Publications by authors named "Amy Chen"

427 Publications

Airway hyperresponsiveness in patients with normal spirometry results and symptoms compatible with asthma: Primary care retrospective chart review.

Can Fam Physician 2021 Mar 16;67(3):e84-e89. Epub 2021 Mar 16.

Associate Professor in the Department of Family and Community Medicine at the University of Toronto.

Objective: To evaluate the proportion of patients with symptoms suggestive of asthma and normal lung function who exhibit airway hyperreactivity with methacholine challenge testing (MCT) in primary care.

Design: Retrospective chart review.

Setting: Primary care lung clinic in Toronto, Ont.

Participants: A total of 69 patients presenting to the lung clinic who had symptoms compatible with asthma, normal spirometry test results, and were referred for MCT.

Main Outcome Measures: Descriptive statistics, frequency counts, independent tests, and tests were used to examine differences in the proportion of clinical and demographic variables identified in patients with or without a positive MCT result. Effect size was determined between MCT-positive and MCT-negative patients for both categorical ( coefficient) and continuous (Hedges ) data.

Results: Twenty-one patients (30.4%) had positive MCT results, and 48 patients (69.6%) had negative MCT results. Family history of asthma and reduced baseline and postbronchodilator forced expiratory volume in 1 second were associated with a positive MCT result.

Conclusion: The findings of this study provide insight into the utility of simple spirometry for asthma diagnosis and the need to further clarify the role of MCT in the primary care setting.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.46747/cfp.6703e84DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7963022PMC
March 2021

Current Trainee and Workforce Patterns for Thyroid and Parathyroid Surgery in the United States.

Endocr Pract 2021 Feb 23. Epub 2021 Feb 23.

Thyroid/Parathyroid Endocrine Surgical Division, Massachusetts Eye and Ear Infirmary, Boston, Massachusetts.

Objective: Thyroid and parathyroid surgery is performed by both general surgeons and otolaryngologists. We describe the proportion of surgeries performed by specialty, providing data to support decisions about when and to whom to direct research, education, and quality improvement interventions.

Methods: We tabulated case numbers for privately insured patients undergoing thyroid and parathyroid surgery in Marketscan: 2010-2016 and trainee case logs for residents and fellows in general surgery and otolaryngology. Summary statistics and tests for trends and differences were calculated.

Results: Marketscan data captured 114 500 thyroid surgeries. The proportion performed by each specialty was not significantly different. Otolaryngologists performed 58 098 and general surgeons performed 56 402. Otolaryngologists more commonly performed hemithyroidectomy (n = 25 148, 43.29% of all thyroid surgeries performed by otolaryngologists) compared to general surgeons (n = 20 353, 36.09% of all thyroid surgeries performed by general surgeons). Marketscan data captured 21 062 parathyroid surgeries: 6582 (31.25%) were performed by otolaryngologists, and 14 480 (68.75%) were performed by general surgeons. The case numbers of otolaryngology and general surgery trainees completing residency and fellowship varied 6- to 9-fold across different sites. The wide variation may reflect both the level of exposure a particular training program offers and trainee level of interest.

Conclusion: Thyroid surgical care is equally provided by general surgeons and otolaryngologists. Both specialties contribute significantly to parathyroid surgical care. Both specialties should provide input into and be targets of research, quality, and education interventions.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.eprac.2021.02.010DOI Listing
February 2021

The Transcriptomic and Phenotypic Response of the Melanized Yeast to Ionizing Particle Exposure.

Front Microbiol 2020 12;11:609996. Epub 2021 Jan 12.

Center for Biomolecular Science and Engineering, United States Naval Research Laboratory, Washington, DC, United States.

Fungi can tolerate extremely high doses of ionizing radiation compared with most other eukaryotes, a phenomenon encompassing both the recovery from acute exposure and the growth of melanized fungi in chronically contaminated environments such as nuclear disaster sites. This observation has led to the use of fungi in radiobiology studies, with the goal of finding novel resistance mechanisms. However, it is still not entirely clear what underlies this phenomenon, as genetic studies have not pinpointed unique responses to ionizing radiation in the most resistant fungi. Additionally, little work has been done examining how fungi (other than budding yeast) respond to irradiation by ionizing particles (e.g., protons, α-particles), although particle irradiation may cause distinct cellular damage, and is more relevant for human risks. To address this paucity of data, in this study we have characterized the phenotypic and transcriptomic response of the highly radioresistant yeast to irradiation by three separate ionizing radiation sources: protons, deuterons, and α-particles. The experiment was performed with both melanized and non-melanized strains of , to determine the effect of this pigment on the response. No significant difference in survival was observed between these strains under any condition, suggesting that melanin does not impart protection to acute irradiation to these particles. The transcriptomic response during recovery to particle exposure was similar to that observed after γ-irradiation, with DNA repair and replication genes upregulated, and genes involved in translation and ribosomal biogenesis being heavily repressed, indicating an attenuation of cell growth. However, a comparison of global gene expression showed clear clustering of particle and γ-radiation groups. The response elicited by particle irradiation was, in total, more complex. Compared to the γ-associated response, particle irradiation resulted in greater changes in gene expression, a more diverse set of differentially expressed genes, and a significant induction of gene categories such as autophagy and protein catabolism. Additionally, analysis of individual particle responses resulted in identification of the first unique expression signatures and individual genes for each particle type that could be used as radionuclide discrimination markers.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fmicb.2020.609996DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7835796PMC
January 2021

Iterative Adaptation of a Tuberculosis Digital Medication Adherence Technology to Meet User Needs: Qualitative Study of Patients and Health Care Providers Using Human-Centered Design Methods.

JMIR Form Res 2020 Dec 8;4(12):e19270. Epub 2020 Dec 8.

Department of Surgery, University of California, San Francisco, San Francisco, CA, United States.

Background: Digital adherence technologies have been widely promoted as a means to improve tuberculosis medication adherence. However, uptake of these technologies has been suboptimal by both patients and health workers. Not surprisingly, studies have not demonstrated significant improvement in treatment outcomes.

Objective: This study aimed to optimize a well-known digital adherence technology, 99DOTS, for end user needs in Uganda. We describe the findings of the ideation phase of the human-centered design methodology to adapt 99DOTS according to a set of design principles identified in the previous inspiration phase.

Methods: 99DOTS is a low-cost digital adherence technology wherein tuberculosis medication blister packs are encased within an envelope that reveals toll-free numbers that patients can call to report dosing. We identified 2 key areas for design and testing: (1) the envelope, including the form factor, content, and depiction of the order of pill taking; and (2) the patient call-in experience. We conducted 5 brainstorming sessions with all relevant stakeholders to generate a suite of potential prototype concepts. Senior investigators identified concepts to further develop based on feasibility and consistency with the predetermined design principles. Prototypes were revised with feedback from the entire team. The envelope and call-in experience prototypes were tested and iteratively revised through focus groups with health workers (n=52) and interviews with patients (n=7). We collected and analyzed qualitative feedback to inform each subsequent iteration.

Results: The 5 brainstorming sessions produced 127 unique ideas that we clustered into 6 themes: rewards, customization, education, logistics, wording and imagery, and treatment countdown. We developed 16 envelope prototypes, 12 icons, and 28 audio messages for prototype testing. In the final design, we altered the pill packaging envelope by adding a front flap to conceal the pills and reduce potential stigma associated with tuberculosis. The flap was adorned with either a blank calendar or map of Uganda. The inside cover contained a personalized message from a local health worker including contact information, pictorial pill-taking instructions, and a choice of stickers to tailor education to the patient and phase of treatment. Pill-taking order was indicated with colors, chevron arrows, and small mobile phone icons. Last, the call-in experience when patients report dosing was changed to a rotating series of audio messages centered on the themes of prevention, encouragement, and reassurance that tuberculosis is curable.

Conclusions: We demonstrated the use of human-centered design as a promising tool to drive the adaptation of digital adherence technologies to better address the needs and motivations of end users. The next phase of research, known as the implementation phase in the human-centered design methodology, will investigate whether the adapted 99DOTS platform results in higher levels of engagement from patients and health workers, and ultimately improves tuberculosis treatment outcomes.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2196/19270DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7755538PMC
December 2020

Targeting the myeloid checkpoint receptor SIRPα potentiates innate and adaptive immune responses to promote anti-tumor activity.

J Hematol Oncol 2020 11 30;13(1):160. Epub 2020 Nov 30.

ALX Oncology, Burlingame, CA, USA.

Background: Signal regulatory protein α (SIRPα) is a myeloid-lineage inhibitory receptor that restricts innate immunity through engagement of its cell surface ligand CD47. Blockade of the CD47-SIRPα interaction synergizes with tumor-specific antibodies and T-cell checkpoint inhibitors by promoting myeloid-mediated antitumor functions leading to the induction of adaptive immunity. Inhibition of the CD47-SIRPα interaction has focused predominantly on targeting CD47, which is expressed ubiquitously and contributes to the accelerated blood clearance of anti-CD47 therapeutics. Targeting SIRPα, which is myeloid-restricted, may provide a differential pharmacokinetic, safety, and efficacy profile; however, SIRPα polymorphisms and lack of pan-allelic and species cross-reactive agents have limited the clinical translation of antibodies against SIRPα. Here, we report the development of humanized AB21 (hAB21), a pan-allelic anti-SIRPα antibody that binds human, cynomolgus monkey, and mouse SIRPα alleles with high affinity and blocks the interaction with CD47.

Methods: Human macrophages derived from donors with various SIRPα v1 and v2 allelic status were used to assess the ability of hAB21 to enhance phagocytosis. HAB21_IgG subclasses were evaluated for targeted depletion of peripheral blood mononuclear cells, phagocytosis and in vivo efficacy in xenograft models. Combination therapy with anti-PD1/anti-PD-L1 in several syngeneic models was performed. Immunophenotyping of tissues from MC38 tumor-bearing mice treated with AB21 and anti-PD-1 was evaluated. PK, PD and tolerability of hAB21 were evaluated in cynomolgus monkeys.

Results: SIRPα blockade with hAB21 promoted macrophage-mediated antibody-dependent phagocytosis of tumor cells in vitro and improved responses to rituximab in the Raji human tumor xenograft mouse model. Combined with PD-1/PD-L1 blockade, AB21 improved response rates by facilitating monocyte activation, dendritic cell activation, and T cell effector functions resulting in long term, durable antitumor immunity. In cynomolgus monkeys, hAB21 has a half-life of 5.3 days at 10 mg/kg and complete target occupancy with no hematological toxicity or adverse findings at doses up to 30 mg/kg.

Conclusions: The in vitro and in vivo antitumor activity of hAB21 broadly recapitulates that of CD47 targeted therapies despite differences in ligand expression, binding partners, and function, validating the CD47-SIRPα axis as a fundamental myeloid checkpoint pathway and its blockade as promising therapeutic intervention for treatment of human malignancies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s13045-020-00989-wDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7706287PMC
November 2020

Adaptive evolution of a melanized fungus reveals robust augmentation of radiation resistance by abrogating non-homologous end-joining.

Environ Microbiol 2020 Oct 19. Epub 2020 Oct 19.

Center for Biomolecular Sciences and Engineering, US Naval Research Laboratory, Washington, DC, USA.

Fungi have been observed to exhibit resistance to high levels of ionizing radiation despite sharing most DNA repair mechanisms with other eukaryotes. Radioresistance, in fact, is such a common feature in fungi that it is difficult to identify species that exhibit widely different radiosensitivities, which in turn has hampered the identification of genetic elements responsible for this resistance phenotype. Due to the inherent mutagenic properties of radiation exposure, however, this can be addressed through adaptive laboratory evolution for increased ionizing radiation resistance. Here, using the black yeast Exophiala dermatitidis, we demonstrate that resistance to γ-radiation can be greatly increased through repeated rounds of irradiation and outgrowth. Moreover, we find that the small genome size of fungi situates them as a relatively simple functional genomics platform for identification of mutations associated with ionizing radiation resistance. This enabled the identification of genetic mutations in genes encoding proteins with a broad range of functions from 10 evolved strains. Specifically, we find that greatly increased resistance to γ-radiation is achieved in E. dermatitidis through disruption of the non-homologous end-joining pathway, with three individual evolutionary paths converging to abolish this DNA repair process. This result suggests that non-homologous end-joining, even in haploid cells where homologous chromosomes are not present during much of the cell cycle, is an impediment to repair of radiation-induced lesions in this organism, and that the relative levels of homologous and non-homologous repair in a given fungal species may play a major role in its radiation resistance.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.15285DOI Listing
October 2020

Oral Intubation Attempts in Patients With a Laryngectomy: A Significant Safety Threat.

Otolaryngol Head Neck Surg 2020 Oct 13:194599820960728. Epub 2020 Oct 13.

American Board of Otolaryngology-Head and Neck Surgery, Houston, Texas, USA.

It is impossible to secure the airway of a patient with "neck-only" breathing transorally or transnasally. Surgical removal of the larynx (laryngectomy) or tracheal rerouting (tracheoesophageal diversion or laryngotracheal separation) creates anatomic discontinuity. Misguided attempts at oral intubation of neck breathers may cause hypoxic brain injury or death. We present national data from the American Academy of Otolaryngology-Head and Neck Surgery, the American Head and Neck Society, and the United Kingdom's National Reporting and Learning Service. Over half of US otolaryngologist respondents reported instances of attempted oral intubations among patients with laryngectomy, with a mortality rate of 26%. UK audits similarly revealed numerous resuscitation efforts where misunderstanding of neck breather status led to harm or death. Such data underscore the critical importance of staff education, patient engagement, effective signage, and systems-based best practices to reliably clarify neck breather status and provide necessary resources for safe patient airway management.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1177/0194599820960728DOI Listing
October 2020

Proteomics Reveals Distinct Changes Associated with Increased Gamma Radiation Resistance in the Black Yeast .

Genes (Basel) 2020 Sep 25;11(10). Epub 2020 Sep 25.

Center for Bio/Molecular Science & Engineering, Naval Research Laboratory, Washington, DC 20375, USA.

The yeast exhibits high resistance to γ-radiation in comparison to many other fungi. Several aspects of this phenotype have been characterized, including its dependence on homologous recombination for the repair of radiation-induced DNA damage, and the transcriptomic response invoked by acute γ-radiation exposure in this organism. However, these findings have yet to identify unique γ-radiation exposure survival strategies-many genes that are induced by γ-radiation exposure do not appear to be important for recovery, and the homologous recombination machinery of this organism is not unique compared to more sensitive species. To identify features associated with γ-radiation resistance, here we characterized the proteomes of two strains-the wild type and a hyper-resistant strain developed through adaptive laboratory evolution-before and after γ-radiation exposure. The results demonstrate that protein intensities do not change substantially in response to this stress. Rather, the increased resistance exhibited by the evolved strain may be due in part to increased basal levels of single-stranded binding proteins and a large increase in ribosomal content, possibly allowing for a more robust, induced response during recovery. This experiment provides evidence enabling us to focus on DNA replication, protein production, and ribosome levels for further studies into the mechanism of γ-radiation resistance in and other fungi.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/genes11101128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7650708PMC
September 2020

Phase Ib Study of Chemoprevention with Green Tea Polyphenon E and Erlotinib in Patients with Advanced Premalignant Lesions (APL) of the Head and Neck.

Clin Cancer Res 2020 Nov 17;26(22):5860-5868. Epub 2020 Sep 17.

Department of Hematology and Medical Oncology, Emory University Winship Cancer Institute, Atlanta, Georgia.

Purpose: On the basis of synergistic effects between green tea polyphenon E (PPE) and EGFR-tyrosine kinase inhibitor in preclinical studies, we conducted a phase Ib study of the PPE and erlotinib combination in patients with advanced premalignant lesions (APL) of the oral cavity and larynx.

Patients And Methods: Patients were treated with a fixed dose of PPE (200 mg three times a day) and dose escalation of erlotinib (50, 75, 100 mg daily) for 6 months with tissue biopsy at baseline and 6 months. Primary endpoints were safety and toxicity; secondary endpoints were evaluation of pathologic response, cancer-free survival (CFS), overall survival (OS), and biomarker modulation.

Results: Among 21 enrolled patients, 19 began treatment and 17 completed 6 months of treatment with PPE and erlotinib. Main characteristics of treated patients: 15 severe dysplasia or carcinoma and 17 oral cavity. Only skin rash was associated with dose-limiting toxicity and MTD. Recommended doses for phase II studies are PPE 600 mg daily plus erlotinib 100 mg daily for 6 months. Pathologic responses in 17 evaluable patients: pathologic complete response (47%) and pathologic partial response (18%). The 5-year CFS and OS were 66.3% and 93%, respectively. Among tested biomarkers, only phosphorylated ERK was correlated with response to treatment.

Conclusions: Treatment with PPE and erlotinib combination was well tolerated in patients with APLs of the head and neck, and showed a high rate of pathologic response with excellent CFS. This combination deserves further investigation for the chemoprevention and/or prevention of second primary tumors in early-stage head and neck cancer.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1158/1078-0432.CCR-20-2276DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8016407PMC
November 2020

Indications and outcomes of superselective neck dissection: A review and analysis of the literature.

Laryngoscope Investig Otolaryngol 2020 Aug 25;5(4):672-676. Epub 2020 Jun 25.

Department of Otolaryngology-Head and Neck Surgery Emory University Atlanta Georgia USA.

Superselective neck dissection, defined as dissection of two or less contiguous neck levels, has recently been introduced to reduce surgical morbidity of neck dissection while maintaining favorable oncologic outcomes. The purpose of this review is to report the results of superselective neck dissection when applied to specific settings: the management of regional disease after chemoradiation, head and neck squamous cell carcinoma with clinical N0 necks, and high risk papillary thyroid carcinoma.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/lio2.421DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7444773PMC
August 2020

Using a 22-Layer U-Net to Perform Segmentation of Squamous Cell Carcinoma on Digitized Head and Neck Histological Images.

Proc SPIE Int Soc Opt Eng 2020 Feb 16;11320. Epub 2020 Mar 16.

Dept. of Bioengineering, University of Texas at Dallas, TX.

Squamous cell carcinoma (SCC) comprises over 90 percent of tumors in the head and neck. The diagnosis process involves performing surgical resection of tissue and creating histological slides from the removed tissue. Pathologists detect SCC in histology slides, and may fail to correctly identify tumor regions within the slides. In this study, a dataset of patches extracted from 200 digitized histological images from 84 head and neck SCC patients was used to train, validate and test the segmentation performance of a fully-convolutional U-Net architecture. The neural network achieved a pixel-level segmentation AUC of 0.89 on the testing group. The average segmentation time for whole slide images was 72 seconds. The training, validation, and testing process in this experiment produces a model that has the potential to help segment SCC images in histological images with improved speed and accuracy compared to the manual segmentation process performed by pathologists.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1117/12.2549061DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7261613PMC
February 2020

Ethical framework for head and neck endocrine surgery in the COVID-19 pandemic.

Head Neck 2020 Jul 13;42(7):1418-1419. Epub 2020 May 13.

Oregon Health Sciences University, Portland, Oregon, USA.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/hed.26240DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7272909PMC
July 2020

Development of Clickable Photoaffinity Ligands for Metabotropic Glutamate Receptor 2 Based on Two Positive Allosteric Modulator Chemotypes.

ACS Chem Neurosci 2020 06 22;11(11):1597-1609. Epub 2020 May 22.

Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences and Department of Pharmacology, Monash University, 399 Royal Parade, Parkville, Victoria 3052, Australia.

The metabotropic glutamate receptor 2 (mGlu) is a transmembrane-spanning class C G protein-coupled receptor that is an attractive therapeutic target for multiple psychiatric and neurological disorders. A key challenge has been deciphering the contribution of mGlu relative to other closely related mGlu receptors in mediating different physiological responses, which could be achieved through the utilization of subtype selective pharmacological tools. In this respect, allosteric modulators that recognize ligand-binding sites distinct from the endogenous neurotransmitter glutamate offer the promise of higher receptor-subtype selectivity. We hypothesized that mGlu-selective positive allosteric modulators could be derivatized to generate bifunctional pharmacological tools. Here we developed clickable photoaffinity probes for mGlu based on two different positive allosteric modulator scaffolds that retained similar pharmacological activity to parent compounds. We demonstrate successful probe-dependent incorporation of a commercially available clickable fluorophore using bioorthogonal conjugation. Importantly, we also show the limitations of using these probes to assess fluorescence of mGlu in intact cells where significant nonspecific membrane binding is evident.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1021/acschemneuro.0c00009DOI Listing
June 2020

Tumor detection of the thyroid and salivary glands using hyperspectral imaging and deep learning.

Biomed Opt Express 2020 Mar 18;11(3):1383-1400. Epub 2020 Feb 18.

The University of Texas at Dallas, Department of Bioengineering, Richardson, TX 75080, USA.

The performance of hyperspectral imaging (HSI) for tumor detection is investigated in specimens from the thyroid ( = 200) and salivary glands ( = 16) from 82 patients. Tissues were imaged with HSI in broadband reflectance and autofluorescence modes. For comparison, the tissues were imaged with two fluorescent dyes. Additionally, HSI was used to synthesize three-band RGB multiplex images to represent the human-eye response and Gaussian RGBs, which are referred to as HSI-synthesized RGB images. Using histological ground truths, deep learning algorithms were developed for tumor detection. For the classification of thyroid tumors, HSI-synthesized RGB images achieved the best performance with an AUC score of 0.90. In salivary glands, HSI had the best performance with 0.92 AUC score. This study demonstrates that HSI could aid surgeons and pathologists in detecting tumors of the thyroid and salivary glands.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1364/BOE.381257DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7075628PMC
March 2020

Application of Cell Impedance as a Screening Tool to Discover Modulators of Intraocular Pressure.

J Ocul Pharmacol Ther 2020 06 13;36(5):269-281. Epub 2020 Mar 13.

Department of Ophthalmology, Novartis Institutes for BioMedical Research, Cambridge, Massachusetts.

To identify new targets and compounds involved in mediating cellular contractility or relaxation in trabecular meshwork (TM) cells and test their efficacy in an model measuring outflow facility. A low-molecular weight compound library composed of 3,957 compounds was screened for cytoskeletal changes using the Acea xCelligence impedance platform in immortalized human NTM5 TM cells. Hits were confirmed by 8-point concentration response and were subsequently evaluated for impedance changes in 2 primary human TM strains, as well as cross-reactivity in bovine primary cells. A recently described bovine whole eye perfusion system was used to evaluate effects of compounds on aqueous outflow facility. The primary screen conducted was robust, with ' values >0.5. Fifty-two compounds were identified in the primary screen and confirmed to have concentration-dependent effects on impedance in NTM5 cells. Of these, 9 compounds representing distinct drug classes were confirmed to modulate impedance in both human primary TM cells and bovine cells. One of these compounds, wortmannin, an inhibitor of phosphoinositide 3-kinase, increased outflow facility by 11%. A robust phenotypic assay was developed that enabled identification of contractility modulators in immortalized TM cells. The screening hits were translatable to primary TM cells and modulated outflow facility in an perfusion assay.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1089/jop.2019.0078DOI Listing
June 2020

A Survey of Antimicrobial Resistance Determinants in Category A Select Agents, Exempt Strains, and Near-Neighbor Species.

Int J Mol Sci 2020 Feb 29;21(5). Epub 2020 Feb 29.

US Naval Research Laboratory, Center for Biomolecular Science & Engineering, Washington, DC 20375, USA.

A dramatic increase in global antimicrobial resistance (AMR) has been well documented. Of particular concern is the dearth of information regarding the spectrum and prevalence of AMR within Category A Select Agents. Here, we performed a survey of horizontally and vertically transferred AMR determinants among Category A agents and their near neighbors. Microarrays provided broad spectrum screening of 127 spp., spp., and spp. strains for the presence/absence of 500+ AMR genes (or families of genes). Detecting a broad variety of AMR genes in each genus, microarray analysis also picked up the presence of an engineered plasmid in a strain. High resolution melt analysis (HRMA) was also used to assess the presence of quinolone resistance-associated mutations in 100 of these strains. Though HRMA was able to detect resistance-causing point mutations in strains, it was not capable of discriminating these point mutations from other nucleotide substitutions (e.g., arising from sequence differences in near neighbors). Though these technologies are well-established, to our knowledge, this is the largest survey of Category A agents and their near-neighbor species for genes covering multiple mechanisms of AMR.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/ijms21051669DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7084191PMC
February 2020

Artificial Neural Network-Based Automatic Detection of Food Intake for Neuromodulation in Treating Obesity and Diabetes.

Obes Surg 2020 Jul;30(7):2547-2557

Departments of Medicine and Biomedical Engineering, Johns Hopkins University, School of Medicine, Baltimore, MD, USA.

Purpose: Neuromodulation, such as vagal nerve stimulation and intestinal electrical stimulation, has been introduced for the treatment of obesity and diabetes. Ideally, neuromodulation should be applied automatically after food intake. The purpose of this study was to develop a method of automatic food intake detection through dynamic analysis of heart rate variability (HRV).

Materials And Methods: Two experiments were conducted: (1) a small sample series with a standard test meal and (2) a large sample series with varying meal size. Electrocardiograms (ECGs) were collected in the fasting and postprandial states. Each ECG was processed to compute the HRV. For each HRV segment, time- and frequency-domain features were derived and used as inputs to train and test an artificial neural network (ANN). The ANN was trained and tested with different cross-validation methods.

Results: The highest classification accuracy reached with leave-one-subject-out-leave-one-sample-out cross-validation was 0.93 in experiment 1 and 0.88 in experiment 2. Retraining the ANN on recordings of a subject drastically increased the achieved accuracy for that subject to values of 0.995 and 0.95 in experiments 1 and 2, respectively.

Conclusions: Automatic food intake detection by ANNs, using features from the HRV, is feasible and may have a great potential for neuromodulation-based treatments of meal-related disorders.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1007/s11695-020-04511-6DOI Listing
July 2020

A Phenotypic Screen Identifies Calcium Overload as a Key Mechanism of β-Cell Glucolipotoxicity.

Diabetes 2020 05 20;69(5):1032-1041. Epub 2020 Feb 20.

Novartis Institutes for BioMedical Research, Cambridge, MA

Type 2 diabetes (T2D) is caused by loss of pancreatic β-cell mass and failure of the remaining β-cells to deliver sufficient insulin to meet demand. β-Cell glucolipotoxicity (GLT), which refers to combined, deleterious effects of elevated glucose and fatty acid levels on β-cell function and survival, contributes to T2D-associated β-cell failure. Drugs and mechanisms that protect β-cells from GLT stress could potentially improve metabolic control in patients with T2D. In a phenotypic screen seeking low-molecular-weight compounds that protected β-cells from GLT, we identified compound A that selectively blocked GLT-induced apoptosis in rat insulinoma cells. Compound A and its optimized analogs also improved viability and function in primary rat and human islets under GLT. We discovered that compound A analogs decreased GLT-induced cytosolic calcium influx in islet cells, and all measured β-cell-protective effects correlated with this activity. Further studies revealed that the active compound from this series largely reversed GLT-induced global transcriptional changes. Our results suggest that taming cytosolic calcium overload in pancreatic islets can improve β-cell survival and function under GLT stress and thus could be an effective strategy for T2D treatment.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.2337/db19-0813DOI Listing
May 2020

The response of the melanized yeast Exophiala dermatitidis to gamma radiation exposure.

Environ Microbiol 2020 04 18;22(4):1310-1326. Epub 2020 Feb 18.

Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA.

The melanized yeast Exophiala dermatitidis is resistant to many environmental stresses and is used as a model for understanding the diverse roles of melanin in fungi. Here, we describe the extent of resistance of E. dermatitidis to acute γ-radiation exposure and the major mechanisms it uses to recover from this stress. We find that melanin does not protect E. dermatitidis from γ-radiation. Instead, environmental factors such as nutrient availability, culture age and culture density are much greater determinants of cell survival after exposure. We also observe a dramatic transcriptomic response to γ-radiation that mobilizes pathways involved in morphological development, protein degradation and DNA repair, and is unaffected by the presence of melanin. Together, these results suggest that the ability of E. dermatitidis to survive γ-radiation exposure is determined by the prior and the current metabolic state of the cells as well as DNA repair mechanisms, and that small changes in these conditions can lead to large effects in radiation resistance, which should be taken into account when understanding how diverse fungi recover from this unique stress.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1111/1462-2920.14936DOI Listing
April 2020

Survival advantage of chemoradiotherapy in anaplastic thyroid carcinoma: Propensity score matched analysis with multiple subgroups.

Head Neck 2020 04 16;42(4):678-687. Epub 2019 Dec 16.

Department of Radiation Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia.

Background: We compared overall survival (OS) between radiation therapy (RT) and chemoradiotherapy (CRT) in patients with anaplastic thyroid carcinoma (ATC) using a large database.

Methods: The National Cancer Data Base was queried for ATC patients diagnosed between 2004 and 2013 who received RT or CRT. Groups were balanced by propensity score matching (PSM) on nine relevant variables. OS was also examined in five paired subgroups given known patient heterogeneity.

Results: Of 858 total patients, 575 received CRT and 283 received RT. CRT was associated with decreased risk of death (hazard ratio [HR] 0.66, P < .001), 1-year OS 25.5% vs 14.3%. A survival advantage to CRT was seen using PSM cohorts (HR 0.75, P = .006). Those receiving definitive surgery saw the greatest benefit to CRT over RT (HR 0.65, P = .009), 1-year OS 39.6% vs 20.4%.

Conclusions: CRT is associated with decreased risk of death in ATC; the magnitude of CRT vs RT benefit varied by subgroup.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/hed.26042DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7082181PMC
April 2020

Melanin Produced by the Fast-Growing Marine Bacterium Vibrio natriegens through Heterologous Biosynthesis: Characterization and Application.

Appl Environ Microbiol 2020 02 18;86(5). Epub 2020 Feb 18.

Center for Biomolecular Science and Engineering, Naval Research Laboratory, Washington, DC, USA

Melanin is a pigment produced by organisms throughout all domains of life. Due to its unique physicochemical properties, biocompatibility, and biostability, there has been an increasing interest in the use of melanin for broad applications. In the vast majority of studies, melanin has been either chemically synthesized or isolated from animals, which has restricted its use to small-scale applications. Using bacteria as biocatalysts is a promising and economical alternative for the large-scale production of biomaterials. In this study, we engineered the marine bacterium , one of the fastest-growing organisms, to synthesize melanin by expressing a heterologous tyrosinase gene and demonstrated that melanin production was much faster than in previously reported heterologous systems. The melanin of was characterized as a polymer derived from dihydroxyindole-2-carboxylic acid (DHICA) and, similarly to synthetic melanin, exhibited several characteristic and useful features. Electron microscopy analysis demonstrated that melanin produced from formed nanoparticles that were assembled as "melanin ghost" structures, and the photoprotective properties of these particles were validated by their protection of cells from UV irradiation. Using a novel electrochemical reverse engineering method, we observed that melanization conferred redox activity to Moreover, melanized bacteria were able to quickly adsorb the organic compound trinitrotoluene (TNT). Overall, the genetic tractability, rapid division time, and ease of culture provide a set of attractive properties that compare favorably to current production strains and warrant the further development of this chassis as a microbial factory for natural product biosynthesis. Melanins are macromolecules that are ubiquitous in nature and impart a large variety of biological functions, including structure, coloration, radiation resistance, free radical scavenging, and thermoregulation. Currently, in the majority of investigations, melanins are either chemically synthesized or extracted from animals, which presents significant challenges for large-scale production. Bacteria have been used as biocatalysts to synthesize a variety of biomaterials due to their fast growth and amenability to genetic engineering using synthetic biology tools. In this study, we engineered the extremely fast-growing bacterium to synthesize melanin nanoparticles by expressing a heterologous tyrosinase gene with inducible promoters. Characterization of the melanin produced from -produced tyrosinase revealed that it exhibited physical and chemical properties similar to those of natural and chemically synthesized melanins, including nanoparticle structure, protection against UV damage, and adsorption of toxic compounds. We anticipate that producing and controlling melanin structures at the nanoscale in this bacterial system with synthetic biology tools will enable the design and rapid production of novel biomaterials for multiple applications.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1128/AEM.02749-19DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7028964PMC
February 2020

Histopathology Feature Mining and Association with Hyperspectral Imaging for the Detection of Squamous Neoplasia.

Sci Rep 2019 11 28;9(1):17863. Epub 2019 Nov 28.

Department of Biomedical Engineering, Emory University and Georgia Institute of Technology, Atlanta, GA, USA.

Hyperspectral imaging (HSI) is a noninvasive optical modality that holds promise for early detection of tongue lesions. Spectral signatures generated by HSI contain important diagnostic information that can be used to predict the disease status of the examined biological tissue. However, the underlying pathophysiology for the spectral difference between normal and neoplastic tissue is not well understood. Here, we propose to leverage digital pathology and predictive modeling to select the most discriminative features from digitized histological images to differentiate tongue neoplasia from normal tissue, and then correlate these discriminative pathological features with corresponding spectral signatures of the neoplasia. We demonstrated the association between the histological features quantifying the architectural features of neoplasia on a microscopic scale, with the spectral signature of the corresponding tissue measured by HSI on a macroscopic level. This study may provide insight into the pathophysiology underlying the hyperspectral dataset.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-54139-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6882850PMC
November 2019

Protein-Protein Interactions, Clustering, and Rheology for Bovine IgG up to High Concentrations Characterized by Small Angle X-Ray Scattering and Molecular Dynamics Simulations.

J Pharm Sci 2020 01 11;109(1):696-708. Epub 2019 Nov 11.

McKetta Department of Chemical Engineering, The University of Texas at Austin, Austin, Texas 78712. Electronic address:

A systematic understanding of intermolecular interactions is necessary for designing concentrated monoclonal and polyclonal antibody solutions with reduced viscosity and enhanced stability. Here, we determine the effects of pH and cosolute on the strength and geometry of short-range anisotropic protein-protein attractions for a polyclonal bovine IgG by comparing intensities [I(q)] obtained from small-angle X-ray scattering to those computed in molecular dynamics simulations with 12-bead models. As our model embodies key features of the protein shape, it can describe the experimental I(q) for solutions of 10-200 mg/mL protein with only a small (<1 kT) variation in the model's well depth. At high concentration, small changes in the interaction potential produce large increases in clustering given the close interprotein spacing. Reducing the pH below the pI or adding NaCl weakens short-range anisotropic attractions but not enough to remove large reversible oligomers that raise viscosity. In contrast, for arginine added at pH 5.5, a uniform attraction model is sufficient to describe the I(q) that plateaus at low q. With primarily monomers and dimers, the viscosity is reduced relative to the other systems that have larger clusters as described with a model that includes the cluster size distribution.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.xphs.2019.11.001DOI Listing
January 2020

Head and Neck Cancer Detection in Digitized Whole-Slide Histology Using Convolutional Neural Networks.

Sci Rep 2019 10 1;9(1):14043. Epub 2019 Oct 1.

Department of Bioengineering, University of Texas at Dallas, Richardson, TX, USA.

Primary management for head and neck cancers, including squamous cell carcinoma (SCC), involves surgical resection with negative cancer margins. Pathologists guide surgeons during these operations by detecting cancer in histology slides made from the excised tissue. In this study, 381 digitized, histological whole-slide images (WSI) from 156 patients with head and neck cancer were used to train, validate, and test an inception-v4 convolutional neural network. The proposed method is able to detect and localize primary head and neck SCC on WSI with an AUC of 0.916 for patients in the SCC testing group and 0.954 for patients in the thyroid carcinoma testing group. Moreover, the proposed method is able to diagnose WSI with cancer versus normal slides with an AUC of 0.944 and 0.995 for the SCC and thyroid carcinoma testing groups, respectively. For comparison, we tested the proposed, diagnostic method on an open-source dataset of WSI from sentinel lymph nodes with breast cancer metastases, CAMELYON 2016, to obtain patch-based cancer localization and slide-level cancer diagnoses. The experimental design yields a robust method with potential to help create a tool to increase efficiency and accuracy of pathologists detecting head and neck cancers in histological images.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1038/s41598-019-50313-xDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6773771PMC
October 2019

Hyperspectral Imaging of Head and Neck Squamous Cell Carcinoma for Cancer Margin Detection in Surgical Specimens from 102 Patients Using Deep Learning.

Cancers (Basel) 2019 Sep 14;11(9). Epub 2019 Sep 14.

Department of Bioengineering, The University of Texas at Dallas, Richardson, TX 75080, USA.

Surgical resection of head and neck (H and N) squamous cell carcinoma (SCC) may yield inadequate surgical cancer margins in 10 to 20% of cases. This study investigates the performance of label-free, reflectance-based hyperspectral imaging (HSI) and autofluorescence imaging for SCC detection at the cancer margin in excised tissue specimens from 102 patients and uses fluorescent dyes for comparison. Fresh surgical specimens ( = 293) were collected during H and N SCC resections ( = 102). The tissue specimens were imaged with reflectance-based HSI and autofluorescence imaging and afterwards with two fluorescent dyes for comparison. A histopathological ground truth was made. Deep learning tools were developed to detect SCC with new patient samples (inter-patient) and machine learning for intra-patient tissue samples. Area under the curve (AUC) of the receiver-operator characteristic was used as the main evaluation metric. Additionally, the performance was estimated in mm increments circumferentially from the tumor-normal margin. In intra-patient experiments, HSI classified conventional SCC with an AUC of 0.82 up to 3 mm from the cancer margin, which was more accurate than proflavin dye and autofluorescence (both < 0.05). Intra-patient autofluorescence imaging detected human papilloma virus positive (HPV+) SCC with an AUC of 0.99 at 3 mm and greater accuracy than proflavin dye ( < 0.05). The inter-patient results showed that reflectance-based HSI and autofluorescence imaging outperformed proflavin dye and standard red, green, and blue (RGB) images ( < 0.05). In new patients, HSI detected conventional SCC in the larynx, oropharynx, and nasal cavity with 0.85-0.95 AUC score, and autofluorescence imaging detected HPV+ SCC in tonsillar tissue with 0.91 AUC score. This study demonstrates that label-free, reflectance-based HSI and autofluorescence imaging methods can accurately detect the cancer margin in ex-vivo specimens within minutes. This non-ionizing optical imaging modality could aid surgeons and reduce inadequate surgical margins during SCC resections.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/cancers11091367DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769839PMC
September 2019

Hyperspectral imaging for head and neck cancer detection: specular glare and variance of the tumor margin in surgical specimens.

J Med Imaging (Bellingham) 2019 Jul 14;6(3):035004. Epub 2019 Sep 14.

University of Texas at Dallas, Department of Bioengineering, Dallas, Texas, United States.

Head and neck squamous cell carcinoma (SCC) is primarily managed by surgical cancer resection. Recurrence rates after surgery can be as high as 55%, if residual cancer is present. Hyperspectral imaging (HSI) is evaluated for detection of SCC in surgical specimens. Several machine learning methods are investigated, including convolutional neural networks (CNNs) and a spectral-spatial classification framework based on support vector machines. Quantitative results demonstrate that additional data preprocessing and unsupervised segmentation can improve CNN results to achieve optimal performance. The methods are trained in two paradigms, with and without specular glare. Classifying regions that include specular glare degrade the overall results, but the combination of the CNN probability maps and unsupervised segmentation using a majority voting method produces an area under the curve value of 0.81 [0.80, 0.83]. As the wavelengths of light used in HSI can penetrate different depths into biological tissue, cancer margins may change with depth and create uncertainty in the ground truth. Through serial histological sectioning, the variance in the cancer margin with depth is investigated and paired with qualitative classification heat maps using the methods proposed for the testing group of SCC patients. The results determined that the validity of the top section alone as the ground truth may be limited to 1 to 2 mm. The study of specular glare and margin variation provided better understanding of the potential of HSI for the use in the operating room.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1117/1.JMI.6.3.035004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6744927PMC
July 2019

Redirecting, Without Dampening, the Enthusiasm of Surgeons.

Authors:
Amy Y Chen

JAMA Otolaryngol Head Neck Surg 2019 Aug 29. Epub 2019 Aug 29.

Emory University, Atlanta, Georgia.

View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1001/jamaoto.2019.2404DOI Listing
August 2019

Preclinical Efficacy and Safety Comparison of CD3 Bispecific and ADC Modalities Targeting BCMA for the Treatment of Multiple Myeloma.

Mol Cancer Ther 2019 11 21;18(11):2008-2020. Epub 2019 Aug 21.

Allogene Therapeutics, Research, South San Francisco, California.

The restricted expression pattern of B-cell maturation antigen (BCMA) makes it an ideal tumor-associated antigen (TAA) for the treatment of myeloma. BCMA has been targeted by both CD3 bispecific antibody and antibody-drug conjugate (ADC) modalities, but a true comparison of modalities has yet to be performed. Here we utilized a single BCMA antibody to develop and characterize both a CD3 bispecific and 2 ADC formats (cleavable and noncleavable) and compared activity both and with the aim of generating an optimal therapeutic. Antibody affinity, but not epitope was influential in drug activity and hence a high-affinity BCMA antibody was selected. Both the bispecific and ADCs were potent and , causing dose-dependent cell killing of myeloma cell lines and tumor regression in orthotopic myeloma xenograft models. Primary patient cells were effectively lysed by both CD3 bispecific and ADCs, with the bispecific demonstrating improved potency, maximal cell killing, and consistency across patients. Safety was evaluated in cynomolgus monkey toxicity studies and both modalities were active based on on-target elimination of B lineage cells. Distinct nonclinical toxicity profiles were seen for the bispecific and ADC modalities. When taken together, results from this comparison of BCMA CD3 bispecific and ADC modalities suggest better efficacy and an improved toxicity profile might be achieved with the bispecific modality. This led to the advancement of a bispecific candidate into phase I clinical trials.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1158/1535-7163.MCT-19-0007DOI Listing
November 2019

Aging and the treatment of basal cell carcinoma.

Clin Dermatol 2019 Jul - Aug;37(4):373-378. Epub 2019 Jun 16.

Stanford University School of Medicine, Stanford, California, USA. Electronic address:

Basal cell carcinoma (BCC) is the most commonly diagnosed type of skin cancer. BCCs are especially prevalent in the elderly population, given their association with cumulative sun exposure and other risk factors. In this contribution, we outline geriatric concepts related to the care of older adults with BCCs. We describe how a patient's life expectancy can be estimated and combined with tumor characteristics to determine lag time to benefit, a concept to better understand whether patients will experience the efficacy of a treatment within their life span. We also review the possibility of current BCC overdiagnosis and summarize the effectiveness, benefits, and risks of common treatments for BCCs, noting that all treatment modalities have special considerations when administered to older adults. In particular, nonsurgical treatments might be preferable for older adults with a limited life expectancy. Ultimately, we argue that the decision of whether and how to treat a BCC should be the result of shared decision-making between the provider and the patient and take into account not only tumor characteristics, but also patient values and preferences.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.clindermatol.2019.06.004DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6952217PMC
January 2020