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2. Navigating Next-Generation Sequencing Laboratory Developed Tests: A Critical Look at Proficiency Testing, US Food and Drug Administration Regulations, and Clinical Laboratory Performance

Author

Harada, Shuko and Mackinnon, Alexander C.

Subjects
United States. Food and Drug Administration -- Laws, regulations and rules, Therapeutics, Physiological -- Laws, regulations and rules, Medical societies -- Laws, regulations and rules, Physical therapy -- Laws, regulations and rules, Genetic engineering -- Laws, regulations and rules, Genetically modified organisms -- Laws, regulations and rules, Medical laboratories -- Laws, regulations and rules, Government regulation, Health, College of American Pathologists
Abstract

Proficiency testing (PT) plays a crucial role in maintaining the quality of clinical laboratories, as mandated by the Clinical Laboratory Improvement Amendments (CLIA). (1) Central to PT is the use [...]

Published
2024
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3. Molecular Characterization of Juxtaglomerular Cell Tumors: Evidence of Alterations in MAPK–RAS Pathway

Author

Lobo, João, Canete-Portillo, Sofia, Pena, Maria Del Carmen Rodriguez, McKenney, Jesse K., Aron, Manju, Massicano, Felipe, Wilk, Brandon M., Gajapathy, Manavalan, Brown, Donna M., Baydar, Dilek E., Matoso, Andres, Rioux-Leclerq, Nathalie, Pan, Chin-Chen, Tretiakova, Maria S., Trpkov, Kiril, Williamson, Sean R., Rais-Bahrami, Soroush, Mackinnon, Alexander C., Harada, Shuko, Worthey, Elizabeth A., and Magi-Galluzzi, Cristina

Published
2024
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18. PD-L1 (22C3) Expression Correlates with Clinical and Molecular Features of Lung Adenocarcinomas in Cytological Samples

Author

Anderson, Sarah A., primary, Harbi, Djamel, additional, Oramas Mogrovejo, Diana, additional, Floyd, Antoinette D., additional, Eltoum, Isam-Eldin, additional, Fatima, Huma, additional, Rosenblum, Frida, additional, Lora Gonzalez, Manuel, additional, Lin, Diana, additional, Mackinnon, Alexander C., additional, Siegal, Gene P., additional, Winokur, Thomas, additional, Yalniz, Ceren, additional, Huo, Lei, additional, Harada, Shuko, additional, and Huang, Xiao, additional

Published
2023
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24. Bronchiolar Adenoma: Expansion of the Concept of Ciliated Muconodular Papillary Tumors With Proposal for Revised Terminology Based on Morphologic, Immunophenotypic, and Genomic Analysis of 25 Cases

Author

Chang, Jason C., Montecalvo, Joseph, Borsu, Laetitia, Lu, Shaohua, Larsen, Brandon T., Wallace, William Dean, Sae-Ow, Wichit, Mackinnon, Alexander C., Kim, Hyunjae R., Bowman, Anita, Sauter, Jennifer L., Arcila, Maria E., Ladanyi, Marc, Travis, William D., and Rekhtman, Natasha

Published
2018
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25. Navigating Next-Generation Sequencing Laboratory Developed Tests: A Critical Look at Proficiency Testing, US Food and Drug Administration Regulations, and Clinical Laboratory Performance.

Author

Shuko Harada and Mackinnon, Alexander C.

Subjects
*PATHOLOGICAL laboratories, *CLINICAL pathology, *SEQUENCE analysis, *INDUSTRIAL property, *GOVERNMENT regulation, *ONCOGENES, *MEDICAL laboratories, *COLORECTAL cancer, *BENCHMARKING (Management), *QUALITY assurance, *SENSITIVITY & specificity (Statistics)
Abstract

The authors reflect on updates on proficiency testing (PT), particularly for next-generation sequencing (NGS) assays. Also cited are the efforts by the U.S. Food and Drug Administration (FDA) in regulating PT programs, the variant allelic frequencies (VAF), and the Sustainable Predictive Oncology Therapeutics and Diagnostics (SOT/Dx) launched by the Tapestry Networks in 2016.

Published
2024
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28. Spindle Cell Sarcoma of the Uterus Harboring MEIS1::NCOA1 Fusion Gene and Mimicking Endometrial Stromal Sarcoma.

Author

Mejbel, Haider A., Harada, Shuko, Stevens, Todd M., Huang, Xiao, Netto, George J., Mackinnon, Alexander C., and Al Diffalha, Sameer

Subjects
GENE fusion, MOLECULAR pathology, SARCOMA, SMOOTH muscle tumors, ENDOMETRIUM, NOSOLOGY, UTERUS
Abstract

MEIS1::NCOA1/2 sarcomas are a newly recognized group of exceedingly rare low-grade spindle cell sarcomas that often involve the genitourinary and gynecologic tracts. Due to its deceptively low-grade morphology and the non-specific immunoprofile, these neoplasms may pose a diagnostic challenge by histologically mimicking other entities such as endometrial stromal sarcoma, smooth muscle tumor, or uterine perivascular epithelioid cell tumor (PEComa). Histologically, MEIS1::NCOA1/2 sarcomas typically show spindle cell proliferation with hyperchromatic nuclei and a generalized cytologic uniformity, arranged in short fascicles and exhibiting alternating zones of hypo- and hypercellularity. Among the previously reported cases, molecular analysis revealed the MEIS1::NCOA2 fusion as the most commonly detected fusion gene, whereas the MEIS1::NCOA1 fusion gene has been reported in only a single case that involved kidney. Herein we report the first case of uterine sarcoma harboring the MEIS1::NCOA1 fusion gene that was initially misclassified as low-grade endometrial stromal sarcoma, demonstrating its clinicopathologic features, and highlighting the essential role of molecular pathology to arrive at the accurate diagnosis that may alter disease classification and inform therapy. [ABSTRACT FROM AUTHOR]

Published
2023
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29. Oral and Inhaled Fosamprenavir Reverses Pepsin‐Induced Damage in a Laryngopharyngeal Reflux Mouse Model

Author

Johnston, Nikki, primary, Samuels, Tina L., additional, Goetz, Christopher J., additional, Arnold, Leggy A., additional, Smith, Brian C., additional, Seabloom, Donna, additional, Wuertz, Beverly, additional, Ondrey, Frank, additional, Wiedmann, Timothy S., additional, Vuksanovic, Nemanja, additional, Silvaggi, Nicholas R., additional, MacKinnon, Alexander C., additional, Miller, James, additional, Bock, Jonathan, additional, and Blumin, Joel H., additional

Published
2022
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33. Oral and Inhaled Fosamprenavir Reverses Pepsin‐Induced Damage in a Laryngopharyngeal Reflux Mouse Model.

Author

Johnston, Nikki, Samuels, Tina L., Goetz, Christopher J., Arnold, Leggy A., Smith, Brian C., Seabloom, Donna, Wuertz, Beverly, Ondrey, Frank, Wiedmann, Timothy S., Vuksanovic, Nemanja, Silvaggi, Nicholas R., MacKinnon, Alexander C., Miller, James, Bock, Jonathan, and Blumin, Joel H.

Abstract

Objective: More than 20% of the US population suffers from laryngopharyngeal reflux. Although dietary/lifestyle modifications and alginates provide benefit to some, there is no gold standard medical therapy. Increasing evidence suggests that pepsin is partly, if not wholly, responsible for damage and inflammation caused by laryngopharyngeal reflux. A treatment specifically targeting pepsin would be amenable to local, inhaled delivery, and could prove effective for endoscopic signs and symptoms associated with nonacid reflux. The aim herein was to identify small molecule inhibitors of pepsin and test their efficacy to prevent pepsin‐mediated laryngeal damage in vivo. Methods: Drug and pepsin binding and inhibition were screened by high‐throughput assays and crystallography. A mouse model of laryngopharyngeal reflux (mechanical laryngeal injury once weekly for 2 weeks and pH 7 solvent/pepsin instillation 3 days/week for 4 weeks) was provided inhibitor by gavage or aerosol (fosamprenavir or darunavir; 5 days/week for 4 weeks; n = 3). Larynges were collected for histopathologic analysis. Results: HIV protease inhibitors amprenavir, ritonavir, saquinavir, and darunavir bound and inhibited pepsin with IC50 in the low micromolar range. Gavage and aerosol fosamprenavir prevented pepsin‐mediated laryngeal damage (i.e., reactive epithelia, increased intraepithelial inflammatory cells, and cell apoptosis). Darunavir gavage elicited mild reactivity and no discernable protection; aerosol protected against apoptosis. Conclusions: Fosamprenavir and darunavir, FDA‐approved therapies for HIV/AIDS, bind and inhibit pepsin, abrogating pepsin‐mediated laryngeal damage in a laryngopharyngeal reflux mouse model. These drugs target a foreign virus, making them ideal to repurpose. Reformulation for local inhaled delivery could further improve outcomes and limit side effects. Level of evidence: NA. Laryngoscope, 133:S1–S11, 2023 [ABSTRACT FROM AUTHOR]

Published
2023
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37. Comparison of Tissue Molecular Biomarker Testing Turnaround Times and Concordance Between Standard of Care and the Biocartis Idylla Platform in Patients With Colorectal Cancer

Author

Tsongalis, Gregory J, primary, Al Turkmani, M Rabie, additional, Suriawinata, Michael, additional, Babcock, Michael J, additional, Mitchell, Kristi, additional, Ding, Yi, additional, Scicchitano, Lisa, additional, Tira, Adrian, additional, Buckingham, Lela, additional, Atkinson, Sara, additional, Lax, Amy, additional, Aisner, Dara L, additional, Davies, Kurtis D, additional, Wood, Holly N, additional, O’Neill, Stacey S, additional, Levine, Edward A, additional, Sequeira, Judy, additional, Harada, Shuko, additional, DeFrank, Gina, additional, Paluri, Ravikumar, additional, Tan, Bradford A, additional, Colabella, Heather, additional, Snead, Christopher, additional, Cruz-Correa, Marcia, additional, Ramirez, Virginia, additional, Rojas, Arnaldo, additional, Huang, Huiya, additional, Mackinnon, Alexander C, additional, Garcia, Fernando U, additional, Cavone, Sharon M, additional, Elfahal, Mutasim, additional, Abel, Gyorgy, additional, Vasef, Mohammad A, additional, Judd, Andrew, additional, Linder, Mark W, additional, Alkhateeb, Khaled, additional, Skinner, William L, additional, Boccia, Ralph, additional, and Patel, Kashyap, additional

Published
2020
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38. Next generation sequencing of PD-L1 for predicting response to immune checkpoint inhibitors

Author

OmniSeq, Conroy, Jeffrey M., Pabla, Sarabjot, Nesline, Mary K., Glenn, Sean T., Papanicolau-Sengos, Antonios, Burgher, Blake, Andreas, Jonathan, Giamo, Vincent, Wang, Yirong, Lenzo, Felicia L., Bshara, Wiam, Khalil, Maya, Dy, Grace K., Madden, Katherine G., Shirai, Keisuke, Dragnev, Konstantin, Tafe, Laura J., Zhu, Jason, Labriola, Matthew, Marin, Daniele, McCall, Shannon J., Clarke, Jeffrey, George, Daniel J., Zhang, Tian, Zibelman, Matthew, Ghatalia, Pooja, Aráujo-Fernández, Isabel, Cruz Merino, L. de la, Singavi, Arun, George, Ben, MacKinnon, Alexander C., Thompson, Jonathan, Singh, Rajbir, Jacob, Robin, Kasuganti, Deepa, Shah, Neel, Day, Roger, Galluzzi, Lorenzo, Gardner, Mark, Morrison, Carl, OmniSeq, Conroy, Jeffrey M., Pabla, Sarabjot, Nesline, Mary K., Glenn, Sean T., Papanicolau-Sengos, Antonios, Burgher, Blake, Andreas, Jonathan, Giamo, Vincent, Wang, Yirong, Lenzo, Felicia L., Bshara, Wiam, Khalil, Maya, Dy, Grace K., Madden, Katherine G., Shirai, Keisuke, Dragnev, Konstantin, Tafe, Laura J., Zhu, Jason, Labriola, Matthew, Marin, Daniele, McCall, Shannon J., Clarke, Jeffrey, George, Daniel J., Zhang, Tian, Zibelman, Matthew, Ghatalia, Pooja, Aráujo-Fernández, Isabel, Cruz Merino, L. de la, Singavi, Arun, George, Ben, MacKinnon, Alexander C., Thompson, Jonathan, Singh, Rajbir, Jacob, Robin, Kasuganti, Deepa, Shah, Neel, Day, Roger, Galluzzi, Lorenzo, Gardner, Mark, and Morrison, Carl

Abstract

[Background] PD-L1 immunohistochemistry (IHC) has been traditionally used for predicting clinical responses to immune checkpoint inhibitors (ICIs). However, there are at least 4 different assays and antibodies used for PD-L1 IHC, each developed with a different ICI. We set to test if next generation RNA sequencing (RNA-seq) is a robust method to determine PD-L1 mRNA expression levels and furthermore, efficacy of predicting response to ICIs as compared to routinely used, standardized IHC procedures., [Methods] A total of 209 cancer patients treated on-label by FDA-approved ICIs, with evaluable responses were assessed for PD-L1 expression by RNA-seq and IHC, based on tumor proportion score (TPS) and immune cell staining (ICS). A subset of serially diluted cases was evaluated for RNA-seq assay performance across a broad range of PD-L1 expression levels., [Results] Assessment of PD-L1 mRNA levels by RNA-seq demonstrated robust linearity across high and low expression ranges. PD-L1 mRNA levels assessed by RNA-seq and IHC (TPS and ICS) were highly correlated (p < 2e-16). Sub-analyses showed sustained correlation when IHC results were classified as high or low by clinically accepted cut-offs (p < 0.01), and results did not differ by tumor type or anti-PD-L1 antibody used. Overall, a combined positive PD-L1 result (≥1% IHC TPS and high PD-L1 expression by RNA-Seq) was associated with a 2-to-5-fold higher overall response rate (ORR) compared to a double negative result. Standard assessments of sensitivity, specificity, positive predictive value (PPV), and negative predictive value (NPV) showed that a PD-L1 positive assessment for melanoma samples by RNA-seq had the lowest sensitivity (25%) but the highest PPV (72.7%). Among the three tumor types analyzed in this study, the only non-overlapping confidence interval for predicting response was for “RNA-seq low vs high” in melanoma., [Conclusions] Measurement of PD-L1 mRNA expression by RNA-seq is comparable to PD-L1 expression by IHC both analytically and clinically in predicting ICI response. RNA-seq has the added advantages of being amenable to standardization and avoidance of interpretation bias. PD-L1 by RNA-seq needs to be validated in future prospective ICI clinical studies across multiple histologies.

Published
2019

39. Next generation sequencing of PD-L1 for predicting response to immune checkpoint inhibitors

Author

Conroy, Jeffrey M., primary, Pabla, Sarabjot, additional, Nesline, Mary K., additional, Glenn, Sean T., additional, Papanicolau-Sengos, Antonios, additional, Burgher, Blake, additional, Andreas, Jonathan, additional, Giamo, Vincent, additional, Wang, Yirong, additional, Lenzo, Felicia L., additional, Bshara, Wiam, additional, Khalil, Maya, additional, Dy, Grace K., additional, Madden, Katherine G., additional, Shirai, Keisuke, additional, Dragnev, Konstantin, additional, Tafe, Laura J., additional, Zhu, Jason, additional, Labriola, Matthew, additional, Marin, Daniele, additional, McCall, Shannon J., additional, Clarke, Jeffrey, additional, George, Daniel J., additional, Zhang, Tian, additional, Zibelman, Matthew, additional, Ghatalia, Pooja, additional, Araujo-Fernandez, Isabel, additional, de la Cruz-Merino, Luis, additional, Singavi, Arun, additional, George, Ben, additional, MacKinnon, Alexander C., additional, Thompson, Jonathan, additional, Singh, Rajbir, additional, Jacob, Robin, additional, Kasuganti, Deepa, additional, Shah, Neel, additional, Day, Roger, additional, Galluzzi, Lorenzo, additional, Gardner, Mark, additional, and Morrison, Carl, additional

Published
2019
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40. Immature Chondroid Choristoma: Clinicopathologic, Immunohistochemical, and Molecular Study of an Unusual Benign Skin Tumor

Author

Suster, David, Ronen, Shira, Mackinnon, Alexander C., and Suster, Saul

Abstract

An unusual benign skin tumor is reported occurring in a 68-year-old woman with no significant medical history. The lesion presented as a small skin nodule in the neck. Histologic examination showed a well-circumscribed superficial dermal nodule composed of a solid proliferation of large, round cells with abundant eosinophilic cytoplasm and small centrally placed nuclei displaying a vaguely chondroid appearance. Immunohistochemical studies showed strong positivity of the tumor cells for S100 protein and vimentin and negative staining for SOX10, melanoma cocktail, HMB45, Melan-A, cytokeratin AE1/AE3, inhibin, desmin, smooth muscle actin, CD68, CD164, and neuron specific enolase. Next-generation sequencing using a panel of 50 actionable genes commonly encountered in human neoplasia did not reveal the presence of any mutations. Owing to the remarkable similarity of the lesion to immature cartilage, we consider this to be a benign tumor, most likely resulting from an embryologic defect. We propose the term immature chondroid choristoma to designate this lesion.

Published
2022
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41. Diagnostic utility of one-stop fusion gene panel to detect TFE3/TFEBgene rearrangement and amplification in renal cell carcinomas

Author

Harada, Shuko, Caliò, Anna, Janowski, Karen M., Morlote, Diana, Rodriguez Pena, Maria D., Canete-Portillo, Sofia, Harbi, Djamel, DeFrank, Gina, Magi-Galluzzi, Cristina, Netto, George J., Martignoni, Guido, and Mackinnon, Alexander C.

Abstract

MiT family translocation renal cell carcinoma (MiT-RCC) harbors translocations involving the TFE3or TFEBgenes. RCC with TFEBamplification is also identified and is associated with a more aggressive clinical course. Accurate diagnosis of MiT-RCC is crucial for patient management. In this study, we evaluated the performance of the Archer FusionPlex assay for detection of MiT-RCC with TFE3or TFEBtranslocations and TFEBamplifications. RNA was extracted from 49 RCC FFPE tissue samples with known TFE3/TFEBstatus (26 TFE3FISH positive, 12 TFEBFISH positive, 4 TFEBamplified (1 case both split and amplified), and 8 FISH negative) using the Covaris extraction kit. Target enriched cDNA libraries were prepared using the Archer FusionPlex kit and sequenced on the Illumina NextSeq 550. We demonstrate that the age of the specimen, quality of RNA, and sequencing metrics are important for fusion detection. Fusions were identified in 20 of 21 cases less than 2 years old, and TFE3/TFEBrearrangements were detected in all cases with Fusion QC ≥ 100. The assay identified intrachromosomal inversions in two cases (TFE3-RBM10and NONO-TFE3), usually difficult to identify by FISH assays. TFEBmRNA expression and the TFEB/TFE3mRNA expression ratio were significantly higher in RCCs with TFEBfusion and TFEBgene amplification compared to tumors without TFEBfusion or amplification. A cutoff TFEB/TFE3ratio of 0.5 resulted in 97.3% concordance to FISH results with no false negatives. Our study demonstrates that the FusionPlex assay successfully identifies TFE3and TFEBfusions including intrachromosomal inversions. Age of the specimen and certain sequencing metrics are important for successful fusion detection. Furthermore, mRNA expression levels may be used for predicting cases harboring TFEBamplification, thereby streamlining testing. This assay enables accurate molecular detection of multiple subtypes of MiT-RCCs in a convenient workflow.

Published
2021
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42. Tracking in Anatomic Pathology

Author

Pantanowitz, Liron, Mackinnon, Alexander C., Jr., and Sinard, John H.

Subjects
Biomedical laboratories, Evidence-based medicine, Bar codes, Workflow software, Middleware, Medical schools, Middleware, Database middleware, Workflow software, Health
Abstract

Bar code-based tracking solutions, long present in clinical pathology laboratories, have recently made an appearance in anatomic pathology (AP) laboratories. Tracking of AP 'assets' (specimens, blocks, slides) can enhance laboratory efficiency, promote patient safety, and improve patient care. Routing of excess clinical material into research laboratories and biorepositories are other avenues that can benefit from tracking of AP assets. Implementing tracking is not as simple as installing software and turning it on. Not all tracking solutions are alike. Careful analysis of laboratory workflow is needed before implementing tracking to assure that this solution will meet the needs of the laboratory. Such analysis will likely uncover practices that may need to be modified before a tracking system can be deployed. Costs that go beyond simply that of purchasing software will be incurred and need to be considered in the budgeting process. Finally, people, not technology, are the key to assuring quality. Tracking will require significant changes in workflow and an overall change in the culture of the laboratory. Preparation, training, buy-in, and accountability of the people involved are crucial to the success of this process. This article reviews the benefits, available technology, underlying principles, and implementation of tracking solutions for the AP and research laboratory. (Arch Pathol Lab Med. 2013; 137:1798-1810; doi: 10.5858/arpa.2013-0125-SA), The reason for the success of several well-known companies (eg, Walmart, FedEx, Apple, Toyota) is related in part to their adoption of a lean manufacturing process, prioritization of supply chain [...]

Published
2013
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43. Bronchiolar Adenoma

Author

Chang, Jason C., primary, Montecalvo, Joseph, additional, Borsu, Laetitia, additional, Lu, Shaohua, additional, Larsen, Brandon T., additional, Wallace, William Dean, additional, Sae-Ow, Wichit, additional, Mackinnon, Alexander C., additional, Kim, Hyunjae R., additional, Bowman, Anita, additional, Sauter, Jennifer L., additional, Arcila, Maria E., additional, Ladanyi, Marc, additional, Travis, William D., additional, and Rekhtman, Natasha, additional

Published
2018
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45. TFEBrearranged renal cell carcinoma. A clinicopathologic and molecular study of 13 cases. Tumors harboring MALAT1-TFEB, ACTB-TFEB,and the novel NEAT1-TFEBtranslocations constantly express PDL1

Author

Caliò, Anna, Harada, Shuko, Brunelli, Matteo, Pedron, Serena, Segala, Diego, Portillo, Sofia Canete, Magi-Galluzzi, Cristina, Netto, George J., Mackinnon, Alexander C., and Martignoni, Guido

Abstract

Renal cell carcinomas with t(6;11) chromosome translocation has been classically characterized by the rearrangement of the TFEBgene, located on chromosome 6, and MALAT1gene, located on chromosome 11. Recently, a few other genes have been described as fusion partners in TFEBrearranged renal cell carcinomas. Although most of TFEBrearranged renal cell carcinomas have an indolent behavior, in the rare cases of advanced metastatic disease targeted therapy and predictive markers remain lacking. In the present study, we collected 13 TFEBrearranged renal cell carcinomas, confirmed by FISH, analyzing their morphology and exploring the novel gene partners. Looking for predictive markers, we have also performed PDL1 immunohistochemical analysis by using four different assays (E1L3N, 22C3, SP142, and SP263). MALAT1gene rearrangement has been found in ten tumors, five cases showing classical biphasic morphology with “rosettes”, five cases without “rosettes” mimicking other renal cell carcinomas or epithelioid angiomyolipoma/pure epithelioid PEComa. We identified two different partner genes, ACTBand NEAT1, the latter previously unreported and occurring in a tumor with an unusual solid and cystic appearance. In both cases, the “rosettes” were absent. In one case no gene partner was identified. Overall, in 12 of 13 TFEB-rearranged renal cell carcinomas staining for PDL1 SP263 was observed, whereas the other antibodies were less reliable or more difficult to interpret. In conclusion, we described the third case of ACTB-TFEBrearranged renal cell carcinoma and a novel NEAT1-TFEBrearranged renal cell carcinoma, both without the distinctive biphasic morphology typical of t(6;11) renal cell carcinoma. Finally, PDL1 SP263 was constantly expressed in TFEBrearranged renal cell carcinoma with possible clinical benefit which requires further investigations.

Published
2021
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46. Optimized b-value selection for the discrimination of prostate cancer grades, including the cribriform pattern, using diffusion weighted imaging

Author

Hurrell, Sarah L., primary, McGarry, Sean D., primary, Kaczmarowski, Amy, primary, Iczkowski, Kenneth A., primary, Jacobsohn, Kenneth, primary, Hohenwalter, Mark D., primary, Hall, William A., primary, See, William A., primary, Banerjee, Anjishnu, primary, Charles, David K., primary, Nevalainen, Marja T., primary, and Mackinnon, Alexander C., primary

Published
2017
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