Engineering Papers⌕ Search

SEARCH · Engineering Papers

Results for “Cancer”

Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 1,405 records · Page 78
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Dose Summation Strategies for External Beam Radiation Therapy and Brachytherapy in Gynecologic Malignancy: A Review from the NRG Oncology and NCTN Medical Physics Subcommittees

Definitive, nonsurgical management of gynecologic malignancies involves external beam radiation therapy (EBRT) and/or brachytherapy (BT). Summation of the cumulative dose is critical to assess the total biologic effective dose to targets and organs at risk. Cumulative dose calculation from EBRT and BT can be performed with or without image registration (IR) and biologic dose summation. Among these dose summation strategies, linear addition of dose-volume histogram (DVH) parameters without IR is the global standard for composite dose reporting. This approach stems from an era without image guidance and simple external beam and brachytherapy treatment approaches. With technological advances, EBRT and high-dose-rate BT have evolved to allow for volume-based treatment planning and delivery. Modern conformal therapeutic radiation involves volumetric or intensity modulated EBRT, capable of simultaneously treating multiple targets at different specified dose levels. Therefore, given the complexity of modern radiation treatment, the linear addition of DVH parameters from EBRT and high-dose-rate BT is challenging to represent the combined dose distribution. Deformable image registration (DIR) between EBRT and image guided brachytherapy (IGBT) data sets may provide a more nuanced calculation of multimodal dose accumulation. However, DIR is still nascent in this regard, and needs further development for accuracy and efficiency for clinical use. Biologic dose summation can combine physical dose maps from EBRT and each IGBT fraction, thereby generating a composite DVH from the biologic effective dose. However, accurate radiobiologic parameters are tissue-dependent and not well characterized. A combination of voxel-based DIR and biologic weighted dose maps may be the best approximation of dose accumulation but remains invalidated. The purpose of this report is to review dose summation strategies for EBRT and BT, including conventional equivalent dose in 2-Gy fractions dose summation without image registration, physical dose summation using 3-dimensional rigid IR and DIR, and biologic dose summation. We also provide general clinical workflows for IGBT with a focus on cervical cancer.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Radiation Therapy Enhanced by NBTXR3 Nanoparticles Overcomes Anti-PD1 Resistance and Evokes Abscopal Effects

Radiation combined with PD1 blockade offers significant treatment benefits in several tumor types; however, anti-PD1 resistance precludes such benefits in many cases. Here we attempted to overcome anti-PD1 resistance by combining localized radiation with a radioenhancing nanoparticle (NBTXR3) and systemic anti-PD1 treatment to achieve abscopal effects in an anti-PD1–resistant mouse model of lung cancer.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

The Influence of Severe Radiation-Induced Lymphopenia on Overall Survival in Solid Tumors: A Systematic Review and Meta-Analysis

Emerging evidence suggests a detrimental prognostic association between radiation-induced lymphopenia (RIL) and pathologic response, progression-free survival, and overall survival (OS) in patients who undergo radiation therapy for cancer. The aim of this study was to systematically review and meta-analyze the prognostic impact of RIL on OS in patients with solid tumors.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

High-Content Clonogenic Survival Screen to Identify Chemoradiation Sensitizers

The combination of cytotoxic chemotherapy with radiation therapy (CRT) has resulted in significant improvements in clinical outcomes for patients with many locally advanced unresectable cancers. Only a small proportion of patients achieve pathologic complete responses to CRT; combination of CRT with targeted agents offers the promise of further improving treatment responses. However, numerous clinical trials have failed to show an improvement in clinical outcomes with the addition of targeted agents. To increase the accessibility of our screening method and accelerate the pace at which novel combinations with CRT are identified and incorporated into standard practices for treatments, we report details on screening method optimization, data generation, and downstream data analysis.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Prospective Clinical Investigation of the Efficacy of Combination Radiation Therapy With Immune Checkpoint Inhibition

Immune checkpoint inhibitors (ICIs) lead to durable responses in a subset of patients with cancer, but most patients do not respond to ICI, prompting interest in combining immunotherapy with other therapeutic regimens. Preclinical evidence supports the potential for therapeutic synergy between immunotherapy and radiation therapy through modulation of the tumor microenvironment and antitumor immune responses. Local therapy also has the potential to overcome localized sites of relative immune suppression and resistance. Prospective clinical trials have been initiated to test these hypotheses in the clinic as well as to investigate the toxicities and adverse events associated with combination immunotherapy and radiation therapy. In this review, we discuss the emerging results from prospective clinical trials of combination immunotherapy and radiation therapy, the safety and efficacy of their combination, concordance with preclinical and retrospective data, and some of the remaining open questions to be addressed by future clinical trials.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Moving Beyond the Standard of Care: Accelerate Testing of Radiation-Drug Combinations

Radiation therapy is a major treatment modality used in > 60% of cancer patients as definitive local treatment for inoperable locoregionally confined tumors and as palliative therapy. Although cytotoxic chemotherapy enhances the effectiveness of treatment, the benefit over radiation therapy alone is modest. There is a need to enhance the effectiveness of local tumor control over what sequentially or concurrently administered cytotoxic chemotherapy provides. Although many biological pathways are known to enhance the effectiveness of radiation therapy, there is currently a paucity of drugs approved for use in combination. Several clinical trials have tested the effectiveness of combining targeted agents or immunotherapies with radiation therapy, but the results of these trials have been negative, likely stemming from the relative lack of preclinical evidence using appropriate experimental standardization or model systems. Accelerating the identification of agents tested in an appropriate clinical context and experimental systems or models would greatly enhance the potential to bring forward early testing of drugs that would not only be safe but also more effective. This article provides an overview of the opportunities and challenges of developing therapeutics to combine with radiation therapy, and some guidance toward preclinical and early clinical testing to improve the chance that advanced phase testing of drug-radiation combinations would be successful in the long term.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Results of a Multi-institutional Phase 2 Clinical Trial for 4DCT-ventilation Functional Avoidance Thoracic Radiation Therapy

Radiation pneumonitis remains a major limitation in the radiation therapy treatment of patients with lung cancer. Functional avoidance radiation therapy uses functional imaging to reduce pulmonary toxic effects by designing radiation therapy plans that reduce doses to functional regions of the lung. Lung functional imaging has been developed that uses 4-dimensional computed tomography (4DCT) imaging to calculate 4DCT-based lung ventilation (4DCT-ventilation). A phase 2 multicenter study was initiated to evaluate 4DCT-ventilation functional avoidance radiation therapy. The study hypothesis was that functional avoidance radiation therapy could reduce the rate of grade ≥2 radiation pneumonitis to 12% compared with a 25% historical rate, with the trial being positive if ≤16.4% of patients experienced grade ≥2 pneumonitis.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Proton Therapy in Supradiaphragmatic Lymphoma: Predicting Treatment-Related Mortality to Help Optimize Patient Selection

In some patients with Hodgkin lymphoma (HL), proton beam therapy (PBT) may reduce the risk of radiation-related cardiovascular disease (CVD) and second cancers (SC) compared with photon radiation therapy (RT). Our aim was to identify patients who benefit the most from PBT in terms of predicted 30-year absolute mortality risks (AMR{sub 30}) from CVD and SC, taking into account individual background, chemotherapy, radiation, and smoking-related risks.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2022

Randomized Phase 3, Double-blind, Placebo-controlled Study of Prophylactic Gabapentin for the Reduction of Oral Mucositis Pain During the Treatment of Oropharyngeal Squamous Cell Carcinoma

The purpose of this paper is to determine whether prophylactic gabapentin usage in patients undergoing definitive concurrent chemotherapy and radiation therapy (chemoRT) for oropharyngeal cancer (OPC) improves treatment-related oral mucositis pain, opioid use, and feeding tube (FT) placement.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2024

Predicting transcription factor activity using prior biological information

Dysregulation of normal transcription factor activity is a common driver of disease. Therefore, the detection of aberrant transcription factor activity is important to understand disease pathogenesis. We have developed Priori, a method to predict transcription factor activity from RNA sequencing data. Priori has two key advantages over existing methods. First, Priori utilizes literature-supported regulatory information to identify transcription factor-target gene relationships. It then applies linear models to determine the impact of transcription factor regulation on the expression of its target genes. Second, results from a third-party benchmarking pipeline reveals that Priori detects aberrant activity from 124 single-gene perturbation experiments with higher sensitivity and specificity than 11 other methods. We applied Priori and other top-performing methods to predict transcription factor activity from two large primary patient datasets. Our work demonstrates that Priori uniquely discovered significant determinants of survival in breast cancer and identified mediators of drug response in leukemia.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Structural delineation and phase-dependent activation of the costimulatory CD27:CD70 complex

CD27 is a tumor necrosis factor (TNF) receptor, which stimulates lymphocytes and promotes their differentiation upon activation by TNF ligand CD70. Activation of the CD27 receptor provides a costimulatory signal to promote T cell, B cell, and NK cell activity to facilitate antitumor and anti-infection immunity. Aberrant increased and focused expression of CD70 on many tumor cells renders CD70 an attractive therapeutic target for direct tumor killing. However, despite their use as drug targets to treat cancers, the molecular basis and atomic details of CD27 and CD70 interaction remain elusive. Here we report the crystal structure of human CD27 in complex with human CD70. Analysis of our structure shows that CD70 adopts a classical TNF ligand homotrimeric assembly to engage CD27 receptors in a 3:3 stoichiometry. By combining structural and rational mutagenesis data with reported disease-correlated mutations, we identified the key amino acid residues of CD27 and CD70 that control this interaction. We also report increased potency for plate-bound CD70 constructs compared with solution-phase ligand in a functional activity to stimulate T-cells in vitro. These findings offer new mechanistic insight into this critical costimulatory interaction.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2025

DOME: Directional medical embedding vectors from Electronic Health Records

Motivation: The increasing availability of Electronic Health Record (EHR) systems has created enormous potential for translational research. Recent developments in representation learning techniques have led to effective large-scale representations of EHR concepts along with knowledge graphs that empower downstream EHR studies. However, most existing methods require training with patient-level data, limiting their abilities to expand the training with multi-institutional EHR data. On the other hand, scalable approaches that only require summary-level data do not incorporate temporal dependencies between concepts. Methods: We introduce a DirectiOnal Medical Embedding (DOME) algorithm to encode temporally directional relationships between medical concepts, using summary-level EHR data. Specifically, DOME first aggregates patient-level EHR data into an asymmetric co-occurrence matrix. Then it computes two Positive Pointwise Mutual Information (PPMI) matrices to correspondingly encode the pairwise prior and posterior dependencies between medical concepts. Following that, a joint matrix factorization is performed on the two PPMI matrices, which results in three vectors for each concept: a semantic embedding and two directional context embeddings. They collectively provide a comprehensive depiction of the temporal relationship between EHR concepts. Results: We highlight the advantages and translational potential of DOME through three sets of validation studies. First, DOME consistently improves existing direction-agnostic embedding vectors for disease risk prediction in several diseases, for example achieving a relative gain of 5.5% in the area under the receiver operating characteristic (AUROC) for lung cancer. Second, DOME excels in directional drug-disease relationship inference by successfully differentiating between drug side effects and indications, correspondingly achieving relative AUROC gain over the state-of-the-art methods by 10.8% and 6.6%. Finally, DOME effectively constructs directional knowledge graphs, which distinguish disease risk factors from comorbidities, thereby revealing disease progression trajectories. The source codes are provided at https://github.com/celehs/Directional-EHRembedding.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2021

Conformational Changes of RORγ During Response Element Recognition and Coregulator Engagement

The retinoic acid receptor-related orphan receptor γ (RORγ) is a ligand-dependent transcription factor of the nuclear receptor super family that underpins metabolic activity, immune function, and cancer progression. Despite being a valuable drug target in health and disease, our understanding of the ligand-dependent activities of RORγ is far from complete. Like most nuclear receptors, RORγ must recruit coregulatory protein to enact the RORγ target gene program. To date, a majority of structural studies have been focused exclusively on the RORγ ligand-binding domain and the ligand-dependent recruitment of small peptide segments of coregulators. Herein, we examine the ligand-dependent assembly of full length RORγ:coregulator complexes on cognate DNA response elements using structural proteomics and small angle x-ray scattering. The results from our studies suggest that RORγ becomes elongated upon DNA recognition, preventing long range interdomain crosstalk. We also determined that the DNA binding domain adopts a sequence-specific conformation, and that coregulatory protein may be able to ‘sense’ the ligand- and DNA-bound status of RORγ. We propose a model where ligand-dependent coregulator recruitment may be influenced by the sequence of the DNA to which RORγ is bound. Overall, the efforts described herein will illuminate important aspects of full length RORγ and monomeric orphan nuclear receptor target gene regulation through DNA-dependent conformational changes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2023

Monobody Inhibitor Selective to the Phosphatase Domain of SHP2 and its Use as a Probe for Quantifying SHP2 Allosteric Regulation

SHP2 is a phosphatase/adaptor protein that plays an important role in various signaling pathways. Its mutations are associated with cancers and developmental diseases. SHP2 contains a protein tyrosine phosphatase (PTP) and two SH2 domains. Selective inhibition of these domains has been challenging due to the multitude of homologous proteins in the proteome. Here, we developed a monobody, synthetic binding protein, that bound to and inhibited the SHP2 PTP domain. It was selective to SHP2 PTP over close homologs. A crystal structure of the monobody-PTP complex revealed that the monobody bound both highly conserved residues in the active site and less conserved residues in the periphery, rationalizing its high selectivity. Its epitope overlapped with the interface between the PTP and N-terminal SH2 domains that is formed in auto-inhibited SHP2. By using the monobody as a probe for the accessibility of the PTP active site, we developed a simple, nonenzymatic assay for the allosteric regulation of SHP2. The assay showed that, in the absence of an activating phospho-Tyr ligand, wild-type SHP2 and the “PTP-dead” C459E mutant were predominantly in the closed state in which the PTP active site is inaccessible, whereas the E76K and C459S mutants were in the open, active state. It also revealed that previously developed monobodies to the SH2 domains, ligands lacking a phospho-Tyr, weakly favored the open state. These results provide corroboration for a conformational equilibrium underlying allosteric regulation of SHP2, provide powerful tools for characterizing and controlling SHP2 functions, and inform drug discovery against SHP2.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Design of a bifunctional TEMPO-tertiary amine mesoporous silica catalyst for the three-step cascade synthesis of a chromene derivative

A key challenge is design of materials and processes whereby competing reagents or conditions do not harm the multi-step sequence, thus allowing for more efficient chemical synthesis with elimination of work-up and separation steps. In this work, a three-step reaction cascade is performed using a porous bifunctional dimethylpropylamine-TEMPO-MCM41 catalyst, converting the commodity chemicals benzyl alcohol, sodium hypochlorite, and malononitrile to a biologically active anti-cancer, and anti-malarial 2-amino-chromene derivative. The cascade first utilizes a TEMPO-catalyzed oxidation of benzyl alcohol to benzaldehyde with NaOCl as the terminal oxidant. This is followed by a two-step, dual base catalyzed Knoevenagel condensation with malononitrile followed by a Michael addition with lawsone. Optimal conditions converting benzyl alcohol to 2-amino-5,10-dioxo-4-phenyl-5,10-dihydro-4H-benzo[g]chromene-3-carbonitrile include the delayed addition of malononitrile and lawsone during the three-step reaction sequence, which results in a 2-amino-chromene yield of over 80%. The importance of stepwise reagent addition is rationalized due to the unfavorable adsorption of acidic lawsone on the surface-grafted base catalyst. Tertiary Brønsted base sites of dimethylpropylamine outperform the more Lewis basic primary propylamine functionalized catalyst. This work outlines a simple and effective method for generating mesoporous materials with two types of active sites via co-condensation and thiol-ene coupling procedures.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Deep-Learning-Derived Evaluation Metrics Enable Effective Benchmarking of Computational Tools for Phosphopeptide Identification

Tandem mass spectrometry (MS/MS)-based phosphoproteomics is a powerful technology for global phosphorylation analysis. However, applying four computational pipelines to a typical mass spectrometry (MS)-based phosphoproteomic dataset from a human cancer study, we observed a large discrepancy among the reported phosphopeptide identification and phosphosite localization results, underscoring a critical need for benchmarking. While efforts have been made to compare performance of computational pipelines using data from synthetic phosphopeptides, evaluations involving real application data have been largely limited to comparing the numbers of phosphopeptide identifications due to the lack of appropriate evaluation metrics. We investigated three deep learning-derived features as potential evaluation metrics: phosphosite probability, Delta RT and spectral similarity. Predicted phosphosite probability is computed by MusiteDeep, which provides high accuracy as previously reported; Delta RT is defined as the absolute retention time (RT) difference between RTs observed and predicted by AutoRT; and spectral similarity is defined as the Pearson’s correlation coefficient between spectra observed and predicted by pDeep2. Using a synthetic peptide dataset, we found that both Delta RT and spectral similarity provided excellent discrimination between correct and incorrect peptide-spectrum matches (PSMs) both when incorrect PSMs involved wrong peptide sequences and even when incorrect PSMs were caused by only incorrect phosphosite localization. Based on these results, we used all the three deep learning-derived features as evaluation metrics to compare different computational pipelines on diverse set of phosphoproteomic datasets and showed their utility in benchmarking performance of the pipelines. The benchmark metrics demonstrated in this study will enable users to select computational pipelines and parameters for routine analysis of phosphoproteomics data and will offer guidance for developers to improve computational methods.

59 BASIC BIOLOGICAL SCIENCES↗