 or with clinical symptoms consistent with COVID-19. In general, we recommend a symptoms-based approach, due to the current lack of confidence in the accuracy of available testing and the clinical significance of prolonged detection of virus via molecular testing.
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http://dx.doi.org/10.1093/ecco-jcc/jjaa135DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7665410PMC
October 2020

Characteristics and outcomes of patients with peripheral artery disease undergoing endovascular revascularization: A community hospital perspective.

Vascular 2020 09 21:1708538120958858. Epub 2020 Sep 21.

Department of Vascular Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.

Background: There are limited data on outcomes for patients with peripheral artery disease undergoing endovascular revascularization by multi-disciplinary teams in a community hospital setting.

Methods: From January 2015 through December 2015, we assembled a multi-disciplinary program comprised of cardiologists, surgeons, radiologists, nurses, and administrative staff for managing patients with peripheral artery disease undergoing endovascular revascularization. Demographic, procedural, and outcomes data were collected with use of a template from the Society for Vascular Surgery Vascular Quality Initiative database. We compared characteristics and outcomes of patients with intermittent claudication and critical limb ischemia. We used Kaplan-Meier methods to estimate the rate of overall survival and freedom from rehospitalization between groups.

Results: After excluding patients with acute limb ischemia ( = 5), peripheral intervention to the upper extremity ( = 6), or abdominal aorta ( = 11), there were 82 patients in the study cohort; 45 had intermittent claudication and 37 had critical limb ischemia. Baseline and procedural characteristics were similar between groups, although critical limb ischemia patients were more likely to have hyperlipidemia (75.7% vs. 53.3%,  = .42). Procedural success was achieved in 91.3% of cases. Actionable access site bleeding occurred in 2.4% of patients. High rates of aspirin (91.5%) and statin (87.8%) were noted at discharge. After two years of post endovascular revascularization, survival was 57.5% for critical limb ischemia patients and 94.4% for intermittent claudication patients ( < .001). Freedom from rehospitalization was 32.7% for critical limb ischemia patients and 83.5% for intermittent claudication patients ( < .001).

Conclusions: We found that favorable outcomes may be achieved with a multi-disciplinary peripheral artery disease program at community hospitals. The incorporation of quality improvement practices may further help to develop standardized and regionalized approaches to care delivery for patients with peripheral artery disease.
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http://dx.doi.org/10.1177/1708538120958858DOI Listing
September 2020

Concomitant marked decline in prevalence of SARS-CoV-2 and other respiratory viruses among symptomatic patients following public health interventions in Australia: data from St Vincent's Hospital and associated screening clinics, Sydney, NSW.

Clin Infect Dis 2020 Aug 25. Epub 2020 Aug 25.

St Vincent's Hospital, Sydney, Australia.

Our Australian hospital tested almost 22,000 symptomatic people over 11 weeks for SARS-CoV-2 in a multiplex PCR assay. Following travel bans and physical distancing, SARS-CoV-2 and other respiratory viruses diagnoses fell dramatically. Increasing rhinovirus diagnoses as social control measures were relaxed may indirectly indicate an elevated risk of COVID-19 resurgence.
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http://dx.doi.org/10.1093/cid/ciaa1256DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7499558PMC
August 2020

Breeder friendly phenotyping.

Plant Sci 2020 Jun 18;295:110396. Epub 2020 Jan 18.

International Maize and Wheat Improvement Centre, Mexico.

The word phenotyping can nowadays invoke visions of a drone or phenocart moving swiftly across research plots collecting high-resolution data sets on a wide array of traits. This has been made possible by recent advances in sensor technology and data processing. Nonetheless, more comprehensive often destructive phenotyping still has much to offer in breeding as well as research. This review considers the 'breeder friendliness' of phenotyping within three main domains: (i) the 'minimum data set', where being 'handy' or accessible and easy to collect and use is paramount, visual assessment often being preferred; (ii) the high throughput phenotyping (HTP), relatively new for most breeders, and requiring significantly greater investment with technical hurdles for implementation and a steeper learning curve than the minimum data set; (iii) detailed characterization or 'precision' phenotyping, typically customized for a set of traits associated with a target environment and requiring significant time and resources. While having been the subject of debate in the past, extra investment for phenotyping is becoming more accepted to capitalize on recent developments in crop genomics and prediction models, that can be built from the high-throughput and detailed precision phenotypes. This review considers different contexts for phenotyping, including breeding, exploration of genetic resources, parent building and translational research to deliver other new breeding resources, and how the different categories of phenotyping listed above apply to each. Some of the same tools and rules of thumb apply equally well to phenotyping for genetic analysis of complex traits and gene discovery.
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http://dx.doi.org/10.1016/j.plantsci.2019.110396DOI Listing
June 2020

Postoperative outcomes in thoracic outlet decompression for acute versus chronic venous thoracic outlet syndrome.

J Vasc Surg Venous Lymphat Disord 2021 Mar 26;9(2):321-328. Epub 2020 May 26.

Department of Vascular Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pa.

Objective: Venous thoracic outlet syndrome (VTOS) is a rare disorder that occurs in young athletes and working adults. There are multiple published reports demonstrating excellent outcomes with thoracic outlet (TO) decompression surgery when patients present acutely (within 2 weeks of symptom onset). Our objective was to assess outcomes after decompression surgery in patients with acute, subacute, chronic, and secondary VTOS. Additionally, we sought to identify risk factors for persistence of symptoms following operative decompression.

Methods: A retrospective chart review was performed for all patients who underwent operative decompression for VTOS at the University of Pittsburgh Medical Center from 2013 to 2017. We examined baseline characteristics, comorbidities, presenting symptoms, interventions performed, and postoperative clinical outcomes. Patients were characterized as acute, subacute, or chronic based on onset of symptoms and presentation to our surgeons (acute <2 weeks, subacute 2 weeks to 3 months, and chronic >3 months). Our outcomes of interest were return to baseline functional status as defined by resumption of sports activity or occupation and axillosubclavian vein patency.

Results: A total of 51 operative decompressions were performed in 48 patients for VTOS. There were 23 operations (45%) performed on patients who presented acutely, 7 (14%) in the subacute group, and 21 (41%) surgeries in patients with chronic symptoms. Of these 51 operations, 4 (7.8%) were deemed unsuccessful-two surgeries were in the acute group, one in the subacute, and one in the chronic group. The 30-day morbidity after 51 first rib resections included no pneumothoraces, no lymphatic leaks, two surgical site hematomas with associated hemothorax in one patient, two surgical site infections, and only two unplanned returns to the operating room for hematoma evacuation and superficial wound infection washout. In terms of preoperative vein patency, those who presented acutely were more likely to have an occluded axillosubclavian vein (P = .029). The Fisher's exact was 0.540, indicating that the proportion of patients returning to baseline functional status were similar when comparing acute presenters with those who present late. A multivariate Cox proportional hazards model was attempted; however, a small sample size greatly limited the power of the study and prohibited identification of risk factors for surgical failure.

Conclusions: Patients with acute and chronic VTOS resumed their preintervention sports activity or vocation after TO decompression in more than 90% of cases with a low incidence of adverse events. Based on our study results, patients with chronic VTOS benefit as much from TO decompression as those with acute VTOS.
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http://dx.doi.org/10.1016/j.jvsv.2020.05.010DOI Listing
March 2021

Australian and New Zealand consensus statement on the management of lymphoma, chronic lymphocytic leukaemia and myeloma during the COVID-19 pandemic.

Intern Med J 2020 06 15;50(6):667-679. Epub 2020 May 15.

Department of Haematology, St Vincent's Hospital, Sydney, New South Wales, Australia.

The COVID-19 pandemic poses a unique challenge to the care of patients with haematological malignancies. Viral pneumonia is known to cause disproportionately severe disease in patients with cancer, and patients with lymphoma, myeloma and chronic lymphocytic leukaemia are likely to be at particular risk of severe disease related to COVID-19. This statement has been developed by consensus among authors from Australia and New Zealand. We aim to provide supportive guidance to clinicians making individual patient decisions during the COVID-19 pandemic, in particular during periods that access to healthcare resources may be limited. General recommendations include those to minimise patient exposure to COVID-19, including the use of telehealth, avoidance of non-essential visits and minimisation of time spent by patients in infusion suites and other clinical areas. This statement also provides recommendations where appropriate in assessing indications for therapy, reducing therapy-associated immunosuppression and reducing healthcare utilisation in patients with specific haematological malignancies during the COVID-19 pandemic. Specific decisions regarding therapy of haematological malignancies will need to be individualised, based on disease risk, risks of immunosuppression, rates of community transmission of COVID-19 and available local healthcare resources.
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http://dx.doi.org/10.1111/imj.14859DOI Listing
June 2020

Tracked Patient Encounters During Advanced Pharmacy Practice Experiences and Skill Self-assessment Using Entrustable Professional Activities.

Am J Pharm Educ 2019 11;83(9):7349

University of Minnesota College of Pharmacy, Minneapolis, Minnesota.

To determine if the number of patient encounters during advanced pharmacy practice experiences (APPEs) relates to student self-assessment of patient care skills using entrustable professional activities (EPAs). During 12-week acute care/institutional (AC/INST) APPEs, 15-week combined community pharmacy and ambulatory care (CPAC) APPEs, and three 5-week AC/INST or CPAC elective APPEs, fourth-year pharmacy students completed patient tracking surveys. Students documented the number of encounters, type of care provided, primary and secondary diagnoses, and special dosing/population considerations. Students completed self-assessment surveys for 12 EPAs. Students rated their ability to perform each EPA using a four-point scale (1=still developing this skill; 4=can do this independently) at the start and after each APPE semester. Data were collected from May 2016 through April 2017. During this time, 165 students completed APPEs. Students reported 79,717 encounters. There was no significant correlation found between total number of encounters and EPA scores. The baseline EPA mean score was 3.1 and semester 3 EPA mean score was 3.7. The mean student-reported EPA scores did increase over time, some more quickly than others. Tracking student patient encounters provided insight into the quantity and variety of patients and conditions seen and level of care provided by students during APPEs. Mean scores on EPAs increased over time with increased exposure to patients. Patient tracking can be used to inform the curriculum by identifying potential gaps in both didactic and experiential education.
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http://dx.doi.org/10.5688/ajpe7349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6920653PMC
November 2019

From QTLs to Adaptation Landscapes: Using Genotype-To-Phenotype Models to Characterize G×E Over Time.

Front Plant Sci 2019 4;10:1540. Epub 2019 Dec 4.

Biometris, Wageningen University and Research Centre, Wageningen, Netherlands.

Genotype by environment interaction (G×E) for the target trait, e.g. yield, is an emerging property of agricultural systems and results from the interplay between a hierarchy of secondary traits involving the capture and allocation of environmental resources during the growing season. This hierarchy of secondary traits ranges from basic traits that correspond to response mechanisms/sensitivities, to intermediate traits that integrate a larger number of processes over time and therefore show a larger amount of G×E. Traits underlying yield differ in their contribution to adaptation across environmental conditions and have different levels of G×E. Here, we provide a framework to study the performance of genotype to phenotype (G2P) modeling approaches. We generate and analyze response surfaces, or adaptation landscapes, for yield and yield related traits, emphasizing the organization of the traits in a hierarchy and their development and interactions over time. We use the crop growth model APSIM-wheat with genotype-dependent parameters as a tool to simulate non-linear trait responses over time with complex trait dependencies and apply it to wheat crops in Australia. For biological realism, APSIM parameters were given a genetic basis of 300 QTLs sampled from a gamma distribution whose shape and rate parameters were estimated from real wheat data. In the simulations, the hierarchical organization of the traits and their interactions over time cause G×E for yield even when underlying traits do not show G×E. Insight into how G×E arises during growth and development helps to improve the accuracy of phenotype predictions within and across environments and to optimize trial networks. We produced a tangible simulated adaptation landscape for yield that we first investigated for its biological credibility by statistical models for G×E that incorporate genotypic and environmental covariables. Subsequently, the simulated trait data were used to evaluate statistical genotype-to-phenotype models for multiple traits and environments and to characterize relationships between traits over time and across environments, as a way to identify traits that could be useful to select for specific adaptation. Designed appropriately, these types of simulated landscapes might also serve as a basis to train other, more deep learning methodologies in order to transfer such network models to real-world situations.
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http://dx.doi.org/10.3389/fpls.2019.01540DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6904366PMC
December 2019

Combining Crop Growth Modeling and Statistical Genetic Modeling to Evaluate Phenotyping Strategies.

Front Plant Sci 2019 27;10:1491. Epub 2019 Nov 27.

Biometris, Wageningen University and Research Centre, Wageningen, Netherlands.

Genomic prediction of complex traits, say yield, benefits from including information on correlated component traits. Statistical criteria to decide which yield components to consider in the prediction model include the heritability of the component traits and their genetic correlation with yield. Not all component traits are easy to measure. Therefore, it may be attractive to include proxies to yield components, where these proxies are measured in (high-throughput) phenotyping platforms during the growing season. Using the Agricultural Production Systems Simulator (APSIM)-wheat cropping systems model, we simulated phenotypes for a wheat diversity panel segregating for a set of physiological parameters regulating phenology, biomass partitioning, and the ability to capture environmental resources. The distribution of the additive quantitative trait locus effects regulating the APSIM physiological parameters approximated the same distribution of quantitative trait locus effects on real phenotypic data for yield and heading date. We use the crop growth model APSIM-wheat to simulate phenotypes in three Australian environments with contrasting water deficit patterns. The APSIM output contained the dynamics of biomass and canopy cover, plus yield at the end of the growing season. Each water deficit pattern triggered different adaptive mechanisms and the impact of component traits differed between drought scenarios. We evaluated multiple phenotyping schedules by adding plot and measurement error to the dynamics of biomass and canopy cover. We used these trait dynamics to fit parametric models and P-splines to extract parameters with a larger heritability than the phenotypes at individual time points. We used those parameters in multi-trait prediction models for final yield. The combined use of crop growth models and multi-trait genomic prediction models provides a procedure to assess the efficiency of phenotyping strategies and compare methods to model trait dynamics. It also allows us to quantify the impact of yield components on yield prediction accuracy even in different environment types. In scenarios with mild or no water stress, yield prediction accuracy benefitted from including biomass and green canopy cover parameters. The advantage of the multi-trait model was smaller for the early-drought scenario, due to the reduced correlation between the secondary and the target trait. Therefore, multi-trait genomic prediction models for yield require scenario-specific correlated traits.
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http://dx.doi.org/10.3389/fpls.2019.01491DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6890853PMC
November 2019

Conjugated linoleic acid as a novel insecticide targeting the agricultural pest Leptinotarsa decemlineata.

PLoS One 2019 14;14(11):e0220830. Epub 2019 Nov 14.

Department of Animal Sciences, University of Wisconsin-Madison, Madison, Wisconsin, United States of America.

The Colorado Potato Beetle, Leptinotarsa decemlineata, is a major agricultural pest of solanaceous crops in the United States. Historically, a multitude of insecticides have been used to control problematic populations. Due to increasing resistance to insecticides, novel compounds and methodologies are warranted for the control of beetle populations. Mixed-isomer conjugated linoleic acid has been studied in-depth for its beneficial properties to mammalian systems. At the same time, studies have demonstrated that conjugated linoleic acid can manipulate fatty acid composition in non-mammalian systems, resulting in embryo mortality. Consequently, experiments were conducted to assess the effects of foliar-applied conjugated linoleic acid on larval growth, embryogenesis, and feeding preference in Colorado potato beetle. Both maternal and deterrent effects of dietary conjugated linoleic acid were assessed. Conjugated linoleic acid demonstrated desirable insecticidal properties, including increased larval mortality, slowed larval development, antifeedant effects, and decreased egg viability after maternal ingestion.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0220830PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6855466PMC
March 2020

CT Three-Dimensional (3D) Modeling Maintains Fluoroscopy Time and Contrast Volume to a Minimum in the Endovascular Treatment of Great Vessel Injury from Iatrogenic Trauma.

Ann Vasc Surg 2020 May 6;65:283.e13-283.e17. Epub 2019 Nov 6.

Department of Vascular Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA.

CT angiography with multislice detector has become the preferred method for assessment of hemodynamically stable patients suspected of great vessel injury from iatrogenic and blunt trauma. The CT images obtained can be transformed into a three-dimensional (3D) model using the software within minutes. This allows the clinician to evaluate the injury and the injury's proximity to other vital structures for operative planning. The 3D modeling provides geometric calibration of the c-arm or image intensifier in regard to optimal cranial/caudal and oblique angles to evaluate and treat the vessel injury. We describe a case of a 28-year-old female undergoing a cesarian section and hysterectomy for placenta percreta, who sustained a right subclavian artery injury (presumed wire injury) from inadvertent right common carotid artery cannulation during placement of a right internal jugular 8 French resuscitative central line. A 3D model was created from the CT angiography to locate the small pseudoaneurysm of the right subclavian artery. The optimal projection was obtained using the 3D reconstructive software to visualize the injury and its relation to the right vertebral artery ostium for endovascular planning. This preoperative maneuver allowed for limited radiation exposure and contrast volume used to treat the injury.
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http://dx.doi.org/10.1016/j.avsg.2019.10.095DOI Listing
May 2020

Portal Vein Thrombosis After Total Pancreatectomy and Islet Autotransplant: Prophylaxis and Graft Impact.

Pancreas 2019 Nov/Dec;48(10):1329-1333

From the Departments of Surgery.

Objectives: To determine the rate of portal vein thrombosis (PVT) based on pharmacologic prophylaxis protocol and the impact of PVT on islet graft function after total pancreatectomy with islet autotransplantation (TPIAT).

Methods: We compared the incidence of PVT, postsurgical bleeding, and thrombotic complications in patients undergoing TPIAT between 2001 and 2018 at the University of Minnesota who received either unfractionated heparin (UFH) or enoxaparin for postoperative PVT prophylaxis. Six-month and 1-year graft function was compared between patients who developed PVT and those who did not.

Results: Twelve patients (6.6%) developed a PVT, which resolved by 6 months after TPIAT in 10 patients. There was no statistically significant difference in PVT rate between patients who received UFH or enoxaparin for prophylaxis (P = 0.54). Patients who received enoxaparin developed other thrombotic complications more often (6% vs 0%, P = 0.02). Islet graft function did not differ in patients who developed PVT versus those who did not.

Conclusions: There was no difference between enoxaparin or UFH prophylaxis in preventing PVT, but there may be a higher incidence of other thrombotic complications with enoxaparin. In the setting of routine screening and anticoagulation therapy, PVT is a self-limited process.
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http://dx.doi.org/10.1097/MPA.0000000000001421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7181460PMC
September 2020

Functional popliteal artery entrapment syndrome: A review of diagnostic and management approaches.

Vasc Med 2019 10 23;24(5):455-460. Epub 2019 Sep 23.

Department of Vascular Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA, USA.

Functional popliteal artery entrapment syndrome (FPAES) presents a challenge for clinicians in the field today. The relative rarity of the disease coupled with its affliction primarily in young, athletic individuals makes it a difficult condition to diagnose. Treatment modalities have been limited to surgical intervention, with more novel methods being developed over the last several years. We present a case report and review the diagnostic and management approaches for FPAES, shedding light on proposed future interventions.
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http://dx.doi.org/10.1177/1358863X19871343DOI Listing
October 2019

Masson tumor (intravascular papillary endothelial hyperplasia) arising in a superficial temporal artery aneurysm.

J Vasc Surg Cases Innov Tech 2019 Sep 29;5(3):388-391. Epub 2019 Aug 29.

Department of Vascular Surgery, University of Pittsburgh Medical Center, Pittsburgh, Pa.

Masson tumor (intravascular papillary endothelial hyperplasia) is a rare proliferation of endothelial cells within the wall of a vessel, often thought to represent an aberrant resolution of a thrombosis. We describe the unique case of a 75-year-old man who presented to the clinic with a tender, spontaneous aneurysmal dilation of his left superficial temporal artery (STA). Only 8% of all STA aneurysms are believed to be spontaneous true aneurysms, with the majority being post-traumatic pseudoaneurysms. After successful surgical resection, pathologic examination demonstrated a Masson tumor within an STA aneurysm. This paper describes a case in which both rare entities were discovered and briefly outlines the diagnostic and therapeutic modalities available.
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http://dx.doi.org/10.1016/j.jvscit.2019.02.013DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6727241PMC
September 2019

Evaluation of the Phenotypic Repeatability of Canopy Temperature in Wheat Using Continuous-Terrestrial and Airborne Measurements.

Front Plant Sci 2019 9;10:875. Epub 2019 Jul 9.

CSIRO Agriculture and Food, Canberra, ACT, Australia.

Infrared canopy temperature (CT) is a well-established surrogate measure of stomatal conductance. There is ample evidence showing that genotypic variation in stomatal conductance is associated with grain yield in wheat. Our goal was to determine when CT repeatability is greatest (throughout the season and within the day) to guide CT deployment for research and wheat breeding. CT was measured continuously with ArduCrop wireless infrared thermometers from post-tillering to physiological maturity, and with airborne thermography on cloudless days from manned helicopter at multiple times before and after flowering. Our experiments in wheat, across two years contrasting for water availability, showed that repeatability for CT was greatest later in the season, during grain-filling, and usually in the afternoon. This was supported by the observation that repeatability for ArduCrop, and more so for airborne CT, was significantly associated ( < 0.0001) with calculated clear-sky solar radiation and to a lesser degree, vapor pressure deficit. Adding vapor pressure deficit to a model comprising either clear-sky solar radiation or its determinants, day-of-year and hour-of-day, made little to no improvement to the coefficient of determination. Phenotypic correlations for airborne CT afternoon sampling events were consistently high between events in the same year, more so for the year when soil water was plentiful ( = 0.7 to 0.9) than the year where soil water was limiting ( = 0.4 to 0.9). Phenotypic correlations for afternoon airborne CT were moderate between years contrasting in soil water availability ( = 0.1 to 0.5) and notably greater on two separate days following irrigation or rain in the drier year, ranging from = 0.39 to 0.53 ( < 0.0001) for the midday events. For ArduCrop CT the pattern of phenotypic correlations, within a given year, was similar for both years: phenotypic correlations were higher during the grain-filling months of October and November and for hours-of-day from 11 onwards. The lowest correlations comprised events from hours-of-day 8 and 9 across all months. The capacity for the airborne method to instantaneously sample CT on hundreds of plots is more suited to large field experiments than the static ArduCrop sensors which measure CT continuously on a single experimental plot at any given time. Our findings provide promising support for the reliable deployment of CT phenotyping for research and wheat breeding, whereby the high repeatability and high phenotypic correlations between afternoon sampling events during grain-filling could enable reliable screening of germplasm from only one or two sampling events.
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http://dx.doi.org/10.3389/fpls.2019.00875DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6629910PMC
July 2019

A Weakly Supervised Deep Learning Framework for Sorghum Head Detection and Counting.

Plant Phenomics 2019 27;2019:1525874. Epub 2019 Jun 27.

International Field Phenomics Research Laboratory, Institute for Sustainable Agro-Ecosystem Services, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Tokyo, Japan.

The yield of cereal crops such as sorghum ( L. Moench) depends on the distribution of crop-heads in varying branching arrangements. Therefore, counting the head number per unit area is critical for plant breeders to correlate with the genotypic variation in a specific breeding field. However, measuring such phenotypic traits manually is an extremely labor-intensive process and suffers from low efficiency and human errors. Moreover, the process is almost infeasible for large-scale breeding plantations or experiments. Machine learning-based approaches like deep convolutional neural network (CNN) based object detectors are promising tools for efficient object detection and counting. However, a significant limitation of such deep learning-based approaches is that they typically require a massive amount of hand-labeled images for training, which is still a tedious process. Here, we propose an active learning inspired weakly supervised deep learning framework for sorghum head detection and counting from UAV-based images. We demonstrate that it is possible to significantly reduce human labeling effort without compromising final model performance ( between human count and machine count is 0.88) by using a semitrained CNN model (i.e., trained with limited labeled data) to perform synthetic annotation. In addition, we also visualize key features that the network learns. This improves trustworthiness by enabling users to better understand and trust the decisions that the trained deep learning model makes.
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http://dx.doi.org/10.34133/2019/1525874DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7706102PMC
June 2019

Lemierre's Syndrome: An Atypical Presentation.

Ann Vasc Surg 2019 Oct 13;60:479.e1-479.e4. Epub 2019 Jun 13.

Department of Vascular Surgery, University of Pittsburgh Medical Center, Pittsburgh, PA.

Septic thrombophlebitis is a rare diagnosis in this era of widespread antibiotic usage. The clinical diagnosis requires astute clinical suspicion and evaluation. We describe an asplenic 63-year-old woman who presented to the emergency department with a 24-hour history of a tender, swollen, right neck and upper chest wall. She denied any recent illnesses, but two years before, she was hospitalized and treated for Streptococcus pneumoniae meningitis and endocarditis. An enhanced computed tomography scan demonstrated inflammatory changes around a thrombosed right internal jugular vein, which extended to the brachiocephalic/superior vena cava junction. A retropharyngeal effusion was present, but no pulmonary or oropharyngeal abscess was identified. Lemierre's syndrome, although rare, must be recognized promptly to reduce morbidity and mortality associated with this condition.
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http://dx.doi.org/10.1016/j.avsg.2019.03.011DOI Listing
October 2019

Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding.

Plant Sci 2019 May 30;282:23-39. Epub 2018 Jun 30.

CSIRO Agriculture and Food, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, QLD 4067, Australia; School of Agriculture and Food Sciences, The University of Queensland, Gatton, QLD 4343, Australia.

New types of phenotyping tools generate large amounts of data on many aspects of plant physiology and morphology with high spatial and temporal resolution. These new phenotyping data are potentially useful to improve understanding and prediction of complex traits, like yield, that are characterized by strong environmental context dependencies, i.e., genotype by environment interactions. For an evaluation of the utility of new phenotyping information, we will look at how this information can be incorporated in different classes of genotype-to-phenotype (G2P) models. G2P models predict phenotypic traits as functions of genotypic and environmental inputs. In the last decade, access to high-density single nucleotide polymorphism markers (SNPs) and sequence information has boosted the development of a class of G2P models called genomic prediction models that predict phenotypes from genome wide marker profiles. The challenge now is to build G2P models that incorporate simultaneously extensive genomic information alongside with new phenotypic information. Beyond the modification of existing G2P models, new G2P paradigms are required. We present candidate G2P models for the integration of genomic and new phenotyping information and illustrate their use in examples. Special attention will be given to the modelling of genotype by environment interactions. The G2P models provide a framework for model based phenotyping and the evaluation of the utility of phenotyping information in the context of breeding programs.
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http://dx.doi.org/10.1016/j.plantsci.2018.06.018DOI Listing
May 2019

Improving process-based crop models to better capture genotype×environment×management interactions.

J Exp Bot 2019 04;70(9):2389-2401

CSIRO Agriculture & Food, Queensland Biosciences Precinct, St Lucia, QLD, Australia.

In spite of the increasing expectation for process-based crop modelling to capture genotype (G) by environment (E) by management (M) interactions to support breeding selections, it remains a challenge to use current crop models to accurately predict phenotypes from genotypes or from candidate genes. We use wheat as a target crop and the APSIM farming systems model (Holzworth et al., 2014) as an example to analyse the current status of process-based crop models with a major focus on need to improve simulation of specific eco-physiological processes and their linkage to underlying genetic controls. For challenging production environments in Australia, we examine the potential opportunities to capture physiological traits, and to integrate genetic and molecular approaches for future model development and applications. Model improvement will require both reducing the uncertainty in simulating key physiological processes and enhancing the capture of key observable traits and underlying genetic control of key physiological responses to environment. An approach consisting of three interactive stages is outlined to (i) improve modelling of crop physiology, (ii) develop linkage from model parameter to genotypes and further to loci or alleles, and (iii) further link to gene expression pathways. This helps to facilitate the integration of modelling, phenotyping, and functional gene detection and to effectively advance modelling of G×E×M interactions. While gene-based modelling is not always needed to simulate G×E×M, including well-understood gene effects can improve the estimation of genotype effects and prediction of phenotypes. Specific examples are given for enhanced modelling of wheat in the APSIM framework.
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http://dx.doi.org/10.1093/jxb/erz092DOI Listing
April 2019

Modelling impact of early vigour on wheat yield in dryland regions.

J Exp Bot 2019 04;70(9):2535-2548

CSIRO Agriculture & Food, Canberra, Australia.

Early vigour, or faster early leaf area development, has been considered an important trait for rainfed wheat in dryland regions such as Australia. However, early vigour is a genetically complex trait, and results from field experiments have been highly variable. Whether early vigour can lead to improved water use efficiency and crop yields is strongly dependent on climate and management conditions across the entire growing season. Here, we present a modelling framework for simulating the impact of early vigour on wheat growth and yield at eight sites representing the major climate types in Australia. On a typical soil with plant available water capacity (PAWC) of 147 mm, simulated yield increase with early vigour associated with larger seed size was on average 4% higher compared with normal vigour wheat. Early vigour through selection of doubled early leaf sizes could increase yield by 16%. Increase in yield was mainly from increase in biomass and grain number, and was reduced at sites with seasonal rainfall plus initial soil water <300 mm. Opportunities exists for development of early vigour wheat varieties for wetter sites. Soil PAWC could play a significant role in delivering the benefit of early vigour and would require particular attention.
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http://dx.doi.org/10.1093/jxb/erz069DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6487594PMC
April 2019

Meta-Analytic and Economic Approaches for Evaluation of Pesticide Impact on Sclerotinia Stem Rot Control and Soybean Yield in the North Central United States.

Phytopathology 2019 Jul 10;109(7):1157-1170. Epub 2019 Jun 10.

1 Department of Plant Pathology, University of Wisconsin-Madison, Madison, WI.

As complete host resistance in soybean has not been achieved, Sclerotinia stem rot (SSR) caused by continues to be of major economic concern for farmers. Thus, chemical control remains a prevalent disease management strategy. Pesticide evaluations were conducted in Illinois, Iowa, Michigan, Minnesota, New Jersey, and Wisconsin from 2009 to 2016, for a total of 25 site-years ( = 2,057 plot-level data points). These studies were used in network meta-analyses to evaluate the impact of 10 popular pesticide active ingredients, and seven common application timings on SSR control and yield benefit, compared with not treating with a pesticide. Boscalid and picoxystrobin frequently offered the best reductions in disease severity and best yield benefit ( < 0.0001). Pesticide applications (one- or two-spray programs) made during the bloom period provided significant reductions in disease severity index (DIX) ( < 0.0001) and led to significant yield benefits ( = 0.0009). Data from these studies were also used in nonlinear regression analyses to determine the effect of DIX on soybean yield. A three-parameter logistic model was found to best describe soybean yield loss (pseudo- = 0.309). In modern soybean cultivars, yield loss due to SSR does not occur until 20 to 25% DIX, and considerable yield loss (-697 kg ha or -10 bu acre) is observed at 68% DIX. Further analyses identified several pesticides and programs that resulted in greater than 60% probability for return on investment under high disease levels.
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http://dx.doi.org/10.1094/PHYTO-04-18-0124-RDOI Listing
July 2019

Weather-Based Models for Assessing the Risk of Sclerotinia sclerotiorum Apothecial Presence in Soybean (Glycine max) Fields.

Plant Dis 2018 Jan 20;102(1):73-84. Epub 2017 Nov 20.

Department of Plant Pathology, University of Wisconsin-Madison.

Sclerotinia stem rot (SSR) epidemics in soybean, caused by Sclerotinia sclerotiorum, are currently responsible for annual yield reductions in the United States of up to 1 million metric tons. In-season disease management is largely dependent on chemical control but its efficiency and cost-effectiveness depends on both the chemistry used and the risk of apothecia formation, germination, and further dispersal of ascospores during susceptible soybean growth stages. Hence, accurate prediction of the S. sclerotiorum apothecial risk during the soybean flowering period could enable farmers to improve in-season SSR management. From 2014 to 2016, apothecial presence or absence was monitored in three irrigated (n = 1,505 plot-level observations) and six nonirrigated (n = 2,361 plot-level observations) field trials located in Iowa (n = 156), Michigan (n = 1,400), and Wisconsin (n = 2,310), for a total of 3,866 plot-level observations. Hourly air temperature, relative humidity, dew point, wind speed, leaf wetness, and rainfall were also monitored continuously, throughout the season, at each location using high-resolution gridded weather data. Logistic regression models were developed for irrigated and nonirrigated conditions using apothecial presence as a binary response variable. Agronomic variables (row width) and weather-related variables (defined as 30-day moving averages, prior to apothecial presence) were tested for their predictive ability. In irrigated soybean fields, apothecial presence was best explained by row width (r = -0.41, P < 0.0001), 30-day moving averages of daily maximum air temperature (r = 0.27, P < 0.0001), and daily maximum relative humidity (r = 0.16, P < 0.05). In nonirrigated fields, apothecial presence was best explained by using moving averages of daily maximum air temperature (r = -0.30, P < 0.0001) and wind speed (r = -0.27, P < 0.0001). These models correctly predicted (overall accuracy of 67 to 70%) apothecial presence during the soybean flowering period for four independent datasets (n = 1,102 plot-level observations or 30 daily mean observations).
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http://dx.doi.org/10.1094/PDIS-04-17-0504-REDOI Listing
January 2018

Aerial Imagery Analysis - Quantifying Appearance and Number of Sorghum Heads for Applications in Breeding and Agronomy.

Front Plant Sci 2018 23;9:1544. Epub 2018 Oct 23.

Agriculture and Food - Commonwealth Scientific and Industrial Research Organisation, St Lucia, QLD, Australia.

Sorghum ( L. Moench) is a C4 tropical grass that plays an essential role in providing nutrition to humans and livestock, particularly in marginal rainfall environments. The timing of head development and the number of heads per unit area are key adaptation traits to consider in agronomy and breeding but are time consuming and labor intensive to measure. We propose a two-step machine-based image processing method to detect and count the number of heads from high-resolution images captured by unmanned aerial vehicles (UAVs) in a breeding trial. To demonstrate the performance of the proposed method, 52 images were manually labeled; the precision and recall of head detection were 0.87 and 0.98, respectively, and the coefficient of determination () between the manual and new methods of counting was 0.84. To verify the utility of the method in breeding programs, a geolocation-based plot segmentation method was applied to pre-processed ortho-mosaic images to extract >1000 plots from original RGB images. Forty of these plots were randomly selected and labeled manually; the precision and recall of detection were 0.82 and 0.98, respectively, and the coefficient of determination between manual and algorithm counting was 0.56, with the major source of error being related to the morphology of plants resulting in heads being displayed both within and outside the plot in which the plants were sown, i.e., being allocated to a neighboring plot. Finally, the potential applications in yield estimation from UAV-based imagery from agronomy experiments and scouting of production fields are also discussed.
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http://dx.doi.org/10.3389/fpls.2018.01544DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6206408PMC
October 2018

Validating Sclerotinia sclerotiorum Apothecial Models to Predict Sclerotinia Stem Rot in Soybean (Glycine max) Fields.

Plant Dis 2018 12 18;102(12):2592-2601. Epub 2018 Oct 18.

Department of Plant Pathology, University of Wisconsin-Madison.

In soybean, Sclerotinia sclerotiorum apothecia are the sources of primary inoculum (ascospores) critical for Sclerotinia stem rot (SSR) development. We recently developed logistic regression models to predict the presence of apothecia in irrigated and nonirrigated soybean fields. In 2017, small-plot trials were established to validate two weather-based models (one for irrigated fields and one for nonirrigated fields) to predict SSR development. Additionally, apothecial scouting and disease monitoring were conducted in 60 commercial fields in three states between 2016 and 2017 to evaluate model accuracy across the growing region. Site-specific air temperature, relative humidity, and wind speed data were obtained through the Integrated Pest Information Platform for Extension and Education (iPiPE) and Dark Sky weather networks. Across all locations, iPiPE-driven model predictions during the soybean flowering period (R1 to R4 growth stages) explained end-of-season disease observations with an accuracy of 81.8% using a probability action threshold of 35%. Dark Sky data, incorporating bias corrections for weather variables, explained end-of-season disease observations with 87.9% accuracy (in 2017 commercial locations in Wisconsin) using a 40% probability threshold. Overall, these validations indicate that these two weather-based apothecial models, using either weather data source, provide disease risk predictions that both reduce unnecessary chemical application and accurately advise applications at critical times.
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http://dx.doi.org/10.1094/PDIS-02-18-0245-REDOI Listing
December 2018

Acute infection of Viabahn stent graft in the popliteal artery.

J Vasc Surg Cases Innov Tech 2017 Jun 25;3(2):69-73. Epub 2017 Apr 25.

Division of Surgery, Mayo Clinic Health System-Franciscan Healthcare, La Crosse, Wisc.

Peripheral stents are increasingly used for treatment of peripheral arterial disease, yet all implanted devices are potentially at risk for infection. We describe a 51-year-old man who underwent stenting in the femoropopliteal artery and presented 3 days later with leg pain, fever, and evidence of peripheral stigmata of embolization. Blood cultures grew methicillin-resistant and remained persistently positive despite antibiotic therapy. At surgical exploration, the popliteal artery had essentially been disintegrated by the infection, with only visible stent graft maintaining arterial continuity. Acute stent graft infections are rare and must be managed promptly to reduce morbidity.
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http://dx.doi.org/10.1016/j.jvscit.2017.02.003DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5757776PMC
June 2017

Supporting quality in experiential education through enhanced faculty engagement.

Curr Pharm Teach Learn 2017 Nov 23;9(6):962-965. Epub 2017 Aug 23.

Pharmaceutical Care and Health Systems, University of Minnesota College of Pharmacy, 308 Harvard St. SE, Minneapolis, MN 55455, United States. Electronic address:

Introduction: There are ongoing assessment and improvement activities related to strategies to improve the quality of education in the complex and resource-intensive area of experiential education (EE). One undescribed approach for design and delivery of EE programs for schools and colleges, with reliance on volunteer preceptors, is to utilize clinical practice faculty in formal partnerships with EE leadership to enhance curriculum and assessment.

Commentary And Implications: Clinical practice faculty, who possess practice setting expertise, can serve as course directors for advanced pharmacy practice experience (APPE) rotations. In this role, they can collaborate with EE faculty and staff to create more course-specific expectations, learning objectives, and criteria for APPE rotation experiences. This model could increase consistency for students and preceptors, using an approach that is analogous to content experts serving as course directors in didactic curriculum. This commentary explores the potential of this strategy to increase quality and consistency in EE.
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http://dx.doi.org/10.1016/j.cptl.2017.07.003DOI Listing
November 2017