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1. Verification and Validation of Modeling of Fluid–Solid Interaction in Explosion-Resistant Designs Using Material Point Method

Author

Mohammed H. Saffarini, Zhen Chen, Ahmed Elbelbisi, Hani Salim, Kyle Perry, Andrew L. Bowman, and Stephen D. Robert

Subjects
explosion, failure evolution, material point method, verification and validation, Building construction, TH1-9745
Abstract

Verifying and validating explosion-resistant design models are challenging tasks due to the difficulties in accurately capturing the failure evolution within a setup influenced by the combined effects of fluid–solid interactions (FSI), blast waves, fragmentation, and impact. Curtain wall system, as a key structural component, is widely used in various types of buildings for its aesthetic appeal and weather protection. Hence, optimizing the explosion-resistance of such systems is necessary to improve building safety. In this work, we develop computational procedures that can be used to enhance the design of blast-resistant structures. This paper focuses on studying a representative component (e.g., window panels) from a typical curtain wall system, as well as a small-scale modeling of shock tube testing. For that, the material point method (MPM) simulations are verified against the finite element method (FEM) simulations, and the computational results are validated against shock tube testing. The work objective is to evaluate the simulation fidelity of explosion responses in several case studies. The first case study demonstrates how the MPM captures damage and fragmentation in a typical confined explosion event involving FSI, thus, providing an improved physical description compared to the FEM. The second case study qualitatively compares the MPM’s ability to simulate the shock tube response with experimental observations. Since the second study validates that the MPM solution is qualitatively consistent with the experimental data, the MPM model is then used in the third case study to establish an FEM model that could capture the same physics. This FEM model can be scaled up to model field experiments. The fourth case study involves the development of an FEM model for a representative curtain wall system component, which is validated against experimental results and then scaled down and employed to validate a corresponding MPM model. The proposed procedure provides a feasible approach to verifying and validating explosion-resistant designs for more general cases.

Published
2024
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2. Understanding the connection between blasting and highwall stability

Author

R. Quentin Eades and Kyle Perry

Subjects
Mining engineering. Metallurgy, TN1-997
Abstract

Surface mines continue to implement highwalls for several reasons, such as increasing recovery, improving margins, and justifying higher stripping ratios. Highwall stability is a complex issue that is dependent upon a variety of mining and geologic factors, and a safe design is necessary for a successful surface operation. To improve highwall stability, it is important to understand the connection between local geology and blasting. Explosives are employed throughout the mining industry for primary rock breakage. There are a number of controlled blasting techniques that can be implemented to improve highwall stability. These include line drilling, smooth wall blasting, trim blasting, buffer blasting, air decking, and presplitting. Each of these techniques have associated advantages and disadvantages. Understanding local geology is necessary for selecting the appropriate controlled blasting technique. Furthermore, understanding the limitations and conditions for successful implementation of each technique is necessary. A discussion of the impact of geologic conditions on highwall stability is provided. Additionally, discussion is provided for the successful incorporation of the controlled blasting techniques listed above, and the associated mining and geologic factors that influence the selection and design of controlled blasting plans. Finally, a new methodology is proposed. Keywords: Controlled blasting, Highwall stability, Presplitting, Surface mining

Published
2019
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3. Evaluation of the 20 L dust explosibility testing chamber and comparison to a modified 38 L vessel for underground coal

Author

Robert Eades, Kyle Perry, Catherine Johnson, and Jacob Miller

Subjects
Mining engineering. Metallurgy, TN1-997
Abstract

The phenomenon of combustible dust explosions is present within many industries. Tests for explosibility of dust clouds per ASTM E1226 use a 20 L explosive chamber that places the combustible dust directly below the dispersion nozzle which generates a thorough mixture for testing purposes. However, in the underground coal mining industry, there are a number of geologic, mining, and regulatory factors that change the deposition scheme of combustible coal dust. This causes the atmosphere of a coal mine to have a variable rock dust-coal dust mixture at the time of ignition. To investigate the impact of this variable atmosphere, a series of lean explosibility tests were conducted on a sample of Pittsburgh Pulverized coal dust. These explosibility tests were conducted in a 38 L chamber with a 5 kJ Sobbe igniter. The 38 L chamber generates a variable air-dust mixture prior to ignition. The test results indicate that the 38 L chamber experiences reduced explosive pressures, and lower explosibility index values when compared to the 20 L chamber. Keywords: Dust explosion, Coal mining, Coal dust, Explosibility testing

Published
2018
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6. Evaluation of a 38 L Explosive Chamber for Testing Coal Dust Explosibility

Author

Robert Eades and Kyle Perry

Subjects
Heat, QC251-338.5
Abstract

Coal dust explosions are the deadliest disasters facing the coal mining industry. Research has been conducted globally on this topic for decades. The first explosibility tests in the United States were performed by the Bureau of Mines using a 20 L chamber. This serves as the basis for all standardized tests used for combustible dusts. The purpose of this paper is to investigate the use of a new 38 L chamber for testing coal dust explosions. The 38 L chamber features design modifications to model the unique conditions present in an underground coal mine when compared to other industries where combustible dust hazards are present. A series of explosibility tests were conducted within the explosive chamber using a sample of Pittsburgh pulverized coal dust and a five kJ Sobbe igniter. Analysis to find the maximum pressure ratio and Kst combustible dust parameter was performed for each trial. Based upon this analysis, observations are made for each concentration regarding whether the explosibility test was under-fueled or over-fueled. Based upon this analysis, a recommendation for future explosibility testing concentrations is made.

Published
2019
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7. Predictive value of grade point average (GPA), Medical College Admission Test (MCAT), internal examinations (Block) and National Board of Medical Examiners (NBME) scores on Medical Council of Canada qualifying examination part I (MCCQE-1) scores

Author

Banibrata Roy, Kyle Perry, Ira Ripstein, and Barry Cohen

Subjects
Education (General), L7-991, Medicine (General), R5-920
Abstract

Background: To determine whether the pre-medical Grade Point Average (GPA), Medical College Admission Test (MCAT), Internal examinations (Block) and National Board of Medical Examiners (NBME) scores are correlated with and predict the Medical Council of Canada Qualifying Examination Part I (MCCQE-1) scores. Methods: Data from 392 admitted students in the graduating classes of 2010-2013 at University of Manitoba (UofM), College of Medicine was considered. Pearson’s correlation to assess the strength of the relationship, multiple linear regression to estimate MCCQE-1 score and stepwise linear regression to investigate the amount of variance were employed. Results: Complete data from 367 (94%) students were studied. The MCCQE-1 had a moderate-to-large positive correlation with NBME scores and Block scores but a low correlation with GPA and MCAT scores. The multiple linear regression model gives a good estimate of the MCCQE-1 (R2 =0.604). Stepwise regression analysis demonstrated that 59.2% of the variation in the MCCQE-1 was accounted for by the NBME, but only 1.9% by the Block exams, and negligible variation came from the GPA and the MCAT. Conclusions: Amongst all the examinations used at UofM, the NBME is most closely correlated with MCCQE-1.

Published
2016

8. Visceral Adipose MicroRNA 223 Is Upregulated in Human and Murine Obesity and Modulates the Inflammatory Phenotype of Macrophages.

Author

Jeffrey A Deiuliis, Rafay Syed, Dheeraj Duggineni, Jessica Rutsky, Palanivel Rengasamy, Jie Zhang, Kun Huang, Bradley Needleman, Dean Mikami, Kyle Perry, Jeffrey Hazey, and Sanjay Rajagopalan

Subjects
Medicine, Science
Abstract

Obesity in humans and mice is typified by an activated macrophage phenotype in the visceral adipose tissue (VAT) leading to increased macrophage-mediated inflammation. microRNAs (miRNAs) play an important role in regulating inflammatory pathways in macrophages, and in this study we compared miRNA expression in the VAT of insulin resistant morbidly obese humans to a non-obese cohort with normal glucose tolerance. miR-223-3p was found to be significantly upregulated in the whole omental tissue RNA of 12 human subjects, as were 8 additional miRNAs. We then confirmed that miR-223 upregulation was specific to the stromal vascular cells of human VAT, and found that miR-223 levels were unchanged in adipocytes and circulating monocytes of the non-obese and obese. miR-223 ablation increased basal / unstimulated TLR4 and STAT3 expression and LPS-stimulated TLR4, STAT3, and NOS2 expression in primary macrophages. Conversely, miR-223 mimics decreased TLR4 expression in primary macrophage, at the same time it negatively regulated FBXW7 expression, a well described suppressor of Toll-like receptor 4 (TLR4) signaling. We concluded that the abundance of miR-223 in macrophages significantly modulates macrophage phenotype / activation state and response to stimuli via effects on the TLR4/FBXW7 axis.

Published
2016
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10. Visceral adipose inflammation in obesity is associated with critical alterations in tregulatory cell numbers.

Author

Jeffrey Deiuliis, Zubair Shah, Nilay Shah, Bradley Needleman, Dean Mikami, Vimal Narula, Kyle Perry, Jeffrey Hazey, Thomas Kampfrath, Madhukar Kollengode, Qinghua Sun, Abhay R Satoskar, Carey Lumeng, Susan Moffatt-Bruce, and Sanjay Rajagopalan

Subjects
Medicine, Science
Abstract

The development of insulin resistance (IR) in mouse models of obesity and type 2 diabetes mellitus (DM) is characterized by progressive accumulation of inflammatory macrophages and subpopulations of T cells in the visceral adipose. Regulatory T cells (Tregs) may play a critical role in modulating tissue inflammation via their interactions with both adaptive and innate immune mechanisms. We hypothesized that an imbalance in Tregs is a critical determinant of adipose inflammation and investigated the role of Tregs in IR/obesity through coordinated studies in mice and humans.Foxp3-green fluorescent protein (GFP) "knock-in" mice were randomized to a high-fat diet intervention for a duration of 12 weeks to induce DIO/IR. Morbidly obese humans without overt type 2 DM (n = 13) and lean controls (n = 7) were recruited prospectively for assessment of visceral adipose inflammation. DIO resulted in increased CD3(+)CD4(+), and CD3(+)CD8(+) cells in visceral adipose with a striking decrease in visceral adipose Tregs. Treg numbers in visceral adipose inversely correlated with CD11b(+)CD11c(+) adipose tissue macrophages (ATMs). Splenic Treg numbers were increased with up-regulation of homing receptors CXCR3 and CCR7 and marker of activation CD44. In-vitro differentiation assays showed an inhibition of Treg differentiation in response to conditioned media from inflammatory macrophages. Human visceral adipose in morbid obesity was characterized by an increase in CD11c(+) ATMs and a decrease in foxp3 expression.Our experiments indicate that obesity in mice and humans results in adipose Treg depletion. These changes appear to occur via reduced local differentiation rather than impaired homing. Our findings implicate a role for Tregs as determinants of adipose inflammation.

Published
2011
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13. ETS-related Gene (ERG) is Differentially Expressed in Dermatofibroma (Fibrous Histiocytoma) as Compared With Dermatofibrosarcoma Protuberans and Hypertrophic Scars: A Pilot Immunohistochemical Study

Author

Meredith, Hengy, Jesse, Veenstra, Kyle, Perry, David M, Ozog, and Ben J, Friedman

Subjects
Diagnosis, Differential, Medical Laboratory Technology, Skin Neoplasms, Histology, Cicatrix, Hypertrophic, Histiocytoma, Benign Fibrous, Transcriptional Regulator ERG, Keloid, Dermatofibrosarcoma, Biomarkers, Tumor, Humans, Pilot Projects, Pathology and Forensic Medicine
Abstract

Immunohistochemical staining can be of great utility in differentiating various cutaneous spindle cell neoplasms, particularly when the histomorphologic appearance of the lesions is inconclusive. Nuclear staining for ETS-related gene (ERG), a highly sensitive endothelial cell marker, has seldom been studied in the context of cutaneous spindle cell neoplasms. Little is known about its specificity for vascular differentiation. In this pilot study, immunohistochemical analysis for ERG was performed on 15 dermatofibromas (DF), 10 keloids, and 9 dermatofibrosarcoma protuberans (DFSP) tumors. Consistent nuclear expression of ERG was found in DF [100% (15/15) of the lesions demonstrated50% labeling of tumor cells with moderate to strong intensity]. However, ERG expression was largely absent in DFSP [89% (8/9) of the lesions demonstrating50% labeling staining, generally of mild intensity] and hypertrophic scars-keloids [80% (8/10) without expression]. On the basis of the results of this pilot study, immunohistochemical staining for ERG may prove useful in helping to differentiate DF from DFSP and hypertrophic scars in the context of partial biopsy sampling. If replicated in a larger number of samples, this finding could mitigate the use of costly sequencing panels and potentially avoid unnecessary reexcisions in certain contexts.

Published
2022

14. Improving the Diagnostic Yield of High-Resolution Esophageal Manometry for GERD: The 'Straight Leg-Raise' International Study

Author

Stefano Siboni, Ivan Kristo, Benjamin D. Rogers, Nicola De Bortoli, Anthony Hobson, Brian Louie, Yeong Yeh Lee, Vincent Tee, Salvatore Tolone, Elisa Marabotto, Pierfrancesco Visaggi, Jordan Haworth, Megan Ivy, Garrett Greenan, Chiara Facchini, Takahiro Masuda, Fumiaki Yano, Kyle Perry, Gokulakrishnan Balasubramanian, Dimitrios Theodorou, Tania Triantafyllou, Lorenzo Cusmai, Sara Boveri, Sebastian F. Schoppmann, C. Prakash Gyawali, and Luigi Bonavina

Subjects
Hepatology, Gastroenterology
Abstract

The straight leg raise (SLR) maneuver during high-resolution manometry (HRM) can assess esophagogastric junction (EGJ) barrier function by measuring changes in intraesophageal pressure (IEP) when intra-abdominal pressure is increased. We aimed to determine whether increased esophageal pressure during SLR predicts pathologic esophageal acid exposure time (AET).Adult patients with persistent gastroesophageal reflux disease (GERD) symptoms undergoing HRM and pH-impedance or wireless pH study off proton pump inhibitor were prospectively studied between July 2021 and March 2022. After the HRM Chicago 4.0 protocol, patients were requested to elevate 1 leg at 45º for 5 seconds while supine. The SLR maneuver was considered effective when intra-abdominal pressure increased by 50%. IEPs were recorded 5 cm above the lower esophageal sphincter at baseline and during SLR. GERD was defined as AET greater than 6%.The SLR was effective in 295 patients (81%), 115 (39%) of whom had an AET greater than 6%. Hiatal hernia (EGJ type 2 or 3) was seen in 135 (46%) patients. Compared with patients with an AET less than 6%, peak IEP during SLR was significantly higher in the GERD group (29.7 vs 13.9 mm Hg; P.001). Using receiver operating characteristic analysis, an increase of 11 mm Hg of peak IEP from baseline during SLR was the optimal cut-off value to predict an AET greater than 6% (area under the receiver operating characteristic curve, 0.84; sensitivity, 79%; and specificity, 85%), regardless of the presence of hiatal hernia. On multivariable analysis, an IEP pressure increase during the SLR maneuver, EGJ contractile integral, EGJ subtype 2, and EGJ subtype 3, were found to be significant predictors of AET greater than 6% CONCLUSIONS: The SLR maneuver can predict abnormal an AET, thereby increasing the diagnostic value of HRM when GERD is suspected.gov ID: NCT04813029.

Published
2022

16. Impact of psychiatric disorders on patient satisfaction after Nissen Fundoplication

Author

Carla N, Holcomb, Noah J, Switzer, Anahita, Jalilvand, Patricia, Belle, Monet, McNally, and Kyle, Perry

Subjects
Adult, Male, Patient Satisfaction, Mental Disorders, Gastroesophageal Reflux, Fundoplication, Humans, Female, Laparoscopy, Middle Aged, Retrospective Studies
Abstract

Anxiety and depression have been associated with an increased perception of gastroesophageal reflux symptoms, but there is a paucity of data regarding the outcomes of laparoscopic Nissen Fundoplication (LNF) in this patient population.We performed a retrospective cohort study including all patients undergoing LNF between 2011 and 2017. Patients were stratified by baseline usage of serotonin-modulating medication or benzodiazepines as a proxy for depression and anxiety, respectively. Outcome measures included postoperative gastroesophageal health-related quality of life (GERD-HRQL) scores and overall satisfaction rates after surgery. A p value of 0.05 was considered statistically significant.The population consisted of 271 patients of which 103 patients had depression and 44 patients had anxiety. Patients with depression reported no significant difference in pre- or postoperative GERD-HRQL scores compared to patients without depression and long-term satisfaction rates after surgery were similar in both groups at 76% vs 71%, respectively (p = 0.55). Patients with anxiety reported higher baseline HRQL scores (34 vs. 29, p = 0.05). At long-term follow-up (15 months), patients with anxiety reported slightly worse HRQL scores compared to controls (7 vs. 4, p = 0.11) despite no difference in usage of anti-acid medications or need for endoscopic dilations between the two groups. Patients with anxiety were less likely to report being "satisfied" after surgery (40% vs. 71%, p = 0.01) compared to controls.Patients with anxiety have higher subjective reporting of GERD symptoms and are more likely to report being "satisfied" during long-term follow-up after LNF. Patients on medication for depression appear to have similar reporting of GERD symptoms and derive as much benefit from LNF as patients that are not. While LNF does improve the symptom burden in patients with anxiety, satisfaction is rarely achieved in long-term follow-up.

Published
2019

17. Proceedings of the 39th International Conference on Ground Control in Mining

Author

Ted Klemetti, Brijes Mishra, Heather Lawson, Michael Murphy, Kyle Perry, Ted Klemetti, Brijes Mishra, Heather Lawson, Michael Murphy, and Kyle Perry

Subjects
Mining engineering--Congresses, Mine roof control--Congresses, Ground control (Mining)--Congresses
Abstract

Read what industry thought leaders are saying about research and advancements in ground control science. The International Conference on Ground Control in Mining (ICGCM) has a rich history in advancing ground control techniques and knowledge. It provides a unique platform for researchers, regulators, consultants, manufacturers, and mine operators to present and exchange challenging industry topics as well as to expedite solutions to ground control problems that require immediate attention. This proceedings from the 39th International Conference is no exception. It includes 37 peer-reviewed research papers from industry experts covering topics of importance for today and in the future.

Published
2020

18. Predictive value of grade point average (GPA), Medical College Admission Test (MCAT), internal examinations (Block) and National Board of Medical Examiners (NBME) scores on Medical Council of Canada qualifying examination part I (MCCQE-1) scores

Author

Barry Cohen, Kyle Perry, Ira Ripstein, and Banibrata Roy

Subjects
Medicine (General), Complete data, medicine.medical_specialty, 020205 medical informatics, business.industry, Block (permutation group theory), Education (General), 02 engineering and technology, Multiple linear regression model, Stepwise regression, Positive correlation, Predictive value, Entrance exam, 03 medical and health sciences, R5-920, 0302 clinical medicine, Major Contribution, Linear regression, 0202 electrical engineering, electronic engineering, information engineering, Physical therapy, Medicine, General Materials Science, 030212 general & internal medicine, L7-991, business
Abstract

Background: To determine whether the pre-medical Grade Point Average (GPA), Medical College Admission Test (MCAT), Internal examinations (Block) and National Board of Medical Examiners (NBME) scores are correlated with and predict the Medical Council of Canada Qualifying Examination Part I (MCCQE-1) scores.Methods: Data from 392 admitted students in the graduating classes of 2010-2013 at University of Manitoba (UofM), College of Medicine was considered. Pearson’s correlation to assess the strength of the relationship, multiple linear regression to estimate MCCQE-1 score and stepwise linear regression to investigate the amount of variance were employed.Results: Complete data from 367 (94%) students were studied. The MCCQE-1 had a moderate-to-large positive correlation with NBME scores and Block scores but a low correlation with GPA and MCAT scores. The multiple linear regression model gives a good estimate of the MCCQE-1 (R2 =0.604). Stepwise regression analysis demonstrated that 59.2% of the variation in the MCCQE-1 was accounted for by the NBME, but only 1.9% by the Block exams, and negligible variation came from the GPA and the MCAT.Conclusions: Amongst all the examinations used at UofM, the NBME is most closely correlated with MCCQE-1.

Published
2016

19. Soft Tissue Pathology for Clinicians

Author

Kyle Perry and Kyle Perry

Subjects
Pathology, Oncology, Medicine, Surgery
Abstract

This text is constructed to educate clinicians on the general classification and diagnostic approach to soft tissue tumors, such that they feel more empowered to discuss the relevant features of particular cases with their pathology colleagues. Particular consideration is given to diagnostically and prognostically relevant ancillary studies. The first section addresses the basic foundations of soft tissue pathology, including common morphologic patterns, approach to grading, concepts of immunohistochemistry and molecular studies. Following this introductory section, each soft tissue tumor is presented according to its morphologic differentiation. Sections include lipomatous tumors, fibrous lesions, fibrohistiocytic tumors, neural and nerve sheath tumors, and smooth muscle neoplasms. Each entity is presented in a consistent and organized manner, first discussing the clinical presentation and then addressing the gross and microscopic features. Following this, the immunohistochemical and molecular findings are presented The text then briefly discusses prognosis and treatment. Representative photographs of the microscopic appearance will be included in a large format. Soft Tissue Pathology for Clinicians will further patient care by concisely educating the clinician on the relevant aspects of soft tissue diagnostics.

Published
2017

20. Fibroblastic/Myofibroblastic Tumors

Author

Kyle Perry

Subjects
Pathology, medicine.medical_specialty, Elastofibroma, Solitary fibrous tumor, Soft Tissue Neoplasm, Chemistry, medicine, Dermatofibrosarcoma protuberans, Immunohistochemistry, Superficial Fibromatosis, Nodular fasciitis, medicine.disease, Myofibroblast
Abstract

Fibroblastic and myofibroblastic tumors represent a large group of soft tissue neoplasms that are made up of cells resembling those found in tendons or ligaments. Fibroblasts appear as spindle cells with elongated nuclei and variable amounts of associated eosinophilic collagen deposition (Fig. 5.1). Myofibroblasts can be spindled or star-shaped and demonstrate some muscle-type antigens (e.g. smooth muscle actin) by immunohistochemistry. The behavior of these tumors can span from completely benign to malignant [1].

Published
2017

21. Tumors of Uncertain Differentiation

Author

Kyle Perry

Subjects
Pathology, medicine.medical_specialty, Soft Tissue Neoplasm, Desmoplastic small-round-cell tumor, business.industry, Epithelioid sarcoma, Intramuscular Myxoma, Extraskeletal Myxoid Chondrosarcoma, medicine.disease, Alveolar soft part sarcoma, medicine, Hemosiderotic Fibrolipomatous Tumor, business, Extrarenal Rhabdoid Tumor
Abstract

Although numerous soft tissue neoplasms resemble various connective tissues in the body, some have no identifiable histologic counterpart. Like other diagnostic groups, the behavior of tumors of uncertain differentiation varies from benign to highly malignant. Repetitive genetic aberrations are frequent among these neoplasms and can be used for diagnostic purposes.

Published
2017

23. Neural and Nerve Sheath Lesions

Author

Kyle Perry

Subjects
Pathology, medicine.medical_specialty, business.industry, Connective tissue, Malignant peripheral nerve sheath tumor, Schwannoma, medicine.disease, Myelin, Perineurioma, medicine.anatomical_structure, nervous system, medicine, Neurofibroma, Perineurium, business, Nerve sheath neoplasm
Abstract

Peripheral nerves are composed of axons that are supported and insulated by a myelin substance produced by surrounding Schwann cells. These axons are further organized into bundles that are supported and surrounded by connective tissue and covered by perineurium. In neural and nerve sheath neoplasms, one or a combination of these anatomic structures proliferate to form a soft tissue mass.

Published
2017

24. Gastrointestinal Stromal Tumor

Author

Kyle Perry

Subjects
Leiomyosarcoma, Gastrointestinal tract, Pathology, medicine.medical_specialty, Stromal cell, Soft Tissue Neoplasm, business.industry, medicine.disease, Interstitial cell of Cajal, symbols.namesake, Leiomyoma, Perineurioma, medicine, symbols, Stromal tumor, business
Abstract

The gastrointestinal tract (GI) can be affected by many of the same soft tissue neoplasms that involve other parts of the body, such as leiomyosarcoma, leiomyoma, schwannoma, and perineurioma. A few soft tissue neoplasms, however, are unique to the gastrointestinal tract. Of these, gastrointestinal stromal tumor is one of the most common. This tumor emanates from the interstitial cells of Cajal that normally coordinate peristalsis for digestion.

Published
2017

25. Critical Concepts in Soft Tissue Pathology

Author

Kyle Perry

Subjects
medicine.medical_specialty, Open biopsy, Soft Tissue Neoplasm, medicine.diagnostic_test, business.industry, Soft tissue, Interventional radiology, Soft tissue pathology, medicine.disease, medicine, Specimen Handling, Radiology, Sarcoma, business, Image-Guided Biopsy
Abstract

With recent advances in interventional radiology, the diagnosis of soft tissue neoplasms is increasingly made on image-guided needle core biopsies. This less invasive technique is often preferred to an open biopsy procedure; however, appropriate specimen handling and communication are critical in ensuring a successful pathologic diagnosis with such limited tissue. Wide excision, often after neoadjuvant radiation or chemotherapy, is the common surgical approach for intermediate- to high-grade sarcomas. In these resection specimens, the pathologist typically assesses the tumor for characteristics such astreatment effect, depth of invasion, and involvement of the surgical margins.

Published
2017

28. Skeletal Muscle Tumors

Author

Kyle Perry

Subjects
Myofilament, Pathology, medicine.medical_specialty, Soft tissue, Skeletal muscle, Biology, Rhabdomyoma, medicine.disease, medicine.anatomical_structure, Alveolar rhabdomyosarcoma, medicine, Immunohistochemistry, Embryonal rhabdomyosarcoma, Myogenin
Abstract

Histologically, skeletal muscle cells are distinguished by eosinophilic cytoplasm containing light and dark striations that correspond to the alternating arrangement of thin and thick myofilaments (Fig. 8. 1). These cells can be seen in varying degrees in soft tissue tumors with skeletal muscle differentiation. However, in tumors that are poorly differentiated, rhabdomyoblastic differentiation must sometimes be confirmed by immunohistochemical stains for skeletal muscle markers (e.g., myogenin) [1].

Published
2017

29. Smooth Muscle and Perivascular Tumors

Author

Kyle Perry

Subjects
Pathology, medicine.medical_specialty, Cutaneous Leiomyoma, Genitourinary system, business.industry, fungi, medicine.disease, Glomus tumor, Leiomyoma, Cytoplasm, Eosinophilic, Smooth Muscle Tumor, medicine, business, Cutaneous leiomyosarcoma
Abstract

Smooth muscle is present in almost any part of the body, including the gastrointestinal, genitourinary, and vascular systems. Similarly, smooth muscle tumors can also be found in almost any anatomic location. Morphologically, the neoplastic cells of smooth muscle tumors are noted to have eosinophilic cytoplasm and elongated or ovoid nuclei (Fig. 7.1a).

Published
2017

30. Histologic Examination and Ancillary Studies in Soft Tissue Pathology

Author

Kyle Perry

Subjects
medicine.medical_specialty, medicine.diagnostic_test, Clinical history, business.industry, Soft tissue, Medicine, Soft tissue pathology, Radiology, Differential diagnosis, business, Preliminary diagnosis, Fluorescence in situ hybridization
Abstract

After reviewing the clinical history, a pathologist will typically assess the microscopic features of a tumor on an H&E slide to generate a differential diagnosis from which ancillary tests are ordered. Common ancillary tests include immunohistochemical stains, conventional karyotyping, fluorescence in situ hybridization, and reverse transcription PCR, among others. In addition to these studies, pathologists can freeze, section, and examine representative tissue during an operative procedure and render a preliminary diagnosis to the surgeon. Understanding the uses and limitations of these tests can help the clinician fully leverage the services of the pathology lab in the diagnosis and care of patients with soft tissue sarcomas.

Published
2017

31. Cartilaginous and Osseous Tumors of Soft Tissue

Author

Kyle Perry

Subjects
Basophilic, Extraskeletal Osteosarcoma, Pathology, medicine.medical_specialty, Extraskeletal mesenchymal chondrosarcoma, Chemistry, Osteoid, Eosinophilic, medicine, Soft tissue, Extraskeletal chondroma, Matrix (biology), medicine.disease
Abstract

Although usually associated with the bone, tumors with osteoid or chondroid matrix can occur in the soft tissue and are primarily identified by their associated matrix material. Chondroid material has an amorphous eosinophilic to basophilic appearance (Fig. 11.1). The unmineralized part of the bone known as osteoid has an eosinophilic appearance (Fig. 11.2).

Published
2017

32. 31st Annual Meeting and Associated Programs of the Society for Immunotherapy of Cancer (SITC 2016): part two

Author

Casey Ager, Matthew Reilley, Courtney Nicholas, Todd Bartkowiak, Ashvin Jaiswal, Michael Curran, Tina C. Albershardt, Anshika Bajaj, Jacob F. Archer, Rebecca S. Reeves, Lisa Y. Ngo, Peter Berglund, Jan ter Meulen, Caroline Denis, Hormas Ghadially, Thomas Arnoux, Fabien Chanuc, Nicolas Fuseri, Robert W. Wilkinson, Nicolai Wagtmann, Yannis Morel, Pascale Andre, Michael B. Atkins, Matteo S. Carlino, Antoni Ribas, John A. Thompson, Toni K. Choueiri, F. Stephen Hodi, Wen-Jen Hwu, David F. McDermott, Victoria Atkinson, Jonathan S. Cebon, Bernie Fitzharris, Michael B. Jameson, Catriona McNeil, Andrew G. Hill, Eric Mangin, Malidi Ahamadi, Marianne van Vugt, Mariëlle van Zutphen, Nageatte Ibrahim, Georgina V. Long, Robyn Gartrell, Zoe Blake, Ines Simoes, Yichun Fu, Takuro Saito, Yingzhi Qian, Yan Lu, Yvonne M. Saenger, Sadna Budhu, Olivier De Henau, Roberta Zappasodi, Kyle Schlunegger, Bruce Freimark, Jeff Hutchins, Christopher A. Barker, Jedd D. Wolchok, Taha Merghoub, Elena Burova, Omaira Allbritton, Peter Hong, Jie Dai, Jerry Pei, Matt Liu, Joel Kantrowitz, Venus Lai, William Poueymirou, Douglas MacDonald, Ella Ioffe, Markus Mohrs, William Olson, Gavin Thurston, Cristian Capasso, Federica Frascaro, Sara Carpi, Siri Tähtinen, Sara Feola, Manlio Fusciello, Karita Peltonen, Beatriz Martins, Madeleine Sjöberg, Sari Pesonen, Tuuli Ranki, Lukasz Kyruk, Erkko Ylösmäki, Vincenzo Cerullo, Fabio Cerignoli, Biao Xi, Garret Guenther, Naichen Yu, Lincoln Muir, Leyna Zhao, Yama Abassi, Víctor Cervera-Carrascón, Mikko Siurala, João Santos, Riikka Havunen, Suvi Parviainen, Akseli Hemminki, Angus Dalgleish, Satvinder Mudan, Mark DeBenedette, Ana Plachco, Alicia Gamble, Elizabeth W. Grogan, John Krisko, Irina Tcherepanova, Charles Nicolette, Pooja Dhupkar, Ling Yu, Eugenie S. Kleinerman, Nancy Gordon, Italia Grenga, Lauren Lepone, Sofia Gameiro, Karin M. Knudson, Massimo Fantini, Kwong Tsang, James Hodge, Renee Donahue, Jeffrey Schlom, Elizabeth Evans, Holm Bussler, Crystal Mallow, Christine Reilly, Sebold Torno, Maria Scrivens, Cathie Foster, Alan Howell, Leslie Balch, Alyssa Knapp, John E. Leonard, Mark Paris, Terry Fisher, Siwen Hu-Lieskovan, Ernest Smith, Maurice Zauderer, William Fogler, Marilyn Franklin, Matt Thayer, Dan Saims, John L. Magnani, Jian Gong, Michael Gray, George Fromm, Suresh de Silva, Louise Giffin, Xin Xu, Jason Rose, Taylor H. Schreiber, Sofia R. Gameiro, Paul E. Clavijo, Clint T. Allen, James W. Hodge, Kwong Y. Tsang, Jane Grogan, Nicholas Manieri, Eugene Chiang, Patrick Caplazi, Mahesh Yadav, Patrick Hagner, Hsiling Chiu, Michelle Waldman, Anke Klippel, Anjan Thakurta, Michael Pourdehnad, Anita Gandhi, Ian Henrich, Laura Quick, Rob Young, Margaret Chou, Andrew Hotson, Stephen Willingham, Po Ho, Carmen Choy, Ginna Laport, Ian McCaffery, Richard Miller, Kimberly A. Tipton, Kenneth R. Wong, Victoria Singson, Chihunt Wong, Chanty Chan, Yuanhiu Huang, Shouchun Liu, Jennifer H. Richardson, W. Michael Kavanaugh, James West, Bryan A. Irving, Ritika Jaini, Matthew Loya, Charis Eng, Melissa L. Johnson, Alex A. Adjei, Mateusz Opyrchal, Suresh Ramalingam, Pasi A. Janne, George Dominguez, Dmitry Gabrilovich, Laura de Leon, Jeannette Hasapidis, Scott J. Diede, Peter Ordentlich, Scott Cruickshank, Michael L. Meyers, Matthew D. Hellmann, Pawel Kalinski, Amer Zureikat, Robert Edwards, Ravi Muthuswamy, Nataša Obermajer, Julie Urban, Lisa H. Butterfield, William Gooding, Herbert Zeh, David Bartlett, Olga Zubkova, Larissa Agapova, Marina Kapralova, Liudmila Krasovskaia, Armen Ovsepyan, Maxim Lykov, Artem Eremeev, Vladimir Bokovanov, Olga Grigoryeva, Andrey Karpov, Sergey Ruchko, Alexandr Shuster, Danny N. Khalil, Luis Felipe Campesato, Yanyun Li, Adam S. Lazorchak, Troy D. Patterson, Yueyun Ding, Pottayil Sasikumar, Naremaddepalli Sudarshan, Nagaraj Gowda, Raghuveer Ramachandra, Dodheri Samiulla, Sanjeev Giri, Rajesh Eswarappa, Murali Ramachandra, David Tuck, Timothy Wyant, Jasmin Leshem, Xiu-fen Liu, Tapan Bera, Masaki Terabe, Birgit Bossenmaier, Gerhard Niederfellner, Yoram Reiter, Ira Pastan, Leiming Xia, Yang Xia, Yangyang Hu, Yi Wang, Yangyi Bao, Fu Dai, Shiang Huang, Elaine Hurt, Robert E. Hollingsworth, Lawrence G. Lum, Alfred E. Chang, Max S. Wicha, Qiao Li, Thomas Mace, Neil Makhijani, Erin Talbert, Gregory Young, Denis Guttridge, Darwin Conwell, Gregory B. Lesinski, Rodney JM Macedo Gonzales, Austin P. Huffman, Ximi K. Wang, Ran Reshef, Andy MacKinnon, Jason Chen, Matt Gross, Gisele Marguier, Peter Shwonek, Natalija Sotirovska, Susanne Steggerda, Francesco Parlati, Amani Makkouk, Mark K. Bennett, Ethan Emberley, Tony Huang, Weiqun Li, Silinda Neou, Alison Pan, Jing Zhang, Winter Zhang, Netonia Marshall, Thomas U. Marron, Judith Agudo, Brian Brown, Joshua Brody, Christopher McQuinn, Matthew Farren, Hannah Komar, Reena Shakya, Thomas Ludwug, Y. Maurice Morillon, Scott A. Hammond, John W. Greiner, Pulak R. Nath, Anthony L. Schwartz, Dragan Maric, David D. Roberts, Aung Naing, Kyriakos P. Papadopoulos, Karen A. Autio, Deborah J. Wong, Manish Patel, Gerald Falchook, Shubham Pant, Patrick A. Ott, Melinda Whiteside, Amita Patnaik, John Mumm, Filip Janku, Ivan Chan, Todd Bauer, Rivka Colen, Peter VanVlasselaer, Gail L. Brown, Nizar M. Tannir, Martin Oft, Jeffrey Infante, Evan Lipson, Ajay Gopal, Sattva S. Neelapu, Philippe Armand, Stephen Spurgeon, John P. Leonard, Rachel E. Sanborn, Ignacio Melero, Thomas F. Gajewski, Matthew Maurer, Serena Perna, Andres A. Gutierrez, Raphael Clynes, Priyam Mitra, Satyendra Suryawanshi, Douglas Gladstone, Margaret K. Callahan, James Crooks, Sheila Brown, Audrey Gauthier, Marc Hillairet de Boisferon, Andrew MacDonald, Laura Rosa Brunet, William T. Rothwell, Peter Bell, James M. Wilson, Fumi Sato-Kaneko, Shiyin Yao, Shannon S. Zhang, Dennis A. Carson, Cristina Guiducci, Robert L. Coffman, Kazutaka Kitaura, Takaji Matsutani, Ryuji Suzuki, Tomoko Hayashi, Ezra E. W. Cohen, David Schaer, Yanxia Li, Julie Dobkin, Michael Amatulli, Gerald Hall, Thompson Doman, Jason Manro, Frank Charles Dorsey, Lillian Sams, Rikke Holmgaard, Krishnadatt Persaud, Dale Ludwig, David Surguladze, John S. Kauh, Ruslan Novosiadly, Michael Kalos, Kyla Driscoll, Hardev Pandha, Christy Ralph, Kevin Harrington, Brendan Curti, Wallace Akerley, Sumati Gupta, Alan Melcher, David Mansfield, David R. Kaufman, Emmett Schmidt, Mark Grose, Bronwyn Davies, Roberta Karpathy, Darren Shafren, Katerina Shamalov, Cyrille Cohen, Naveen Sharma, James Allison, Tala Shekarian, Sandrine Valsesia-Wittmann, Christophe Caux, Aurelien Marabelle, Brian M. Slomovitz, Kathleen M. Moore, Hagop Youssoufian, Marshall Posner, Poonam Tewary, Alan D. Brooks, Ya-Ming Xu, Kithsiri Wijeratne, Leslie A. A. Gunatilaka, Thomas J. Sayers, John P. Vasilakos, Tesha Alston, Simon Dovedi, James Elvecrog, Iwen Grigsby, Ronald Herbst, Karen Johnson, Craig Moeckly, Stefanie Mullins, Kristen Siebenaler, Julius SternJohn, Ashenafi Tilahun, Mark A. Tomai, Katharina Vogel, Eveline E. Vietsch, Anton Wellstein, Martin Wythes, Stefano Crosignani, Joseph Tumang, Shilpa Alekar, Patrick Bingham, Sandra Cauwenberghs, Jenny Chaplin, Deepak Dalvie, Sofie Denies, Coraline De Maeseneire, JunLi Feng, Kim Frederix, Samantha Greasley, Jie Guo, James Hardwick, Stephen Kaiser, Katti Jessen, Erick Kindt, Marie-Claire Letellier, Wenlin Li, Karen Maegley, Reece Marillier, Nichol Miller, Brion Murray, Romain Pirson, Julie Preillon, Virginie Rabolli, Chad Ray, Kevin Ryan, Stephanie Scales, Jay Srirangam, Jim Solowiej, Al Stewart, Nicole Streiner, Vince Torti, Konstantinos Tsaparikos, Xianxian Zheng, Gregory Driessens, Bruno Gomes, Manfred Kraus, Chunxiao Xu, Yanping Zhang, Giorgio Kradjian, Guozhong Qin, Jin Qi, Xiaomei Xu, Bo Marelli, Huakui Yu, Wilson Guzman, Rober Tighe, Rachel Salazar, Kin-Ming Lo, Jessie English, Laszlo Radvanyi, Yan Lan, Michael Postow, Yasin Senbabaoglu, Billel Gasmi, Hong Zhong, Cailian Liu, Daniel Hirschhorhn-Cymerman, Yuanyuan Zha, Gregory Malnassy, Noreen Fulton, Jae-Hyun Park, Wendy Stock, Yusuke Nakamura, Hongtao Liu, Xiaoming Ju, Rachelle Kosoff, Kimberly Ramos, Brandon Coder, Robert Petit, Michael Princiotta, Kyle Perry, Jun Zou, Ainhoa Arina, Christian Fernandez, Wenxin Zheng, Michael A. Beckett, Helena J. Mauceri, Yang-Xin Fu, Ralph R. Weichselbaum, Whitney Lewis, Yanyan Han, Yeting Wu, Chou Yang, Jing Huang, Dongyun Wu, Jin Li, Xiaoling Liang, Xiangjun Zhou, Jinlin Hou, Raffit Hassan, Thierry Jahan, Scott J. Antonia, Hedy L. Kindler, Evan W. Alley, Somayeh Honarmand, Weiqun Liu, Meredith L. Leong, Chan C. Whiting, Nitya Nair, Amanda Enstrom, Edward E. Lemmens, Takahiro Tsujikawa, Sushil Kumar, Lisa M. Coussens, Aimee L. Murphy, Dirk G. Brockstedt, Sven D. Koch, Martin Sebastian, Christian Weiss, Martin Früh, Miklos Pless, Richard Cathomas, Wolfgang Hilbe, Georg Pall, Thomas Wehler, Jürgen Alt, Helge Bischoff, Michael Geissler, Frank Griesinger, Jens Kollmeier, Alexandros Papachristofilou, Fatma Doener, Mariola Fotin-Mleczek, Madeleine Hipp, Henoch S. Hong, Karl-Josef Kallen, Ute Klinkhardt, Claudia Stosnach, Birgit Scheel, Andreas Schroeder, Tobias Seibel, Ulrike Gnad-Vogt, Alfred Zippelius, Ha-Ram Park, Yong-Oon Ahn, Tae Min Kim, Soyeon Kim, Seulki Kim, Yu Soo Lee, Bhumsuk Keam, Dong-Wan Kim, Dae Seog Heo, Shari Pilon-Thomas, Amy Weber, Jennifer Morse, Krithika Kodumudi, Hao Liu, John Mullinax, Amod A. Sarnaik, Luke Pike, Andrew Bang, Tracy Balboni, Allison Taylor, Alexander Spektor, Tyler Wilhite, Monica Krishnan, Daniel Cagney, Brian Alexander, Ayal Aizer, Elizabeth Buchbinder, Mark Awad, Leena Ghandi, Jonathan Schoenfeld, Elizabeth Lessey-Morillon, Lisa Ridnour, Neil H. Segal, Manish Sharma, Dung T. Le, Robert L. Ferris, Andrew D. Zelenetz, Ronald Levy, Izidore S. Lossos, Caron Jacobson, Radhakrishnan Ramchandren, John Godwin, A. Dimitrios Colevas, Roland Meier, Suba Krishnan, Xuemin Gu, Jaclyn Neely, John Timmerman, Claire I. Vanpouille-Box, Silvia C. Formenti, Sandra Demaria, Erik Wennerberg, Aranzazu Mediero, Bruce N. 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Cron, Ayelet Sivan, Keston Aquino-Michaels, Marco Orecchioni, Davide Bedognetti, Wouter Hendrickx, Claudia Fuoco, Filomena Spada, Francesco Sgarrella, Gianni Cesareni, Francesco Marincola, Kostas Kostarelos, Alberto Bianco, Lucia Delogu, Jessica Roelands, Sabri Boughorbel, Julie Decock, Scott Presnell, Ena Wang, Franco M. Marincola, Peter Kuppen, Michele Ceccarelli, Darawan Rinchai, Damien Chaussabel, Lance Miller, Andrew Nguyen, J. Zachary Sanborn, Charles Vaske, Shahrooz Rabizadeh, Kayvan Niazi, Steven Benz, Shashank Patel, Nicholas Restifo, James White, Sam Angiuoli, Mark Sausen, Sian Jones, Maria Sevdali, John Simmons, Victor Velculescu, Luis Diaz, Theresa Zhang, Jennifer S. Sims, Sunjay M. Barton, Angela Kadenhe-Chiweshe, Filemon Dela Cruz, Andrew T. Turk, Christopher F. Mazzeo, Andrew L. Kung, Jeffrey N. Bruce, Darrell J. Yamashiro, Eileen P. Connolly, Jason Baird, Marka Crittenden, David Friedman, Hong Xiao, Rom Leidner, Bryan Bell, Kristina Young, Michael Gough, Zhen Bian, Koby Kidder, Yuan Liu, Emily Curran, Xiufen Chen, Leticia P. Corrales, Justin Kline, Ethan G. Aguilar, Jennifer Guerriero, Alaba Sotayo, Holly Ponichtera, Alexandra Pourzia, Sara Schad, Ruben Carrasco, Suzan Lazo, Roderick Bronson, Anthony Letai, Richard S. Kornbluth, Sachin Gupta, James Termini, Elizabeth Guirado, Geoffrey W. Stone, Christina Meyer, Laura Helming, Nicholas Wilson, Robert Hofmeister, Natalie J. Neubert, Laure Tillé, David Barras, Charlotte Soneson, Petra Baumgaertner, Donata Rimoldi, David Gfeller, Mauro Delorenzi, Silvia A. Fuertes Marraco, Daniel E. Speiser, Tara S. Abraham, Bo Xiang, Michael S. Magee, Scott A. Waldman, Adam E. Snook, Wojciech Blogowski, Ewa Zuba-Surma, Marta Budkowska, Daria Salata, Barbara Dolegowska, Teresa Starzynska, Leo Chan, Srinivas Somanchi, Kelsey McCulley, Dean Lee, Nico Buettner, Feng Shi, Paisley T. Myers, Stuart Curbishley, Sarah A. Penny, Lora Steadman, David Millar, Ellen Speers, Nicola Ruth, Gabriel Wong, Robert Thimme, David Adams, Mark Cobbold, Remy Thomas, Mariam Al-Muftah, Michael KK Wong, Michael Morse, Joseph I. Clark, Howard L. Kaufman, Gregory A. Daniels, Hong Hua, Tharak Rao, Janice P. Dutcher, Kai Kang, Yogen Saunthararajah, Vamsidhar Velcheti, Vikas Kumar, Firoz Anwar, Amita Verma, Zinal Chheda, Gary Kohanbash, John Sidney, Kaori Okada, Shruti Shrivastav, Diego A. Carrera, Shuming Liu, Naznin Jahan, Sabine Mueller, Ian F. Pollack, Angel M. Carcaboso, Alessandro Sette, Yafei Hou, Hideho Okada, Jessica J. Field, Weiping Zeng, Vincent FS Shih, Che-Leung Law, Peter D. Senter, Shyra J. Gardai, Nicole M. Okeley, Jennifer G. Abelin, Abu Z. Saeed, Stacy A. Malaker, Jeffrey Shabanowitz, Stephen T. Ward, Donald F. Hunt, Pam Profusek, Laura Wood, Dale Shepard, Petros Grivas, Kerstin Kapp, Barbara Volz, Detlef Oswald, Burghardt Wittig, Manuel Schmidt, Julian P. Sefrin, Lars Hillringhaus, Valeria Lifke, Alexander Lifke, Anna Skaletskaya, Jose Ponte, Thomas Chittenden, Yulius Setiady, Eva Sivado, Vincent Thomas, Meddy El Alaoui, Sébastien Papot, Charles Dumontet, Mike Dyson, John McCafferty, Said El Alaoui, Praveen K. Bommareddy, Andrew Zloza, Frederick Kohlhapp, Ann W. Silk, Sachin Jhawar, Tomas Paneque, Jenna Newman, Pedro Beltran, Felicia Cao, Bang-Xing Hong, Tania Rodriguez-Cruz, Xiao-Tong Song, Stephen Gottschalk, Hugo Calderon, Sam Illingworth, Alice Brown, Kerry Fisher, Len Seymour, Brian Champion, Emma Eriksson, Jessica Wenthe, Ann-Charlotte Hellström, Gabriella Paul-Wetterberg, Angelica Loskog, Ioanna Milenova, Magnus Ståhle, Justyna Jarblad-Leja, Gustav Ullenhag, Anna Dimberg, Rafael Moreno, Ramon Alemany, Sharad Goyal, Ann Silk, Janice Mehnert, Nashat Gabrail, Jennifer Bryan, Daniel Medina, Leah Mitchell, Kader Yagiz, Fernando Lopez, Daniel Mendoza, Anthony Munday, Harry Gruber, Douglas Jolly, Steven Fuhrmann, Sasa Radoja, Wei Tan, Aldo Pourchet, Alan Frey, Ian Mohr, Matthew Mulvey, Robert H. I. Andtbacka, Merrick Ross, Sanjiv Agarwala, Kenneth Grossmann, Matthew Taylor, John Vetto, Rogerio Neves, Adil Daud, Hung Khong, Stephanie M. Meek, Richard Ungerleider, Scott Welden, Maki Tanaka, Matthew Williams, Sigrun Hallmeyer, Bernard Fox, Zipei Feng, Christopher Paustian, Carlo Bifulco, Sadia Zafar, Otto Hemminki, Simona Bramante, Lotta Vassilev, Hongjie Wang, Andre Lieber, Silvio Hemmi, Tanja de Gruijl, Anna Kanerva, Tameem Ansari, Srividya Sundararaman, Diana Roen, Paul Lehmann, Anja C. Bloom, Lewis H. Bender, Ian B. Walters, Jay A. Berzofsky, Fanny Chapelin, Eric T. Ahrens, Jeff DeFalco, Michael Harbell, Amy Manning-Bog, Alexander Scholz, Danhui Zhang, Gilson Baia, Yann Chong Tan, Jeremy Sokolove, Dongkyoon Kim, Kevin Williamson, Xiaomu Chen, Jillian Colrain, Gregg Espiritu Santo, Ngan Nguyen, Wayne Volkmuth, Norman Greenberg, William Robinson, Daniel Emerling, Charles G. Drake, Daniel P. Petrylak, Emmanuel S. Antonarakis, Adam S. Kibel, Nancy N. Chang, Tuyen Vu, Dwayne Campogan, Heather Haynes, James B. Trager, Nadeem A. Sheikh, David I. Quinn, Peter Kirk, Murali Addepalli, Thomas Chang, Ping Zhang, Marina Konakova, Katsunobu Hagihara, Steven Pai, Laurie VanderVeen, Palakshi Obalapur, Peiwen Kuo, Phi Quach, Lawrence Fong, Deborah H. Charych, Jonathan Zalevsky, John L. Langowski, Yolanda Kirksey, Ravi Nutakki, Shalini Kolarkar, Rhoneil Pena, Ute Hoch, Stephen K. Doberstein, John Cha, Zach Mallon, Myra Perez, Amanda McDaniel, Snjezana Anand, Darrin Uecker, Richard Nuccitelli, Eva Wieckowski, Ravikumar Muthuswamy, Roshni Ravindranathan, Ariana N. Renrick, Menaka Thounaojam, Portia Thomas, Samuel Pellom, Anil Shanker, Duafalia Dudimah, Alan Brooks, Yu-Lin Su, Tomasz Adamus, Qifang Zhang, Sergey Nechaev, Marcin Kortylewski, Spencer Wei, Clark Anderson, Chad Tang, Jonathan Schoenhals, Efrosini Tsouko, John Heymach, Patricia de Groot, Joe Chang, Kenneth R. Hess, Adi Diab, Padmanee Sharma, David Hong, James Welsh, Andrea J. Parsons, Jardin Leleux, Stephane Ascarateil, Marie Eve Koziol, Dina Bai, Peihong Dai, Weiyi Wang, Ning Yang, Stewart Shuman, Liang Deng, Patrick Dillon, Gina Petroni, David Brenin, Kim Bullock, Walter Olson, Mark E. Smolkin, Kelly Smith, Carmel Nail, Craig L. Slingluff, Meenu Sharma, Faisal Fa’ak, Louise Janssen, Hiep Khong, Zhilan Xiao, Yared Hailemichael, Manisha Singh, Christina Vianden, Willem W. Overwijk, Andrea Facciabene, Pierini Stefano, Fang Chongyung, Stavros Rafail, Michael Nielsen, Peter Vanderslice, Darren G. Woodside, Robert V. Market, Ronald J. Biediger, Upendra K. Marathi, Kevin Hollevoet, Nick Geukens, Paul Declerck, Nathalie Joly, Laura McIntosh, Eustache Paramithiotis, Magnus Rizell, Malin Sternby, Bengt Andersson, Alex Karlsson-Parra, Rui Kuai, Lukasz Ochyl, Anna Schwendeman, James Moon, Weiwen Deng, Thomas E. Hudson, Bill Hanson, Chris S. Rae, Joel Burrill, Justin Skoble, George Katibah, Michele deVries, Peter Lauer, Thomas W. Dubensky, Xin Chen, Li Zhou, Xiubao Ren, Charu Aggarwal, Drishty Mangrolia, Roger Cohen, Gregory Weinstein, Matthew Morrow, Joshua Bauml, Kim Kraynyak, Jean Boyer, Jian Yan, Jessica Lee, Laurent Humeau, Sandra Oyola, Susan Duff, David Weiner, Zane Yang, Mark Bagarazzi, Douglas G. McNeel, Jens Eickhoff, Robert Jeraj, Mary Jane Staab, Jane Straus, Brian Rekoske, Glenn Liu, Marit Melssen, William Grosh, Nikole Varhegyi, Nadejda Galeassi, Donna H. Deacon, Elizabeth Gaughan, Maurizio Ghisoli, Minal Barve, Robert Mennel, Gladice Wallraven, Luisa Manning, Neil Senzer, John Nemunaitis, Masahiro Ogasawara, Shuichi Ota, Kaitlin M. Peace, Diane F. Hale, Timothy J. Vreeland, Doreen O. Jackson, John S. Berry, Alfred F. Trappey, Garth S. Herbert, Guy T. Clifton, Mark O. Hardin, Anne Toms, Na Qiao, Jennifer Litton, George E. Peoples, Elizabeth A. Mittendorf, Lila Ghamsari, Emilio Flano, Judy Jacques, Biao Liu, Jonathan Havel, Vladimir Makarov, Timothy A. Chan, Jessica B. Flechtner, John Facciponte, Stefano Ugel, Francesco De Sanctis, George Coukos, Sébastien Paris, Agnes Pottier, Laurent Levy, Bo Lu, Federica Cappuccini, Emily Pollock, Richard Bryant, Freddie Hamdy, Adrian Hill, Irina Redchenko, Hussein Sultan, Takumi Kumai, Valentyna Fesenkova, Esteban Celis, Ingrid Fernando, Claudia Palena, Justin M. David, Elizabeth Gabitzsch, Frank Jones, James L. Gulley, Mireia Uribe Herranz, Hiroshi Wada, Atsushi Shimizu, Toshihiro Osada, Satoshi Fukaya, Eiji Sasaki, Milad Abolhalaj, David Askmyr, Kristina Lundberg, Ann-Sofie Albrekt, Lennart Greiff, Malin Lindstedt, Dallas B. Flies, Tomoe Higuchi, Wojciech Ornatowski, Jaryse Harris, Sarah F. Adams, Todd Aguilera, Marjan Rafat, Laura Castellini, Hussein Shehade, Mihalis Kariolis, Dadi Jang, Rie vonEbyen, Edward Graves, Lesley Ellies, Erinn Rankin, Albert Koong, Amato Giaccia, Reham Ajina, Shangzi Wang, Jill Smith, Mariaelena Pierobon, Sandra Jablonski, Emanuel Petricoin, Louis M. Weiner, Lorcan Sherry, John Waller, Mark Anderson, Alison Bigley, Chantale Bernatchez, Cara Haymaker, Harriet Kluger, Michael Tetzlaff, Natalie Jackson, Ivan Gergel, Mary Tagliaferri, Patrick Hwu, Mario Snzol, Michael Hurwitz, Theresa Barberi, Allison Martin, Rahul Suresh, David Barakat, Sarah Harris-Bookman, Charles Drake, Alan Friedman, Sara Berkey, Stephanie Downs-Canner, Robert P. Edwards, Tyler Curiel, Kunle Odunsi, Tullia C. Bruno, Brandon Moore, Olivia Squalls, Peggy Ebner, Katherine Waugh, John Mitchell, Wilbur Franklin, Daniel Merrick, Martin McCarter, Brent Palmer, Jeffrey Kern, Dario Vignali, Jill Slansky, Anissa S. H. Chan, Xiaohong Qiu, Kathryn Fraser, Adria Jonas, Nadine Ottoson, Keith Gordon, Takashi O. Kangas, Steven Leonardo, Kathleen Ertelt, Richard Walsh, Mark Uhlik, Jeremy Graff, Nandita Bose, Ravi Gupta, Nitin Mandloi, Kiran Paul, Ashwini Patil, Rekha Sathian, Aparna Mohan, Malini Manoharan, Amitabha Chaudhuri, Yu Chen, Jing Lin, Yun-bin Ye, Chun-wei Xu, Gang Chen, Zeng-qing Guo, Andrey Komarov, Alex Chenchik, Michael Makhanov, Costa Frangou, Yi Zheng, Carla Coltharp, Darryn Unfricht, Ryan Dilworth, Leticia Fridman, Linying Liu, Milind Rajopadhye, Peter Miller, Fernando Concha-Benavente, Julie Bauman, Sumita Trivedi, Raghvendra Srivastava, James Ohr, Dwight Heron, Uma Duvvuri, Seungwon Kim, Heather Torrey, Toshi Mera, Yoshiaki Okubo, Eva Vanamee, Rosemary Foster, Denise Faustman, Edward Stack, Daisuke Izaki, Kristen Beck, Dan Tong Jia, Paul Armenta, Ashley White-Stern, Douglas Marks, Bret Taback, Basil Horst, Laura Hix Glickman, David B. Kanne, Kelsey S. Gauthier, Anthony L. Desbien, Brian Francica, Justin L. Leong, Leonard Sung, Ken Metchette, Shailaja Kasibhatla, Anne Marie Pferdekamper, Lianxing Zheng, Charles Cho, Yan Feng, Jeffery M. McKenna, John Tallarico, Steven Bender, Chudi Ndubaku, Sarah M. McWhirter, Elena Gonzalez Gugel, Charles J. M. Bell, Adiel Munk, Luciana Muniz, Nina Bhardwaj, Fei Zhao, Kathy Evans, Christine Xiao, Alisha Holtzhausen, Brent A. Hanks, Nathalie Scholler, Catherine Yin, Pien Van der Meijs, Andrew M. Prantner, Cecile M. Krejsa, Leia Smith, Brian Johnson, Daniel Branstetter, Paul L. Stein, Juan C. Jaen, Joanne BL Tan, Ada Chen, Timothy Park, Jay P. Powers, Holly Sexton, Guifen Xu, Steve W. Young, Ulrike Schindler, Wentao Deng, David John Klinke, Hannah M. Komar, Gregory Serpa, Omar Elnaggar, Philip Hart, Carl Schmidt, Mary Dillhoff, Ming Jin, Michael C. 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Fugle, Rachidi Saleh, Shaoli Sun, Jennifer Wu, Bei Liu, Zihai Li, Zachary S. Morris, Emily I. Guy, Clinton Heinze, Jasdeep Kler, Monica M. Gressett, Lauryn R. Werner, Stephen D. Gillies, Alan J. Korman, Hans Loibner, Jacquelyn A. Hank, Alexander L. Rakhmilevich, Paul M. Harari, Paul M. Sondel, Erica Huelsmann, Joseph Broucek, Dorothee Brech, Tobias Straub, Martin Irmler, Johannes Beckers, Florian Buettner, Elke Schaeffeler, Matthias Schwab, Elfriede Noessner, Alison Wolfreys, Andre Da Costa, John Silva, Andrea Crosby, Ludovicus Staelens, Graham Craggs, Annick Cauvin, Sean Mason, Alison M. Paterson, Andrew C. Lake, Caroline M. Armet, Rachel W. O’Connor, Jonathan A. Hill, Emmanuel Normant, Ammar Adam, Detlev M. Biniszkiewicz, Scott C. Chappel, Vito J. Palombella, Pamela M. Holland, Annette Becker, Manmohan R. Leleti, Eric Newcomb, Joanne B. L. Tan, Suthee Rapisuwon, Arash Radfar, Kellie Gardner, Geoffrey Gibney, Michael Atkins, Keith R. Rennier, Robert Crowder, Ping Wang, Russell K. Pachynski, Rosa M. Santana Carrero, Sarai Rivas, Figen Beceren-Braun, Scott Anthony, Kimberly S. Schluns, Deepali Sawant, Maria Chikina, Hiroshi Yano, Creg Workman, Elise Salerno, Ileana Mauldin, Donna Deacon, Sofia Shea, Joel Pinczewski, Thomas Gajewski, Stefani Spranger, Brendan Horton, Akiko Suzuki, Pamela Leland, Bharat H. Joshi, Raj K. Puri, Randy F. Sweis, Riyue Bao, Jason Luke, Marie-Nicole Theodoraki, Frances-Mary Mogundo, Haejung Won, Dayson Moreira, Chan Gao, Xingli Zhao, Priyanka Duttagupta, Jeremy Jones, Massimo D’Apuzzo, and Sumanta Pal

Subjects
0301 basic medicine, Pharmacology, Cancer Research, medicine.medical_specialty, business.industry, medicine.medical_treatment, Immunology, Cancer, Immunotherapy, medicine.disease, 3. Good health, 03 medical and health sciences, 030104 developmental biology, 0302 clinical medicine, Oncology, 030220 oncology & carcinogenesis, Family medicine, Molecular Medicine, Immunology and Allergy, Medicine, business
Abstract

O1 IL-15 primes an mTOR-regulated gene-expression program to prolong anti-tumor capacity of human natural killer cells #### Andreas Lundqvist1, Vincent van Hoef1, Xiaonan Zhang1, Erik Wennerberg2, Julie Lorent1, Kristina Witt1, Laia Masvidal Sanz1, Shuo Liang1, Shannon Murray3, Ola Larsson1

Published
2016

33. IA3, an Aspartic Proteinase Inhibitor from Saccharomyces cerevisiae, Is Intrinsically Unstructured in Solution

Author

Leif Smith, Timothy M. Logan, Omjoy K. Ganesh, Stephen J. Hagen, Arthur S. Edison, Ben M. Dunn, Kyle Perry, Terry B. Green, and Lowri H. Phylip

Subjects
Saccharomyces cerevisiae Proteins, biology, Protein Conformation, Chemistry, Circular Dichroism, Molecular Sequence Data, Proteinase a, Saccharomyces cerevisiae, Endogeny, Ligands, biology.organism_classification, Biochemistry, Protein Structure, Secondary, Yeast, Substrate Specificity, Solutions, Aspartic proteinase inhibitor, Aspartic Acid Endopeptidases, Thermodynamics, Protease Inhibitors, Amino Acid Sequence, Nuclear Magnetic Resonance, Biomolecular, Protein Binding
Abstract

IA(3) is a highly specific and potent 68-amino acid endogenous inhibitor of yeast proteinase A (YprA), and X-ray crystallographic studies have shown that IA(3) binds to YprA as an alpha-helix [Li, M., Phylip, L. H., Lees, W. E., Winther, J. R., Dunn, B. M., Wlodawer, A., Kay, J., and Gustchina, A. (2000) Nat. Struct. Biol. 7, 113-117]. Surprisingly, only residues 2-32 of IA(3) are seen in the X-ray structure, and the remaining residues are believed to be disordered in the complex. We have used circular dichroism (CD) and nuclear magnetic resonance (NMR) spectroscopy to show that IA(3) is unstructured in the absence of YprA. Specifically, IA(3) produced a CD spectrum characteristic of an unstructured peptide, and the (15)N HSQC NMR spectra of IA(3) were characteristic of a polypeptide lacking intrinsic structure. We characterized the unstructured state of IA(3) by using singular-value decomposition (SVD) to analyze the CD data in the presence of TFE, by fully assigning the unbound IA(3) protein by NMR and comparing the chemical shifts to published random-coil values, and by measuring (1)H-(15)N heteronuclear NOEs, which are all consistent with an unfolded protein. The IA(3) samples used for NMR analyses were active and inhibited YprA with an inhibition constant (K(i)) of 1.7 nM, and the addition of YprA led to a large spectral transition in IA(3). Calorimetric (ITC) data also show that the overall enthalpy of the interaction between IA(3) and YprA is exothermic.

Published
2004

34. IA3, A Yeast Proteinase A Inhibitor, Is Intrinsically Unstructured in Solution

Author

Lowri H. Phylip, Kyle Perry, Arthur S. Edison, Terry B. Green, Leif Smith, Ben M. Dunn, Timothy M. Logan, and Stephen J. Hagen

Subjects
Physics, lcsh:T, lcsh:R, Proteinase a, Short Report, lcsh:Medicine, Art history, 030206 dentistry, General Medicine, 010501 environmental sciences, lcsh:Technology, 01 natural sciences, General Biochemistry, Genetics and Molecular Biology, 03 medical and health sciences, 0302 clinical medicine, lcsh:Q, lcsh:Science, 0105 earth and related environmental sciences, General Environmental Science
Abstract

Terry Green, Kyle Perry, Leif Smith, Lowri H. Phylip, Timothy M. Logan, Stephen J. Hagen, Ben M. Dunn, and Arthur S. Edison* Departments of Biochemistry & Molecular Biology and Physics, Box 100245, University of Florida, Gainesville, FL 32610-0245; School of Biosciences, Cardiff University, P. O. Box 911, Cardiff CF10 3US, Wales; Department of Chemistry and Program in Molecular Biophysics, Florida State University, Tallahassee, FL 32306 *art@ascaris.ufbi.ufl.edu

Published
2002

36. Optical fiber probe spectroscopy for laparoscopic monitoring of tissue oxygenation during esophagectomies.

Author

Daniel S. Gareau, Frederic Truffer, Kyle Perry, Thai Pham, C. Kristian Enestvedt, James Dolan, John G. Hunter, and Steven L. Jacques

Subjects
OPTICAL spectroscopy, LAPAROSCOPY, HYPERBARIC oxygenation, ESOPHAGECTOMY, SURGICAL anastomosis, BLOOD vessels, SURGICAL excision, PERFUSION
Abstract

Anastomotic complication is a major morbidity associated with esophagectomy. Gastric ischemia after conduit creation contributes to anastomotic complications, but a reliable method to assess oxygenation in the gastric conduit is lacking. We hypothesize that fiber optic spectroscopy can reliably assess conduit oxygenation, and that intraoperative gastric ischemia will correlate with the development of anastomotic complications. A simple optical fiber probe spectrometer is designed for nondestructive laparoscopic measurement of blood content and hemoglobin oxygen saturation in the stomach tissue microvasculature during human esophagectomies. In 22 patients, the probe measured the light transport in stomach tissue between two fibers spaced 3-mm apart (500- to 650-nm wavelength range). The stomach tissue site of measurement becomes the site of a gastroesophageal anastamosis following excision of the cancerous esophagus and surgical ligation of two of the three gastric arteries that provide blood perfusion to the anastamosis. Measurements are made at each of five steps throughout the surgery. The resting baseline saturation is 0.51±0.15 and decreases to 0.35±0.20 with ligation. Seven patients develop anastomotic complications, and a decreased saturation at either of the last two steps (completion of conduit and completion of anastamosis) is predictive of complication with a sensitivity of 0.71 when the specificity equaled 0.71. [ABSTRACT FROM AUTHOR]

Published
2010
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