297 results on '"Michael Lam"'
Search Results
2. Diagnostic Accuracy of Office Blood Pressure Measurement and Home Blood Pressure Monitoring for Hypertension Screening Among Adults: Results From the IDH Study
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Hiroyuki Mizuno, Eunhee Choi, Kazuomi Kario, Paul Muntner, Chloe L. Fang, Justin Liu, Dona N. Sangapalaarachchi, Michael Lam, Yuichiro Yano, Joseph E. Schwartz, and Daichi Shimbo
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ambulatory blood pressure monitoring ,home blood pressure monitoring ,hypertension screening ,office blood pressure measurement ,Diseases of the circulatory (Cardiovascular) system ,RC666-701 - Abstract
Background Using high awake blood pressure (BP; ≥130/80 mm Hg) on ambulatory BP monitoring (ABPM) as a reference, the purpose of this study was to determine the accuracy of high office BP (≥130/80 mm Hg) at an initial visit and high confirmatory office BP (≥130/80 mm Hg), and separately, high home BP (≥130/80 mm Hg) among participants with high office BP (≥130/80 mm Hg) at an initial office visit. Methods and Results The accuracy of office BP measurements using the oscillometric method for detecting high BP on ABPM was determined among 379 participants with complete office BP and ABPM data in the IDH (Improving the Detection of Hypertension) study. For detecting high BP on ABPM, the accuracy of high confirmatory office BP using the oscillometric method and, separately, high home BP was also determined among the subgroup of 122 participants with high office BP at an initial visit and complete home BP monitoring data. High office BP had moderate sensitivity (0.61 [95% CI, 0.53–0.68]) and high specificity (0.85 [95% CI, 0.80–0.90]) for high awake BP. High confirmatory office BP and high home BP had moderate sensitivity (0.69 [95% CI, 0.59–0.79] and 0.79 [95% CI, 0.71–0.87], respectively) and low and moderate specificity (0.44 [95% CI, 0.27–0.61] and 0.72 [95% CI, 0.56–0.88], respectively). Conclusions Many individuals with high BP on ABPM do not have high office BP. Confirmatory office BP and home blood pressure monitoring also had limited ability to identify individuals with high BP on ABPM.
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- 2023
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3. 342 Improving TCR-T cell function against solid tumors with immune enhancing edits
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Amy Becker, Troy Luster, Ishina Balwani, Erica Del Aguila, Nishit Patel, Birgit Schultes, Justin Oh, Nachiket Narendra Shevale, Ivy Dutta, Nazia Ali, Nithila Saravanan, James Peter, Yurui Guo, Hanan Dahche, Jingyu Peng, Bo Han, Dai Liu, Aaron Prodeus, and Michael Lam
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Published
- 2023
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- View/download PDF
4. Autologous humanized mouse models to study combination and single-agent immunotherapy for colorectal cancer patient-derived xenografts
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Preeti Kanikarla Marie, Alexey V. Sorokin, Lea A. Bitner, Rebecca Aden, Michael Lam, Ganiraju Manyam, Melanie N. Woods, Amanda Anderson, Anna Capasso, Natalie Fowlkes, Michael J. Overman, David G. Menter, and Scott Kopetz
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humanized mice ,immunotherapy ,colorectal cancer ,pre-clinical studies ,T cells ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
Designing studies of immunotherapy is limited due to a lack of pre-clinical models that reliably predict effective immunotherapy responses. To address this gap, we developed humanized mouse models of colorectal cancer (CRC) incorporating patient-derived xenografts (PDX) with human peripheral blood mononuclear cells (PBMC). Humanized mice with CRC PDXs were generated via engraftment of autologous (isolated from the same patients as the PDXs) or allogeneic (isolated from healthy donors) PBMCs. Human T cells were detected in mouse blood, tissues, and infiltrated the implanted PDXs. The inclusion of anti-PD-1 therapy revealed that tumor responses in autologous but not allogeneic models were more comparable to that of patients. An overall non-specific graft-vs-tumor effect occurred in allogeneic models and negatively correlated with that seen in patients. In contrast, autologous humanized mice more accurately correlated with treatment outcomes by engaging pre-existing tumor specific T-cell populations. As autologous T cells appear to be the major drivers of tumor response thus, autologous humanized mice may serve as models at predicting treatment outcomes in pre-clinical settings for therapies reliant on pre-existing tumor specific T-cell populations.
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- 2022
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5. Demonstration of III-nitride vertical-cavity surface-emitting lasers with a topside dielectric curved mirror
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Nathan C. Palmquist, Jared A. Kearns, Stephen Gee, Arturo Juan, Srinivas Gandrothula, Michael Lam, Steven P. Denbaars, and Shuji Nakamura
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GaN VCSEL ,tunnel junction ,long cavity ,nanoporous ,Physics ,QC1-999 - Abstract
We report long cavity (65 λ ) GaN-based vertical-cavity surface-emitting lasers (VCSELs) with a topside dielectric concave mirror, an ion implanted current aperture, and a bottomside nanoporous GaN distributed Bragg reflector. Under pulsed operation, a VCSEL with a 10 μ m aperture and a curved mirror with a radius of curvature of 120 μ m had a threshold current density of 14 kA cm ^−2 , and a maximum output power of 370 μ W for a lasing mode at 404.5 nm. The longitudinal performance has a side-mode suppression ratio of 30 dB up to a current density of approximately 40 kA cm ^−2 . Multiple transverse mode profiles are observed across several devices.
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- 2023
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6. Applications of Extended Reality in Ophthalmology: Systematic Review
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Chee Wui Ong, Marcus Chun Jin Tan, Michael Lam, and Victor Teck Chang Koh
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Computer applications to medicine. Medical informatics ,R858-859.7 ,Public aspects of medicine ,RA1-1270 - Abstract
BackgroundVirtual reality, augmented reality, and mixed reality make use of a variety of different software and hardware, but they share three main characteristics: immersion, presence, and interaction. The umbrella term for technologies with these characteristics is extended reality. The ability of extended reality to create environments that are otherwise impossible in the real world has practical implications in the medical discipline. In ophthalmology, virtual reality simulators have become increasingly popular as tools for surgical education. Recent developments have also explored diagnostic and therapeutic uses in ophthalmology. ObjectiveThis systematic review aims to identify and investigate the utility of extended reality in ophthalmic education, diagnostics, and therapeutics. MethodsA literature search was conducted using PubMed, Embase, and Cochrane Register of Controlled Trials. Publications from January 1, 1956 to April 15, 2020 were included. Inclusion criteria were studies evaluating the use of extended reality in ophthalmic education, diagnostics, and therapeutics. Eligible studies were evaluated using the Oxford Centre for Evidence-Based Medicine levels of evidence. Relevant studies were also evaluated using a validity framework. Findings and relevant data from the studies were extracted, evaluated, and compared to determine the utility of extended reality in ophthalmology. ResultsWe identified 12,490 unique records in our literature search; 87 met final eligibility criteria, comprising studies that evaluated the use of extended reality in education (n=54), diagnostics (n=5), and therapeutics (n=28). Of these, 79 studies (91%) achieved evidence levels in the range 2b to 4, indicating poor quality. Only 2 (9%) out of 22 relevant studies addressed all 5 sources of validity evidence. In education, we found that ophthalmic surgical simulators demonstrated efficacy and validity in improving surgical performance and reducing complication rates. Ophthalmoscopy simulators demonstrated efficacy and validity evidence in improving ophthalmoscopy skills in the clinical setting. In diagnostics, studies demonstrated proof-of-concept in presenting ocular imaging data on extended reality platforms and validity in assessing the function of patients with ophthalmic diseases. In therapeutics, heads-up surgical systems had similar complication rates, procedural success rates, and outcomes in comparison with conventional ophthalmic surgery. ConclusionsExtended reality has promising areas of application in ophthalmology, but additional high-quality comparative studies are needed to assess their roles among incumbent methods of ophthalmic education, diagnostics, and therapeutics.
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- 2021
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7. Inducible pesticide tolerance in Daphnia pulex influenced by resource availability
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Vanessa P. Wuerthner, Jared Jaeger, Paige S. Garramone, Connor O. Loomis, Yelena Pecheny, Rachel Reynolds, Lindsey Deluna, Samantha Klein, Michael Lam, Jessica Hua, and George A. Meindl
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acetylcholine esterase inhibitor ,carbamate ,ecotoxicology ,zooplankton ,Ecology ,QH540-549.5 - Abstract
Abstract Pesticides are a ubiquitous contaminant in aquatic ecosystems. Despite the relative sensitivity of aquatic species to pesticides, growing evidence suggests that populations can respond to pesticides by evolving higher baseline tolerance or inducing a higher tolerance via phenotypic plasticity. While both mechanisms can allow organisms to persist when faced with pesticides, resource allocation theory suggests that tolerance may be related to resource acquisition by the organism. Using Daphnia pulex, we investigated how algal resource availability influenced the baseline and inducible tolerance of D. pulex to a carbamate insecticide, carbaryl. Individuals reared in high resource environments had a higher baseline carbaryl tolerance compared to those reared in low resource environments. However, D. pulex from low resource treatments exposed to sublethal concentrations of carbaryl early in development induced increased tolerance to a lethal concentration of carbaryl later in life. Only individuals reared in the low resource environment induced carbaryl tolerance. Collectively, this highlights the importance of considering resource availability in our understanding of pesticide tolerance.
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- 2019
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8. Clinical, Pathological, and Molecular Characteristics of CpG Island Methylator Phenotype in Colorectal Cancer: A Systematic Review and Meta-analysis
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Shailesh M. Advani, Pragati Advani, Stacia M. DeSantis, Derek Brown, Helena M. VonVille, Michael Lam, Jonathan M. Loree, Amir Mehrvarz Sarshekeh, Jan Bressler, David S. Lopez, Carrie R. Daniel, Michael D. Swartz, and Scott Kopetz
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Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
BACKGROUND: CpG island methylator phenotype (CIMP) tumors, comprising 20% of colorectal cancers, are associated with female sex, age, right-sided location, and BRAF mutations. However, other factors potentially associated with CIMP have not been robustly examined. This meta-analysis provides a comprehensive assessment of the clinical, pathologic, and molecular characteristics that define CIMP tumors. METHODS: We conducted a comprehensive search of the literature from January 1999 through April 2018 and identified 122 articles, on which comprehensive data abstraction was performed on the clinical, pathologic, molecular, and mutational characteristics of CIMP subgroups, classified based on the extent of DNA methylation of tumor suppressor genes assessed using a variety of laboratory methods. Associations of CIMP with outcome parameters were estimated using pooled odds ratio or standardized mean differences using random-effects model. RESULTS: We confirmed prior associations including female sex, older age, right-sided tumor location, poor differentiation, and microsatellite instability. In addition to the recognized association with BRAF mutations, CIMP was also associated with PIK3CA mutations and lack of mutations in KRAS and TP53. Evidence of an activated immune response was seen with high rates of tumor-infiltrating lymphocytes (but not peritumoral lymphocytes), Crohn-like infiltrates, and infiltration with Fusobacterium nucleatum bacteria. Additionally, CIMP tumors were associated with advance T-stage and presence of perineural and lymphovascular invasion. CONCLUSION: The meta-analysis highlights key features distinguishing CIMP in colorectal cancer, including molecular characteristics of an active immune response. Improved understanding of this unique molecular subtype of colorectal cancer may provide insights into prevention and treatment.
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- 2018
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9. Platelet Metabolism and Other Targeted Drugs; Potential Impact on Immunotherapy
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Preeti Kanikarla-Marie, Michael Lam, Alexey V. Sorokin, Michael J. Overman, Scott Kopetz, and David G. Menter
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platelets ,cyclooxygenase ,platelet inhibitors ,non-steroidal anti-inflammatory drugs ,aspirin ,immunotherapy ,Neoplasms. Tumors. Oncology. Including cancer and carcinogens ,RC254-282 - Abstract
The role of platelets in cancer progression has been well recognized in the field of cancer biology. Emerging studies are elaborating further the additional roles and added extent that platelets play in promoting tumorigenesis. Platelets release factors that support tumor growth and also form heterotypic aggregates with tumor cells, which can provide an immune-evasive advantage. Their most critical role may be the inhibition of immune cell function that can negatively impact the body’s ability in preventing tumor establishment and growth. This review summarizes the importance of platelets in tumor progression, therapeutic response, survival, and finally the notion of immunotherapy modulation being likely to benefit from the inclusion of platelet inhibitors.
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- 2018
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10. Task2Vec: Task Embedding for Meta-Learning.
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Alessandro Achille, Michael Lam, Rahul Tewari, Avinash Ravichandran, Subhransu Maji, Charless C. Fowlkes, Stefano Soatto, and Pietro Perona
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- 2019
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11. Rethinking the Hyperparameters for Fine-tuning.
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Hao Li, Pratik Chaudhari, Hao Yang, Michael Lam, Avinash Ravichandran, Rahul Bhotika, and Stefano Soatto
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- 2020
12. The Role of Diffusion in Crystallization of Hard-Sphere Colloids
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Michael Lam, Boris Khusid, Lou Kondic, and William V Meyer
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Physics (General) - Published
- 2021
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13. Unsupervised Video Summarization with Adversarial LSTM Networks.
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Behrooz Mahasseni, Michael Lam, and Sinisa Todorovic
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- 2017
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14. Fine-Grained Recognition as HSnet Search for Informative Image Parts.
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Michael Lam, Behrooz Mahasseni, and Sinisa Todorovic
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- 2017
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15. Bintrafusp Alfa, an Anti-PD-L1:TGFβ Trap Fusion Protein, in Patients with ctDNA-positive, Liver-limited Metastatic Colorectal Cancer
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Van K. Morris, Michael J. Overman, Michael Lam, Christine M. Parseghian, Benny Johnson, Arvind Dasari, Kanwal Raghav, Bryan K. Kee, Ryan Huey, Robert A. Wolff, John Paul Shen, June Li, Isabel Zorrilla, Ching-Wei D. Tzeng, Hop S. Tran Cao, Yun Shin Chun, Timothy E. Newhook, Nicolas Vauthey, Dzifa Duose, Raja Luthra, Cara Haymaker, and Scott Kopetz
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Article - Abstract
Identification of circulating tumor DNA (ctDNA) following curative intent therapies is a surrogate for microscopic residual disease for patients with metastatic colorectal cancer (mCRC). Preclinically, in micrometastatic microsatellite stable (MSS) colorectal cancer, increased TGFβ signaling results in exclusion of antitumor cytotoxic T cells from the tumor microenvironment. Bintrafusp alfa (BA) is a bifunctional fusion protein composed of the extracellular domain of the TGFβRII receptor (“TGFβ trap”) and anti-PD-L1 antibody. Patients with liver-limited, MSS mCRC and with detected ctDNA after complete resection of all known tumors and standard-of-care therapy were treated with 1,200 mg of BA intravenously every 14 days for six doses. The primary endpoint was ctDNA clearance. Radiographic characteristics at recurrence were compared using independent t tests to historical data from a similar cohort of patients with liver-limited mCRC who underwent observation. Only 4 of 15 planned patients received BA before the study was stopped early for loss of equipoise. There was no grade ≥3 adverse event. None of the patients cleared ctDNA. All patients developed radiographic recurrence by the first planned restaging. Although not detectable at prior to treatment, TGFβ3 was found in circulation in all patients at cycle 2 day 1. Compared with a historical cohort, patients administered BA developed more metastases (15 vs. 2, P = 0.005) and greater tumor volumes (9 cm vs. 2 cm, P = 0.05). Treatment with BA in patients with ctDNA-detected, liver-limited mCRC did not clear ctDNA and was associated with large-volume recurrence, highlighting the potential context-specific complexity of dual TGFβ and PD-L1 inhibition. Significance: Use of ctDNA to identify patients with micrometastatic disease for therapeutic intervention is feasible. Treatment with BA in patients with liver-limited mCRC and with detectable ctDNA after resection generated rapid progression. Approaches targeting TGFβ signaling must consider its pathway complexity in future immunotherapy combination strategies.
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- 2022
16. ℋC-search for structured prediction in computer vision.
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Michael Lam, Janardhan Rao Doppa, Sinisa Todorovic, and Thomas G. Dietterich
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- 2015
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17. Figure SF2 from Bintrafusp Alfa, an Anti-PD-L1:TGFβ Trap Fusion Protein, in Patients with ctDNA-positive, Liver-limited Metastatic Colorectal Cancer
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Scott Kopetz, Cara Haymaker, Raja Luthra, Dzifa Duose, Nicolas Vauthey, Timothy E. Newhook, Yun Shin Chun, Hop S. Tran Cao, Ching-Wei D. Tzeng, Isabel Zorrilla, June Li, John Paul Shen, Robert A. Wolff, Ryan Huey, Bryan K. Kee, Kanwal Raghav, Arvind Dasari, Benny Johnson, Christine M. Parseghian, Michael Lam, Michael J. Overman, and Van K. Morris
- Abstract
Supplemental Figure S2
- Published
- 2023
18. Table S3 from Bintrafusp Alfa, an Anti-PD-L1:TGFβ Trap Fusion Protein, in Patients with ctDNA-positive, Liver-limited Metastatic Colorectal Cancer
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Scott Kopetz, Cara Haymaker, Raja Luthra, Dzifa Duose, Nicolas Vauthey, Timothy E. Newhook, Yun Shin Chun, Hop S. Tran Cao, Ching-Wei D. Tzeng, Isabel Zorrilla, June Li, John Paul Shen, Robert A. Wolff, Ryan Huey, Bryan K. Kee, Kanwal Raghav, Arvind Dasari, Benny Johnson, Christine M. Parseghian, Michael Lam, Michael J. Overman, and Van K. Morris
- Abstract
Supplemental Table S3
- Published
- 2023
19. Data from Bintrafusp Alfa, an Anti-PD-L1:TGFβ Trap Fusion Protein, in Patients with ctDNA-positive, Liver-limited Metastatic Colorectal Cancer
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Scott Kopetz, Cara Haymaker, Raja Luthra, Dzifa Duose, Nicolas Vauthey, Timothy E. Newhook, Yun Shin Chun, Hop S. Tran Cao, Ching-Wei D. Tzeng, Isabel Zorrilla, June Li, John Paul Shen, Robert A. Wolff, Ryan Huey, Bryan K. Kee, Kanwal Raghav, Arvind Dasari, Benny Johnson, Christine M. Parseghian, Michael Lam, Michael J. Overman, and Van K. Morris
- Abstract
Identification of circulating tumor DNA (ctDNA) following curative intent therapies is a surrogate for microscopic residual disease for patients with metastatic colorectal cancer (mCRC). Preclinically, in micrometastatic microsatellite stable (MSS) colorectal cancer, increased TGFβ signaling results in exclusion of antitumor cytotoxic T cells from the tumor microenvironment. Bintrafusp alfa (BA) is a bifunctional fusion protein composed of the extracellular domain of the TGFβRII receptor (“TGFβ trap”) and anti-PD-L1 antibody. Patients with liver-limited, MSS mCRC and with detected ctDNA after complete resection of all known tumors and standard-of-care therapy were treated with 1,200 mg of BA intravenously every 14 days for six doses. The primary endpoint was ctDNA clearance. Radiographic characteristics at recurrence were compared using independent t tests to historical data from a similar cohort of patients with liver-limited mCRC who underwent observation. Only 4 of 15 planned patients received BA before the study was stopped early for loss of equipoise. There was no grade ≥3 adverse event. None of the patients cleared ctDNA. All patients developed radiographic recurrence by the first planned restaging. Although not detectable at prior to treatment, TGFβ3 was found in circulation in all patients at cycle 2 day 1. Compared with a historical cohort, patients administered BA developed more metastases (15 vs. 2, P = 0.005) and greater tumor volumes (9 cm vs. 2 cm, P = 0.05). Treatment with BA in patients with ctDNA-detected, liver-limited mCRC did not clear ctDNA and was associated with large-volume recurrence, highlighting the potential context-specific complexity of dual TGFβ and PD-L1 inhibition.Significance:Use of ctDNA to identify patients with micrometastatic disease for therapeutic intervention is feasible. Treatment with BA in patients with liver-limited mCRC and with detectable ctDNA after resection generated rapid progression. Approaches targeting TGFβ signaling must consider its pathway complexity in future immunotherapy combination strategies.
- Published
- 2023
20. Supplemental Figure 3 from Classifying Colorectal Cancer by Tumor Location Rather than Sidedness Highlights a Continuum in Mutation Profiles and Consensus Molecular Subtypes
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Scott Kopetz, Dipen Maru, Michael J. Overman, Funda Meric-Bernstam, Rajyalakshmi Luthra, Jeffrey S. Morris, Yusha Liu, Mark J. Routbort, Russell Broaddus, Kenna Shaw, Cathy Eng, David G. Menter, Shailesh Advani, Van. K Morris, Arvind Dasari, Kanwal Raghav, Alexandra N. Willauer, Michael Lam, Allan A.L. Pereira, and Jonathan M. Loree
- Abstract
Comparison of overall survival based on primary tumor side using a multivariate proportional hazards model controlling for co-variates that differed based on tumor location.
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- 2023
21. Supplemental Figure 1 from Classifying Colorectal Cancer by Tumor Location Rather than Sidedness Highlights a Continuum in Mutation Profiles and Consensus Molecular Subtypes
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Scott Kopetz, Dipen Maru, Michael J. Overman, Funda Meric-Bernstam, Rajyalakshmi Luthra, Jeffrey S. Morris, Yusha Liu, Mark J. Routbort, Russell Broaddus, Kenna Shaw, Cathy Eng, David G. Menter, Shailesh Advani, Van. K Morris, Arvind Dasari, Kanwal Raghav, Alexandra N. Willauer, Michael Lam, Allan A.L. Pereira, and Jonathan M. Loree
- Abstract
Sensitivity analysis comparing mutation prevalence estimates by site of biopsy of tissue used for next generation sequencing panel in metastatic colorectal cancer.
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- 2023
22. Figure S3 from ARID1A Mutation May Define an Immunologically Active Subgroup in Patients with Microsatellite Stable Colorectal Cancer
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Scott Kopetz, Michael J. Overman, Dipen M. Maru, Jaffer A. Ajani, Hey Min Lee, Jonathan M. Loree, Jennifer S. Davis, Jeffrey Morris, John Paul Shen, Jason Willis, Michael Lam, Anuj Verma, Riham Katkhuda, Shailesh M. Advani, Ganiraju C. Manyam, Jason Roszik, Jumanah Alshenaifi, and Amir Mehrvarz Sarshekeh
- Abstract
Supplementary Fig S3. Association of gene size and the differential expression of IFN-γ pathway in genes commonly mutated in MSS CRC
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- 2023
23. Supplemental legend from Classifying Colorectal Cancer by Tumor Location Rather than Sidedness Highlights a Continuum in Mutation Profiles and Consensus Molecular Subtypes
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Scott Kopetz, Dipen Maru, Michael J. Overman, Funda Meric-Bernstam, Rajyalakshmi Luthra, Jeffrey S. Morris, Yusha Liu, Mark J. Routbort, Russell Broaddus, Kenna Shaw, Cathy Eng, David G. Menter, Shailesh Advani, Van. K Morris, Arvind Dasari, Kanwal Raghav, Alexandra N. Willauer, Michael Lam, Allan A.L. Pereira, and Jonathan M. Loree
- Abstract
Supplemental legend
- Published
- 2023
24. Table S1 from ARID1A Mutation May Define an Immunologically Active Subgroup in Patients with Microsatellite Stable Colorectal Cancer
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Scott Kopetz, Michael J. Overman, Dipen M. Maru, Jaffer A. Ajani, Hey Min Lee, Jonathan M. Loree, Jennifer S. Davis, Jeffrey Morris, John Paul Shen, Jason Willis, Michael Lam, Anuj Verma, Riham Katkhuda, Shailesh M. Advani, Ganiraju C. Manyam, Jason Roszik, Jumanah Alshenaifi, and Amir Mehrvarz Sarshekeh
- Abstract
Supplementary Table S1
- Published
- 2023
25. Supplemental Figure 4 from Classifying Colorectal Cancer by Tumor Location Rather than Sidedness Highlights a Continuum in Mutation Profiles and Consensus Molecular Subtypes
- Author
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Scott Kopetz, Dipen Maru, Michael J. Overman, Funda Meric-Bernstam, Rajyalakshmi Luthra, Jeffrey S. Morris, Yusha Liu, Mark J. Routbort, Russell Broaddus, Kenna Shaw, Cathy Eng, David G. Menter, Shailesh Advani, Van. K Morris, Arvind Dasari, Kanwal Raghav, Alexandra N. Willauer, Michael Lam, Allan A.L. Pereira, and Jonathan M. Loree
- Abstract
Summary of the relative prognostic and mutational impact of tumor location in metastatic colorectal cancer. Sub-caption: Relative prevalence of mutations at each site was compared to the median prevalence across all sites and used to calculate relative font size for each gene name. Hazard ratios displayed in the figure utilize rectal location as the reference category.
- Published
- 2023
26. Supplemental Figure 2 from Classifying Colorectal Cancer by Tumor Location Rather than Sidedness Highlights a Continuum in Mutation Profiles and Consensus Molecular Subtypes
- Author
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Scott Kopetz, Dipen Maru, Michael J. Overman, Funda Meric-Bernstam, Rajyalakshmi Luthra, Jeffrey S. Morris, Yusha Liu, Mark J. Routbort, Russell Broaddus, Kenna Shaw, Cathy Eng, David G. Menter, Shailesh Advani, Van. K Morris, Arvind Dasari, Kanwal Raghav, Alexandra N. Willauer, Michael Lam, Allan A.L. Pereira, and Jonathan M. Loree
- Abstract
Sensitivity analysis demonstrating optimal left vs right cut-point to maximize prognostic differences based on side in metastatic colorectal cancer. Sub-caption: Numbers in figure represent the hazard ratio followed by the 95% confidence interval within square brackets. The hazard ratio estimate occurs at the location used to divide left from right in each sensitivity analysis. For example, if the division between right and left occurs between the hepatic flexure and transverse colon, the hazard ratio estimate will be placed on the graph half way between the hepatic flexure and transverse colon (ie. 1.66).
- Published
- 2023
27. Data from Classifying Colorectal Cancer by Tumor Location Rather than Sidedness Highlights a Continuum in Mutation Profiles and Consensus Molecular Subtypes
- Author
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Scott Kopetz, Dipen Maru, Michael J. Overman, Funda Meric-Bernstam, Rajyalakshmi Luthra, Jeffrey S. Morris, Yusha Liu, Mark J. Routbort, Russell Broaddus, Kenna Shaw, Cathy Eng, David G. Menter, Shailesh Advani, Van. K Morris, Arvind Dasari, Kanwal Raghav, Alexandra N. Willauer, Michael Lam, Allan A.L. Pereira, and Jonathan M. Loree
- Abstract
Purpose: Colorectal cancers are classified as right/left-sided based on whether they occur before/after the splenic flexure, with established differences in molecular subtypes and outcomes. However, it is unclear if this division is optimal and whether precise tumor location provides further information.Experimental Design: In 1,876 patients with colorectal cancer, we compared mutation prevalence and overall survival (OS) according to side and location. Consensus molecular subtype (CMS) was compared in a separate cohort of 608 patients.Results: Mutation prevalence differed by side and location for TP53, KRAS, BRAFV600, PIK3CA, SMAD4, CTNNB1, GNAS, and PTEN. Within left- and right-sided tumors, there remained substantial variations in mutation rates. For example, within right-sided tumors, RAS mutations decreased from 70% for cecal, to 43% for hepatic flexure location (P = 0.0001), while BRAFV600 mutations increased from 10% to 22% between the same locations (P < 0.0001). Within left-sided tumors, the sigmoid and rectal region had more TP53 mutations (P = 0.027), less PIK3CA (P = 0.0009), BRAF (P = 0.0033), or CTNNB1 mutations (P < 0.0001), and less MSI (P < 0.0001) than other left-sided locations. Despite this, a left/right division preceding the transverse colon maximized prognostic differences by side and transverse colon tumors had K-modes mutation clustering that appeared more left than right sided. CMS profiles showed a decline in CMS1 and CMS3 and rise in CMS2 prevalence moving distally.Conclusions: Current right/left classifications may not fully recapitulate regional variations in tumor biology. Specifically, the sigmoid-rectal region appears unique and the transverse colon is distinct from other right-sided locations. Clin Cancer Res; 24(5); 1062–72. ©2017 AACR.See related commentary by Dienstmann, p. 989
- Published
- 2023
28. Design of a Barometer-Based Pulse-Taking Device With In Vivo Validation Against High-Frequency Ultrasound Pulse Wave Imaging
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Yuchen Tang, Robert C. Roberts, Cheuk Him Michael Lam, Wai Shan Wong, Mingxiao Yang, Lixing Lao, and Wei-Ning Lee
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Electrical and Electronic Engineering ,Instrumentation - Published
- 2022
29. Distribution and diversity of classical deacylases in bacteria
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Leonie G. Graf, Carlos Moreno-Yruela, Chuan Qin, Sabrina Schulze, Gottfried J. Palm, Ole Schmöker, Nancy Wang, Dianna M. Hocking, Leila Jebeli, Britta Girbardt, Leona Berndt, Babett Dörre, Daniel M. Weis, Markus Janetzky, Dirk Albrecht, Daniela Zühlke, Susanne Sievers, Richard A. Strugnell, Christian A. Olsen, Kay Hofmann, and Michael Lammers
- Subjects
Science - Abstract
Abstract Classical Zn2+-dependent deac(et)ylases play fundamental regulatory roles in life and are well characterized in eukaryotes regarding their structures, substrates and physiological roles. In bacteria, however, classical deacylases are less well understood. We construct a Generalized Profile (GP) and identify thousands of uncharacterized classical deacylases in bacteria, which are grouped into five clusters. Systematic structural and functional characterization of representative enzymes from each cluster reveal high functional diversity, including polyamine deacylases and protein deacylases with various acyl-chain type preferences. These data are supported by multiple crystal structures of enzymes from different clusters. Through this extensive analysis, we define the structural requirements of substrate selectivity, and discovered bacterial de-d-/l-lactylases and long-chain deacylases. Importantly, bacterial deacylases are inhibited by archetypal HDAC inhibitors, as supported by co-crystal structures with the inhibitors SAHA and TSA, and setting the ground for drug repurposing strategies to fight bacterial infections. Thus, we provide a systematic structure-function analysis of classical deacylases in bacteria and reveal the basis of substrate specificity, acyl-chain preference and inhibition.
- Published
- 2024
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30. Indigenous and local knowledge in biocultural approaches to sustainability: a review of the literature in Spanish
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David Patrick Michael Lam, Jan Hanspach, Leonie Burke, and Isabel Díaz-Reviriego
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Ecology ,Automotive Engineering ,Management, Monitoring, Policy and Law ,Ecology, Evolution, Behavior and Systematics ,Nature and Landscape Conservation - Published
- 2022
31. Zero-Shot Learning and Detection of Teeth in Images of Bat Skulls.
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Xu Hu, Michael Lam, Sinisa Todorovic, Thomas G. Dietterich, Maureen A. OLeary, Andrea L. Cirranello, Nancy B. Simmons, and Paúl M. Velazco
- Published
- 2013
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32. Learning to Detect Basal Tubules of Nematocysts in SEM Images.
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Michael Lam, Janardhan Rao Doppa, Xu Hu, Sinisa Todorovic, Thomas G. Dietterich, Abigail Reft, and Marymegan Daly
- Published
- 2013
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33. Dermatological presentations to a regional Victorian hospital emergency department: A 1-year audit
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Claire Ronaldson, Kelly Zhou, Michael Lam, Dillon Ong, Sian Morgan, Aditya Sathe, and Anton N. Isaacs
- Subjects
Public Health, Environmental and Occupational Health ,Family Practice - Abstract
The objective of this study is to describe the epidemiological features of each presentation with a primary dermatological diagnosis to a regional emergency department (ED).1-year retrospective audit.Regional Victorian hospital emergency department.Any presentation to this regional emergency department with a dermatological condition from 1 January 2020 to 31 December 2020.Dermatology presentations to the ED in 2020 and the prevalence of the associated primary diagnosis.In total, 4.7% (n = 1873) of ED presentations had a primary dermatological diagnosis. Of these, 1484 were ≥18 years of age and 389 were ≤17 years of age. Cellulitis (26.1%, n = 388) was the most common primary diagnosis among presentations ≥18 years. Non-specific rash was the most common diagnosis (23.6%, n = 92) in presentations ≤17 years. Indigenous Australians ≥18 years were more likely to be in a younger age group (p 0.01), and dermatitis/eczema presentations ≥18 years (n = 10) were the largest diagnostic group referred to a dermatologist. A total of 134 (7.1%) patients ≥18 years travelled more than 50 km to the ED. There were no dermatological emergencies identified.A high proportion of presentations to this regional ED with a dermatological diagnosis could be well managed by a dermatologist or general practitioner (GP) as an outpatient. The findings of this study inform the need for future rural public dermatology services. Options include teledermatology, or a public weekly or fortnightly rapid review dermatology clinic with a visiting dermatologist, in the absence of a dermatologist onsite.
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- 2022
34. Adolescent Δ-9-tetrahydrocannabinol exposure induces differential acute and long-term neuronal and molecular disturbances in dorsal vs. ventral hippocampal subregions
- Author
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Marta, De Felice, Chaochao, Chen, Mar, Rodríguez-Ruiz, Hanna J, Szkudlarek, Michael, Lam, Selvi, Sert, Shawn N, Whitehead, Ken K-C, Yeung, Walter J, Rushlow, and Steven R, Laviolette
- Abstract
Chronic exposure to Δ-9-tetrahydrocannabinol (THC) during adolescence is associated with long-lasting cognitive impairments and enhanced susceptibility to anxiety and mood disorders. Previous evidence has revealed functional and anatomical dissociations between the posterior vs. anterior portions of the hippocampal formation, which are classified as the dorsal and ventral regions in rodents, respectively. Notably, the dorsal hippocampus is critical for cognitive and contextual processing, whereas the ventral region is critical for affective and emotional processing. While adolescent THC exposure can induce significant morphological disturbances and glutamatergic signaling abnormalities in the hippocampus, it is not currently understood how the dorsal vs. ventral hippocampal regions are affected by THC during neurodevelopment. In the present study, we used an integrative combination of behavioral, molecular, and neural assays in a neurodevelopmental rodent model of adolescent THC exposure. We report that adolescent THC exposure induces long-lasting memory deficits and anxiety like-behaviors concomitant with a wide range of differential molecular and neuronal abnormalities in dorsal vs. ventral hippocampal regions. In addition, using matrix-assisted laser desorption/ionization imaging mass spectrometry (MALDI-IMS), we show for the first time that adolescent THC exposure induces significant and enduring dysregulation of GABA and glutamate levels in dorsal vs. ventral hippocampus. Finally, adolescent THC exposure induced dissociable dysregulations of hippocampal glutamatergic signaling, characterized by differential glutamatergic receptor expression markers, profound alterations in pyramidal neuronal activity and associated oscillatory patterns in dorsal vs. ventral hippocampal subregions.
- Published
- 2022
35. Suicide crises among women and mothers during and around the time of pregnancy: Prevalence and timing of initial contact with first responders and health services
- Author
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Carla Meurk, Susan Roberts, Michael Lam, Lisa Wittenhagen, Leonie Callaway, Katherine Moss, Jayne Lucke, Ruth Barker, Elissa Waterson, Catherine Rawlinson, Natasha Malmstrom, Edward Weaver, Elisabeth Hoehn, Emma Bosley, Shelby Watson, and Ed Heffernan
- Subjects
Psychiatry and Mental health ,General Medicine - Abstract
Objectives: Suicide is a leading cause of maternal mortality. Suicidality during and around the time of pregnancy can have detrimental impacts on a child’s development and outcomes. This paper examines prevalence, demographic characteristics, and timing of initial contact with first responders and health services for a cohort of women who experienced suicidality during and around the time of pregnancy. Methods: Findings are drawn from the Partners in Prevention (PiP) study, a population-wide linked data set of suicide-related attendances by police or paramedics in Queensland, Australia. A sub-cohort of women was identified, who were between 6 months preconception and 2 years postpartum at the time of a suicide-related contact with police or paramedics (PiP-Maternal). Findings are compared to other girls and women who had a suicide-related contact with police or paramedics (PiP-Female). Prevalence, demographic characteristics, timing of contact with first responders and health services, re-presentations, and mortality are reported. Results: The PiP-Maternal cohort comprised 3020 individuals and 3400 births. Women in the PiP-Maternal cohort were younger, more likely to be of Aboriginal and/or Torres Strait Islander descent and live outside of a major city than the PiP-Female cohort. There were high rates of out-of-hours calls to police and ambulance, and similar perceived seriousness of the call between women in the PiP-Maternal and PiP-Female cohorts. Women in the PiP-Maternal cohort were less likely to be admitted to an emergency department within 24 hours, even after matching on covariates. Prevalence of suicidality for women who were pregnant and up to 2 years postpartum was 1.32% (95% CI = [1.27, 1.37]). Conclusion: Vulnerabilities and high rates of contact with police or paramedics, coupled with lower levels of follow-up, highlight the critical need to improve service responses for women with mental health needs during these phases of life.
- Published
- 2022
36. Does Verbal Street Harassment Signal Perpetrator Dominance to Male and Female Observers?
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Faye Nitschke and Michael Lam
- Subjects
Physiology ,media_common.quotation_subject ,Behavioural sciences ,Experimental and Cognitive Psychology ,humanities ,Test (assessment) ,Behavioral Neuroscience ,Harm ,Dominance (ethology) ,Intervention (counseling) ,Perception ,Harassment ,Personality ,Psychology ,Social psychology ,media_common - Abstract
It is difficult to explain why verbal street harassment, where typically a male harasser yells sexually harassing statements at a female victim, has survived as a behaviour. We propose that verbal street harassment may signal a harasser’s dominance and aimed to test this in our registered report. Participants (N = 443) read one of two vignettes describing either a street harassment incident (in which a male perpetrator harasses a female victim) or a street incident without harassment. Participants were asked to evaluate whether the male target possessed a range of traits (including dominance) and to evaluate any harm the female target suffered from the incident. Results suggested that the male target who verbally harassed a female victim on the street was perceived by participants as more dominant and as having a darker personality than a male target who did not engage in street harassment. Participants also perceived the female target as more harmed when she was harassed. However, results did not support the predicted interaction of participant sex and incident type on participants’ perceptions of the male and female targets. These results suggest that verbal street harassment may signal a harasser’s dominance which may be why the behaviour has been maintained. To establish whether verbal street meets the conditions to be classed as a costly signal, these findings should be replicated and extended. Understanding why street harassment persists as a behaviour is critical to designing effective intervention to prevent street harassment and protect harassment victims.
- Published
- 2021
37. Acetyl-CoA synthetase activity is enzymatically regulated by lysine acetylation using acetyl-CoA or acetyl-phosphate as donor molecule
- Author
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Chuan Qin, Leonie G. Graf, Kilian Striska, Markus Janetzky, Norman Geist, Robin Specht, Sabrina Schulze, Gottfried J. Palm, Britta Girbardt, Babett Dörre, Leona Berndt, Stefan Kemnitz, Mark Doerr, Uwe T. Bornscheuer, Mihaela Delcea, and Michael Lammers
- Subjects
Science - Abstract
Abstract The AMP-forming acetyl-CoA synthetase is regulated by lysine acetylation both in bacteria and eukaryotes. However, the underlying mechanism is poorly understood. The Bacillus subtilis acetyltransferase AcuA and the AMP-forming acetyl-CoA synthetase AcsA form an AcuA•AcsA complex, dissociating upon lysine acetylation of AcsA by AcuA. Crystal structures of AcsA from Chloroflexota bacterium in the apo form and in complex with acetyl-adenosine-5′-monophosphate (acetyl-AMP) support the flexible C-terminal domain adopting different conformations. AlphaFold2 predictions suggest binding of AcuA stabilizes AcsA in an undescribed conformation. We show the AcuA•AcsA complex dissociates upon acetyl-coenzyme A (acetyl-CoA) dependent acetylation of AcsA by AcuA. We discover an intrinsic phosphotransacetylase activity enabling AcuA•AcsA generating acetyl-CoA from acetyl-phosphate (AcP) and coenzyme A (CoA) used by AcuA to acetylate and inactivate AcsA. Here, we provide mechanistic insights into the regulation of AMP-forming acetyl-CoA synthetases by lysine acetylation and discover an intrinsic phosphotransacetylase allowing modulation of its activity based on AcP and CoA levels.
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- 2024
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38. A phase 1 trial of 4-(N-(S-penicillaminylacetyl)amino)-phenylarsonous acid (PENAO) in patients with advanced solid tumours
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Michael Lam, Philip J. Hogg, David Edmonds, Lisa G. Horvath, Jayesh Desai, Peter Grimison, Anne Hamilton, Peter Savas, Sunit Sarkar, Danny Rischin, James R. Whittle, Ben Tran, Nicole Signal, and James C Kuo
- Subjects
0301 basic medicine ,Pharmacology ,Cancer Research ,medicine.medical_specialty ,business.industry ,Urology ,Urine ,Toxicology ,Discontinuation ,Clinical trial ,03 medical and health sciences ,030104 developmental biology ,0302 clinical medicine ,Oncology ,Pharmacokinetics ,030220 oncology & carcinogenesis ,Toxicity ,medicine ,Pharmacology (medical) ,In patient ,Phenylarsonous acid ,Dosing ,business - Abstract
This phase I study was conducted to evaluate the safety and Maximum Tolerated Dose of PENAO (4-(N-(S-penicillaminylacetyl)amino)-phenylarsonous acid), a second-generation organic arsenical with anti-mitochondrial activity, when given as a continuous intravenous infusion (CIVI), in patients with advanced solid tumours. Eligibility criteria for this trial included age ≥ 18 years, advanced solid tumour, ECOG Performance Status ≤ 1 and adequate organ function. PENAO was administered by CIVI, with dose levels initially increased by infusion duration in a 21-day cycle at a fixed daily dose and then increased daily dose. Standard dose-limiting toxicity (DLT) definitions were used in a “3 + 3” design. Patients had regular monitoring of toxicity and efficacy. Pharmacokinetic assays of serum and urine As were performed. Twenty-six patients were treated across 8 dose levels. The only dose-limiting toxicity (DLT) observed was fatigue, that occurred in one patient treated at the highest dose level of 9 mg/m2/day. No significant organ toxicity or objective responses were observed, although there were two patients with stable disease lasting up to 7 months. Pharmacokinetic analysis unexpectedly indicated a half-life of 9–19 days, invalidating the CIVI dosing resulting in discontinuation of the study before the RP2D was defined. PENAO was administered by CIVI at dose levels up to 9 mg/m2/day with only one DLT noted. Pharmacokinetic studies invalidated the rationale for continuous dosing and led to discontinuation of the trial without defining a RP2D. Future clinical development of PENAO will use intermittent dosing schedule, alone and in combination with rapamycin.
- Published
- 2021
39. Targeted ultra-high performance liquid chromatography-tandem mass spectrometry assay for the quantification of medium-chain phosphatidylcholines in platelets of coronary artery disease patients
- Author
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Tamara Janker, Adrian Brun, Adrian Sievers-Engler, Kristina Dittrich, Meinrad Gawaz, and Michael Lämmerhofer
- Subjects
Biomarker ,Clinical lipidomics ,Mass spectrometry ,Phospholipids ,Acute coronary syndrome ,Analytical chemistry ,QD71-142 - Abstract
In a recent untargeted clinical lipidomics study of platelets of coronary artery disease (CAD) patients, medium-chain phosphatidylcholines (MCPCs) with C8 and C10 fatty acyl residues were found significantly upregulated in the patient group with acute coronary syndrome (ACS) as compared to chronic coronary syndrome (CCS) and healthy controls. To support this finding, this work presents the development and optimization of a targeted UHPLC-QTrap-MS/MS method with multiple reaction monitoring acquisition for the quantitative analysis of MCPCs (PC 10:0/8:0, PC 16:0/8:0, PC 10:0/20:4 and PC 10:0/10:0) in platelets for biomarker validation. A systematic optimization of chromatographic and mass spectrometric parameters was performed. A charged surface hybrid CSH C18 (1.7 µm, 130 Å) column and fine-tuned gradient elution with 2-propanol/acetonitrile and ammonium acetate as additive to the mobile phase was employed in the final method in ESI negative mode. Four selected PC standards (PC 6:0/6:0, PC 8:0/8:0, PC 10:0/10:0 and PC 12:0/12:0), which cover well the carbon and retention rime range of the target analytes, were used for the optimization process and calibration. Quantification was based on matrix-matched calibration with these four selected commercially available MCPC standards as surrogate calibrants and PC 6:0/6:0(d22) as internal standard. Furthermore, an organic solvent and fatty acyl carbon number-corrected response factor approach gave also accuracies within acceptance limits of bioanalytical validation guidelines and has more generic applicability. Compared to the previous untargeted RPLC-ESI-QTOF-MS/MS method, the optimized targeted UHPLC-QTrap-MS/MS assay showed increased sensitivity and selectivity for the detection of medium-chain PCs in platelet samples of CAD (LOQs in the range of 0.5–5 nmol/L). The method performance parameters indicated its suitability for a future biomarker validation study of MCPCs in platelets.
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- 2024
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40. A branded bandage is worth a thousand words: blood branded bandages signal men’s generosity and morality
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Barbara M. Masser, Barnaby J. W. Dixson, and Michael Lam
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Adult ,Male ,Generosity ,medicine.medical_specialty ,media_common.quotation_subject ,Psychological intervention ,Blood Donors ,Morals ,medicine ,Humans ,Aged ,media_common ,business.industry ,Australia ,Hematology ,General Medicine ,Blood collection ,Donor status ,Middle Aged ,Morality ,Bandages ,Blood donor ,Physical therapy ,Female ,business ,Bandage - Abstract
Background and Objective: Recruiting and retaining male donors remain an ongoing challenge for blood collection agencies. Research suggests that interventions based on costly signalling theory that allows donors to unobtrusively but publicly signal their donor status may be effective. However, what functions as such a signal and how it is interpreted has not been determined.Materials and Methods: A total of 242 Australian residents (127 female; 115 male) recruited through an online research platform rated their perceptions of a male target wearing (a) no bandage, (b) a regular unmarked bandage or (c) a blood donor branded bandage.Results: The target wearing a blood donor branded bandage was rated as significantly more generous by female participants and moral compared to both the target who wore no bandage and the target wearing a regular unmarked bandage. The target wearing the unmarked bandage was perceived as significantly less healthy and competent compared to the target not wearing a bandage.Conclusion: A public signal of public donor status conveys the generosity and morality of the wearer. The bandage applied to donors after they have donated can act as such an effective signal, but only when these bandages are clearly branded as resulting from donating blood.
- Published
- 2020
41. Patterns of Industry Payments to Urologists From 2014-2018
- Author
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Annalise Manley, Michael Lam, Martinez Acevedo, Emily K. Clennon, Nicholas H. Chakiryan, Kamran P. Sajadi, and Brian Duty
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Male ,medicine.medical_specialty ,Faculty, Medical ,Time Factors ,Databases, Factual ,Drug Industry ,Urologists ,Urology ,media_common.quotation_subject ,030232 urology & nephrology ,Subspecialty ,Centers for Medicare and Medicaid Services, U.S ,03 medical and health sciences ,0302 clinical medicine ,Manufacturing Industry ,medicine ,Financial Support ,Humans ,Fellowships and Scholarships ,media_common ,Practice setting ,business.industry ,Administrative Personnel ,Payment ,United States ,Equipment and Supplies ,030220 oncology & carcinogenesis ,Family medicine ,Financial transaction ,Workforce ,Education, Medical, Continuing ,Female ,business ,Medicaid - Abstract
To evaluate the patterns of financial transaction between industry and urologists in the first 5 years of reporting in the Open Payments Program (OPP) by comparing transactions over time, between academic and nonacademic urologists, and by provider characteristics among academic urologists.The Center for MedicareMedicaid Services OPP database was queried for General Payments to urologists from 2014-2018. Faculty at ACGME-accredited urology training programs were identified and characterized via publicly available websites. Industry transfers were analyzed by year, practice setting (academic vs nonacademic), provider characteristics, and AUA section. Payment nature and individual corporate contributions were also summarized.A total of 12,521 urologists - representing 75% of the urology workforce in any given year - received $168 million from industry over the study period. There was no significant trend in payments by year (P = .162). Urologists received a median of $1602 over the study period, though 14% received$10,000. Payment varied significantly by practice setting (P.001), with nonacademic urologists receiving more but smaller payments than academic urologists. Among academic urologists, gender (P.001), department chair status (P.001), fellowship training (P.001), and subspecialty (P.001) were significantly associated with amount of payment from industry. Annual payments from industry varied significantly by AUA section.Reporting of physician-industry transactions has not led to a sustained decline in transactions with urologists. Significant differences in industry interaction exist between academic and nonacademic urologists, and values transferred to academic urologists varied by gender, chair status, subspecialty, and AUA section.
- Published
- 2020
42. Exposure to metals (Ca, K, Mn) and road salt (NaCl) differentially affect development and survival in two model amphibians
- Author
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Brianna Sander, Wyatt J. Parker, George A. Meindl, Jessica Hua, Rachel Oltmer, Michael Lam, Courtney Fitzgerald, and Nicholas Schleissmann
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Sodium ,0211 other engineering and technologies ,chemistry.chemical_element ,Salt (chemistry) ,02 engineering and technology ,010501 environmental sciences ,complex mixtures ,01 natural sciences ,Invasive species ,Ecology, Evolution, Behavior and Systematics ,0105 earth and related environmental sciences ,General Environmental Science ,chemistry.chemical_classification ,021110 strategic, defence & security studies ,Ecology ,biology ,Chemistry ,Lithobates pipiens ,Aquatic ecosystem ,fungi ,technology, industry, and agriculture ,biology.organism_classification ,Environmental chemistry ,General Earth and Planetary Sciences ,sense organs ,Surface runoff - Abstract
Human activity has led to widespread chemical alteration of natural environments. Aquatic ecosystems are especially susceptible to chemical changes, including those caused by runoff and invasive sp...
- Published
- 2020
43. Lipase-mediated detoxification of host-derived antimicrobial fatty acids by Staphylococcus aureus
- Author
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Arnaud Kengmo Tchoupa, Ahmed M. A. Elsherbini, Justine Camus, Xiaoqing Fu, Xuanheng Hu, Oumayma Ghaneme, Lea Seibert, Marco Lebtig, Marieke A. Böcker, Anima Horlbeck, Stilianos P. Lambidis, Birgit Schittek, Dorothee Kretschmer, Michael Lämmerhofer, and Andreas Peschel
- Subjects
Biology (General) ,QH301-705.5 - Abstract
Abstract Long-chain fatty acids with antimicrobial properties are abundant on the skin and mucosal surfaces, where they are essential to restrict the proliferation of opportunistic pathogens such as Staphylococcus aureus. These antimicrobial fatty acids (AFAs) elicit bacterial adaptation strategies, which have yet to be fully elucidated. Characterizing the pervasive mechanisms used by S. aureus to resist AFAs could open new avenues to prevent pathogen colonization. Here, we identify the S. aureus lipase Lip2 as a novel resistance factor against AFAs. Lip2 detoxifies AFAs via esterification with cholesterol. This is reminiscent of the activity of the fatty acid-modifying enzyme (FAME), whose identity has remained elusive for over three decades. In vitro, Lip2-dependent AFA-detoxification was apparent during planktonic growth and biofilm formation. Our genomic analysis revealed that prophage-mediated inactivation of Lip2 was rare in blood, nose, and skin strains, suggesting a particularly important role of Lip2 for host – microbe interactions. In a mouse model of S. aureus skin colonization, bacteria were protected from sapienic acid (a human-specific AFA) in a cholesterol- and lipase-dependent manner. These results suggest Lip2 is the long-sought FAME that exquisitely manipulates environmental lipids to promote bacterial growth in otherwise inhospitable niches.
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- 2024
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44. Machine learning insights into thrombo-ischemic risks and bleeding events through platelet lysophospholipids and acylcarnitine species
- Author
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Tobias Harm, Xiaoqing Fu, Moritz Frey, Kristina Dittrich, Adrian Brun, Tatsiana Castor, Oliver Borst, Karin Anne Lydia Müller, Tobias Geisler, Dominik Rath, Michael Lämmerhofer, and Meinrad Paul Gawaz
- Subjects
Medicine ,Science - Abstract
Abstract Coronary artery disease (CAD) often leads to adverse events resulting in significant disease burdens. Underlying risk factors often remain inapparent prior to disease incidence and the cardiovascular (CV) risk is not exclusively explained by traditional risk factors. Platelets inherently promote atheroprogression and enhanced platelet functions and distinct platelet lipid species are associated with disease severity in patients with CAD. Lipidomics data were acquired using mass spectrometry and processed alongside clinical data applying machine learning to model estimates of an increased CV risk in a consecutive CAD cohort (n = 595). By training machine learning models on CV risk measurements, stratification of CAD patients resulted in a phenotyping of risk groups. We found that distinct platelet lipids are associated with an increased CV or bleeding risk and independently predict adverse events. Notably, the addition of platelet lipids to conventional risk factors resulted in an increased diagnostic accuracy of patients with adverse CV events. Thus, patients with aberrant platelet lipid signatures and platelet functions are at elevated risk to develop adverse CV events. Machine learning combining platelet lipidome data and common clinical parameters demonstrated an increased diagnostic value in patients with CAD and might improve early risk discrimination and classification for CV events.
- Published
- 2024
- Full Text
- View/download PDF
45. Methylation-eQTL analysis in cancer research
- Author
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Scott Kopetz, David G. Menter, Yusha Liu, Jeffrey S. Morris, Michael S. Lee, Michael Lam, Jennifer S. Davis, Ganiraju C. Manyam, Kunal Rai, Keith A. Baggerly, Huiqin Chen, Elias Orouji, and Bradley M. Broom
- Subjects
Statistics and Probability ,0303 health sciences ,Methylation ,Computational biology ,Biology ,Quantitative trait locus ,Biochemistry ,Original Papers ,Computer Science Applications ,03 medical and health sciences ,Computational Mathematics ,0302 clinical medicine ,Computational Theory and Mathematics ,CpG site ,030220 oncology & carcinogenesis ,Gene expression ,Expression quantitative trait loci ,DNA methylation ,Epigenetics ,Molecular Biology ,Gene ,030304 developmental biology - Abstract
Motivation DNA methylation is a key epigenetic factor regulating gene expression. While promoter methylation has been well studied, recent publications have revealed that functionally important methylation also occurs in intergenic and distal regions, and varies across genes and tissue types. Given the growing importance of inter-platform integrative genomic analyses, there is an urgent need to develop methods to discover and characterize gene-level relationships between methylation and expression. Results We introduce a novel sequential penalized regression approach to identify methylation-expression quantitative trait loci (methyl-eQTLs), a term that we have coined to represent, for each gene and tissue type, a sparse set of CpG loci best explaining gene expression and accompanying weights indicating direction and strength of association. Using TCGA and MD Anderson colorectal cohorts to build and validate our models, we demonstrate our strategy better explains expression variability than current commonly used gene-level methylation summaries. The methyl-eQTLs identified by our approach can be used to construct gene-level methylation summaries that are maximally correlated with gene expression for use in integrative models, and produce a tissue-specific summary of which genes appear to be strongly regulated by methylation. Our results introduce an important resource to the biomedical community for integrative genomics analyses involving DNA methylation. Availability and implementation We produce an R Shiny app (https://rstudio-prd-c1.pmacs.upenn.edu/methyl-eQTL/) that interactively presents methyl-eQTL results for colorectal, breast and pancreatic cancer. The source R code for this work is provided in the Supplementary Material. Supplementary information Supplementary data are available at Bioinformatics online.
- Published
- 2021
46. Inducible pesticide tolerance inDaphnia pulexinfluenced by resource availability
- Author
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Paige S. Garramone, Michael Lam, Connor O. Loomis, Samantha Klein, Vanessa P. Wuerthner, Lindsey Deluna, Rachel Reynolds, Jessica Hua, George A. Meindl, Yelena Pecheny, and Jared Jaeger
- Subjects
zooplankton ,0106 biological sciences ,Carbamate ,medicine.medical_treatment ,Zoology ,Biology ,010603 evolutionary biology ,01 natural sciences ,Daphnia pulex ,ecotoxicology ,03 medical and health sciences ,chemistry.chemical_compound ,lcsh:QH540-549.5 ,Carbaryl ,medicine ,Ecotoxicology ,Ecology, Evolution, Behavior and Systematics ,Organism ,030304 developmental biology ,Nature and Landscape Conservation ,0303 health sciences ,Phenotypic plasticity ,Ecology ,acetylcholine esterase inhibitor ,Aquatic ecosystem ,fungi ,carbamate ,Pesticide ,biology.organism_classification ,chemistry ,lcsh:Ecology - Abstract
Pesticides are a ubiquitous contaminant in aquatic ecosystems. Despite the relative sensitivity of aquatic species to pesticides, growing evidence suggests that populations can respond to pesticides by evolving higher baseline tolerance or inducing a higher tolerance via phenotypic plasticity. While both mechanisms can allow organisms to persist when faced with pesticides, resource allocation theory suggests that tolerance may be related to resource acquisition by the organism. Using Daphnia pulex, we investigated how algal resource availability influenced the baseline and inducible tolerance of D. pulex to a carbamate insecticide, carbaryl. Individuals reared in high resource environments had a higher baseline carbaryl tolerance compared to those reared in low resource environments. However, D. pulex from low resource treatments exposed to sublethal concentrations of carbaryl early in development induced increased tolerance to a lethal concentration of carbaryl later in life. Only individuals reared in the low resource environment induced carbaryl tolerance. Collectively, this highlights the importance of considering resource availability in our understanding of pesticide tolerance.
- Published
- 2019
47. Circulating inflammation signature predicts overall survival and relapse-free survival in metastatic colorectal cancer
- Author
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Masayoshi Shimizu, Michael J. Overman, David G. Menter, George A. Calin, Hai T. Tran, Scott Kopetz, John V. Heymach, Jean Nicolas Vauthey, Rosa Lizeth Frias, Neeraj Shah, Anastasia D. Katsiampoura, Michael Lam, Jennifer S. Davis, Andreas Varkaris, Cristina Ivan, Jeffrey S. Morris, and Yun Shin Chun
- Subjects
Male ,Cancer Research ,medicine.medical_specialty ,Colorectal cancer ,Population ,Inflammation ,Disease ,Gastroenterology ,Article ,Disease-Free Survival ,Tumour biomarkers ,03 medical and health sciences ,0302 clinical medicine ,Text mining ,Recurrence ,Internal medicine ,Biomarkers, Tumor ,Medicine ,Humans ,Neoplasm Metastasis ,education ,education.field_of_study ,Predictive marker ,business.industry ,Proportional hazards model ,Interleukin-6 ,Interleukin-8 ,Middle Aged ,medicine.disease ,Prognosis ,3. Good health ,Gene Expression Regulation, Neoplastic ,MicroRNAs ,Oncology ,030220 oncology & carcinogenesis ,Cohort ,Female ,medicine.symptom ,Neoplasm Recurrence, Local ,business ,Colorectal Neoplasms - Abstract
Background Metastatic colorectal cancer (mCRC) is a highly heterogeneous disease from a clinical, molecular, and immunological perspective. Current predictive models rely primarily in tissue based genetic analysis, which not always correlate with inflammatory response. Here we evaluated the role of a circulating inflammatory signature as a prognostic marker in mCRC. Methods Two hundred eleven newly diagnosed patients with mCRC were enrolled in the study. One hundred twenty-one patients had unresectable metastases, whereas ninety patients had potentially resectable liver metastases at presentation. Analysis of miR-21, IL-6, and IL-8 in the plasma of peripheral blood was performed at baseline. Patients with high circulating levels of ≥2 of the three inflammation markers (miR-21, IL-6, and IL-8) were considered to have the “Inflammation phenotype-positive CISIG”. Results Positive CISIG was found in 39/90 (43%) and 50/121 (45%) patients in the resectable and unresectable cohort, respectively. In the resectable population the median relapse-free survival was 18.4 compared to 31.4 months (p = 0.001 HR 2.09, 95% CI 1.2–3.67) for positive vs. negative CISIG. In contrast, the individual components were not significant. In the same population the median overall survival was 46.2 compared to 66.0 months (p = 0.0003, HR 2.57, 95% CI 1.26–5.27) for positive vs. negative CISIG, but not significant for the individual components. In the unresectable population, the median overall survival was 13.5 compared to 25.0 months (p = 0.0008, HR 2.49, 95% CI 1.46–4.22) for positive vs. negative CISIG. IL-6 was independently prognostic with overall survival of 16.2 compared to 27.0 months (p = 0.004, HR 1.96, 95% CI 1.24–3.11) for high vs. low IL-6, but not the other components. Using a Cox regression model, we demonstrated that CISIG is an independent predictive marker of survival in patients with unresectable disease (HR 1.8, 95% CI 1.2, 2.8, p
- Published
- 2019
48. Prognostic Implications of Mucinous Differentiation in Metastatic Colorectal Carcinoma Can Be Explained by Distinct Molecular and Clinicopathologic Characteristics
- Author
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Kanwal Pratap Singh Raghav, Van K. Morris, Allan Andresson Lima Pereira, Shailesh Advani, Jonathan M. Loree, Wen Li, Scott Kopetz, Jing Ning, Russell Broaddus, Maliha Khan, Michael J. Overman, Dipen M. Maru, and Michael Lam
- Subjects
Adult ,Male ,0301 basic medicine ,Oncology ,medicine.medical_specialty ,Mucinous Differentiation ,Colorectal cancer ,Adenocarcinoma ,Article ,Cohort Studies ,Young Adult ,03 medical and health sciences ,0302 clinical medicine ,Internal medicine ,Biomarkers, Tumor ,Overall survival ,Histologic type ,Humans ,Medicine ,Aged ,Aged, 80 and over ,business.industry ,Liver Neoplasms ,Gastroenterology ,Microsatellite instability ,DNA Methylation ,Middle Aged ,Prognosis ,medicine.disease ,Adenocarcinoma, Mucinous ,Combined Modality Therapy ,Survival Rate ,Phenotype ,030104 developmental biology ,CpG site ,030220 oncology & carcinogenesis ,Baseline characteristics ,Mutation ,CpG Islands ,Female ,Microsatellite Instability ,Colorectal Neoplasms ,business ,Follow-Up Studies - Abstract
The mucinous histologic subtype accounts for 5% to 20% of colorectal cancer (CRC) cases but remains poorly characterized. The present study characterized the baseline characteristics, mutational profile, and clinical outcomes of patients diagnosed with mucinous CRC.We identified 1877 patients with metastatic CRC with available histologic findings and molecular profiling and summarized the baseline clinical and pathologic characteristics and overall survival (OS) stratified by the histologic type. The data from separate cohorts with consensus molecular subtype (CMS) and CpG island methylator information were also summarized.The mucinous histologic type was found in 277 of the 1877 patients (14.8%) and was associated with an increased prevalence of microsatellite instability (P .001) and a right-sided primary (P .001). An increased frequency of CMS1 (microsatellite instability immune) and lower rates of CMS2 (canonical) were identified, with mucinous compared with nonmucinous adenocarcinoma (P .0001). Mutations in SMAD4 (P .001), GNAS (P .001), ERBB2 (P = .02), BRAF (P .001), and KRAS (P .001) occurred at greater frequencies in the mucinous CRC cases, and TP53 (P .001), APC (P .001), and NRAS mutations (P = .03) were less common. Univariate (hazard ratio [HR], 1.38; 95% confidence interval [CI], 1.17-1.63; P .001) and multivariate analysis (HR, 1.36; 95% CI, 1.12-1.64; P = .002) demonstrated that the mucinous histologic type is associated with worse OS. The features associated with the mucinous histologic subtype were independent predictors for shorter OS, including BRAF (HR, 1.74; 95% CI, 1.35-2.25; P .001) and KRAS (HR, 1.42; 95% CI, 1.22-1.65; P .001) mutations, right-sided location (HR, 1.20; 95% CI, 1.04-1.39; P = .01), and synchronous metastases (HR, 2.92; 95% CI, 2.49-3.42; P .001).Compared with nonmucinous adenocarcinoma, the mucinous histologic type is associated with a worse prognosis, even when controlling for known prognostic features. This unique biologic behavior should be considered in the treatment and prognostic assessment of patients with CRC.
- Published
- 2018
49. Donating blood: is there also a signalling function?
- Author
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Michael Lam
- Subjects
Signalling theory ,Signalling ,Mechanism (biology) ,media_common.quotation_subject ,Intervention (counseling) ,Survival of the fittest ,Perspective (graphical) ,Function (engineering) ,Psychology ,Altruism ,Social psychology ,health care economics and organizations ,media_common - Abstract
Altruism: the desire to benefit others at a cost to the self is the most commonly frequently mentioned reason for donating blood. The behaviour itself, is without a doubt altruistic in the sense that it is unlikely there are any benefits that could outweigh the immediate cost of making the time and effort to give blood to an anonymous human. In studying the altruistic behaviour of donating blood, research has primarily focused on understanding the proximate level explanations of the behaviour. That is, what are the psychological mechanism that triggers the behaviour. However, altruistic behaviours, like all other human behaviours can also be understood from an ultimate perspective. That is, what evolutionary factors could explain the survival of the behaviour and their associated psychological mechanisms. This thesis considers an ultimate explanation of blood donation drawn from Costly Signalling Theory: donating blood also functions as a signal of underlying qualities. The aim of this thesis is to assess the applicability of using Costly Signalling Theory to understand blood donation.In Chapter 1, I provide an overview of research on the link between altruism and donating blood. I detail the importance of distinguishing between ultimate and proximate level explanations to develop a fuller understanding of the behaviour. I further outline the questions that needs to be answered before applying Costly Signalling Theory to develop recruitment intervention for blood donation. In Chapter 2, given the robust link between altruism and donating blood, I empirically test the levels of altruism underlying blood donors and non-donors. Subsequently, in Chapter 3, I examine the qualities signalled by donating blood compared to other forms of helping, such as donating money and volunteering. In Chapter 4, I assess the effectiveness of male blood donors signalling the qualities associated with donating blood (e.g., altruism, trustworthiness) through a subtly marked blood branded bandage. Chapter 5 explores the content communicated by blood donors who had successfully donated blood to understand possible signalling strategies in their communication. Finally, in Chapter 6 I draw together all these findings to discuss the applicability of using Costly Signalling Theory to understand blood donation, practical implications and future directions. Together, the thesis presents a program of research examining the traits signalled by donating blood and the methods that blood donation status could be effectively signalled.
- Published
- 2021
50. ARID1A mutation may define an immunologically active subgroup in patients with microsatellite-stable colorectal cancer
- Author
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Riham Katkhuda, Michael Lam, Hey Min Lee, Jennifer S. Davis, Jaffer A. Ajani, Scott Kopetz, Jeffrey S. Morris, Jason Willis, Shailesh Advani, Michael J. Overman, Jason Roszik, Jonathan M. Loree, Anuj Verma, John Paul Shen, Ganiraju C. Manyam, Jumanah Alshenaifi, Amir Mehrvarz Sarshekeh, and Dipen M. Maru
- Subjects
0301 basic medicine ,Cancer Research ,ARID1A ,Colorectal cancer ,Programmed Cell Death 1 Receptor ,medicine.disease_cause ,Article ,B7-H1 Antigen ,Frameshift mutation ,03 medical and health sciences ,0302 clinical medicine ,medicine ,Biomarkers, Tumor ,Humans ,CTLA-4 Antigen ,Retrospective Studies ,Mutation ,business.industry ,Gene Expression Profiling ,Cancer ,medicine.disease ,Prognosis ,Gene expression profiling ,DNA-Binding Proteins ,030104 developmental biology ,Oncology ,MSH2 ,030220 oncology & carcinogenesis ,Cancer research ,DNA mismatch repair ,Microsatellite Instability ,business ,Colorectal Neoplasms ,Follow-Up Studies ,T-Lymphocytes, Cytotoxic ,Transcription Factors - Abstract
Purpose: AT-rich interactive domain 1A (ARID1A) is commonly mutated in colorectal cancer, frequently resulting in truncation and loss of protein expression. ARID1A recruits MSH2 for mismatch repair during DNA replication. ARID1A deficiency promotes hypermutability and immune activation in preclinical models, but its role in patients with colorectal cancer is being explored. Experimental Design: The DNA sequencing and gene expression profiling of patients with colorectal cancer were extracted from The Cancer Genome Atlas and MD Anderson Cancer Center databases, with validation utilizing external databases, and correlation between ARID1A and immunologic features. IHC for T-cell markers was performed on a separate cohort of patients. Results: Twenty-eight of 417 patients with microsatellite stable (MSS) colorectal cancer (6.7%) had ARID1A mutation. Among 58 genes most commonly mutated in colorectal cancer, ARID1A mutation had the highest increase with frameshift mutation rates in MSS cases (8-fold, P < 0.001). In MSS, ARID1A mutation was enriched in immune subtype (CMS1) and had a strong correlation with IFNγ expression (Δz score +1.91, P < 0.001). Compared with ARID1A wild-type, statistically significant higher expression for key checkpoint genes (e.g., PD-L1, CTLA4, and PDCD1) and gene sets (e.g., antigen presentation, cytotoxic T-cell function, and immune checkpoints) was observed in mutant cases. This was validated by unsupervised differential expression of genes related to immune response and further confirmed by higher infiltration of T cells in IHC of tumors with ARID1A mutation (P = 0.01). Conclusions: The immunogenicity of ARID1A-mutant cases is likely due to an increased level of neoantigens resulting from increased tumor mutational burden and frameshift mutations. Tumors with ARID1A mutation may be more susceptible to immune therapy–based treatment strategies and should be recognized as a unique molecular subgroup in future immune therapy trials.
- Published
- 2021
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