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At least 1,063 records · Page 59
All sourcesNASA NTRSDOE OSTI
DOE OSTI2019

Deep learning and radiomics: the utility of Google TensorFlow™ Inception in classifying clear cell renal cell carcinoma and oncocytoma on multiphasic CT

Purpose: Currently, all solid enhancing renal masses without microscopic fat are considered malignant until proven otherwise and there is substantial overlap in the imaging findings of benign and malignant renal masses, particularly between clear cell RCC (ccRCC) and benign oncocytoma (ONC). Radiomics has attracted increased attention for its utility in pre-operative work-up on routine clinical images. Radiomics based approaches have converted medical images into mineable data and identified prognostic imaging signatures that machine learning algorithms can use to construct predictive models by learning the decision boundaries of the underlying data distribution. The TensorFlow™ framework from Google is a state-of-the-art open-source software library that can be used for training deep learning neural networks for performing machine learning tasks. The purpose of this study was to investigate the diagnostic value and feasibility of a deep learning-based renal lesion classifier using open-source Google TensorFlow™ Inception in differentiating ccRCC from ONC on routine four-phase MDCT in patients with pathologically confirmed renal masses. Methods: With institutional review board approval for this 1996 Health Insurance Portability and Accountability Act compliant retrospective study and a waiver of informed consent, we queried our institution’s pathology, clinical, and radiology databases for histologically proven cases of ccRCC and ONC obtained between January 2000 and January 2016 scanned with a an intravenous contrast-enhanced four-phase renal mass protocol (unenhanced (UN), corticomedullary (CM), nephrographic (NP), and excretory (EX) phases). To extract features to be used for the machine learning model, the entire renal mass was contoured in the axial plane in each of the four phases, resulting in a 3D volume of interest (VOI) representative of the entire renal mass. We investigated thirteen different approaches to convert the acquired VOI data into a set of images that adequately represented each tumor which was used to train the final layer of the neural network model. Training was performed over 4000 iterations. In each iteration, 90% of the data were designated as training data and the remaining 10% served as validation data and a leave-one-out cross-validation scheme was implemented. Accuracy, sensitivity, specificity, positive (PPV) and negative predictive (NPV) values, and CIs were calculated for the classification of the thirteen processing modes. Results: We analyzed 179 consecutive patients with 179 lesions (128 ccRCC and 51 ONC). The ccRCC cohort had a mean size of 3.8 cm (range 0.8–14.6 cm) and the ONC cohort had a mean lesion size of 3.9 cm (range 1.0–13.1 cm). The highest specificity and PPV (52.9% and 80.3%, respectively) were achieved in the EX phase when we analyzed the single mid-slice of the tumor in the axial, coronal and sagittal plane, and when we increased the number of mid-slices of the tumor to three, with an accuracy of 75.4%, which also increased the sensitivity to 88.3% and the PPV to 79.6%. Using the entire tumor volume also showed that classification performance was best in the EX phase with an accuracy of 74.4%, a sensitivity of 85.8% and a PPV of 80.1%. When the entire tumor volume, plus mid-slices from all phases and all planes presented as tiled images, were submitted to the final layer of the neural network we achieved a PPV of 82.5%. Conclusions: The best classification result was obtained in the EX phase among the thirteen classification methods tested. Our proof of concept study is the first step towards understanding the utility of machine learning in the differentiation of ccRCC from ONC on routine CT images. We hope this could lead to future investigation into the development of a multivariate machine learning model which may augment our ability to accurately predict renal lesion histology on imaging.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Can MRI be used to diagnose histologic grade in T1a (< 4 cm) clear cell renal cell carcinomas?

Objective: To assess whether MRI can differentiate low-grade from high-grade T1a cc-RCC. Materials and methods: With IRB approval, 49 consecutive solid < 4 cm cc-RCC (low grade [Grade 1 or 2] N = 38, high grade [Grade 3] N = 11) with pre-operative MRI before nephrectomy were identified between 2013 and 2018. Tumor size, apparent diffusion coefficient (ADC) histogram analysis, enhancement wash-in and wash-out rates, and chemical shift signal intensity index (SI index) were assessed by a blinded radiologist. Subjectively, two blinded Radiologists also assessed for (1) microscopic fat, (2) homogeneity (5-point Likert scale), and (3) ADC signal (relative to renal cortex); discrepancies were resolved by consensus. Outcomes were studied using Chi square, multivariate analysis, logistic regression modeling, and ROC. Inter-observer agreement was assessed using Cohen’s kappa. Results: Tumor size was 24 ± 7 (13–39) mm with no association to grade (p = 0.45). Among quantitative features studied, corticomedullary phase wash-in index (p = 0.015), SI index (p = 0.137), and tenth-centile ADC (p = 0.049) were higher in low-grade tumors. 36.8% (14/38) low-grade tumors versus zero high-grade tumors demonstrated microscopic fat (p = 0.015; Kappa = 0.67). Microscopic fat was specific for low-grade disease (100.0% [71.5–100.0]) with low sensitivity (36.8% [21.8–54.6]). Other subjective features did not differ between groups (p > 0.05). A logistic regression model combining microscopic fat + wash-in index + tenth-centile-ADC yielded area under ROC curve 0.98 (Confidence Intervals 0.94–1.0) with sensitivity/specificity 87.5%/100%. Conclusion: The combination of microscopic fat, higher corticomedullary phase wash-in and higher tenth-centile ADC is highly accurate for diagnosis of low-grade disease among T1a clear cell RCC.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2019

Deficiency of mismatch repair genes is less frequently observed in signet ring cell compared with non-signet ring cell gastric cancer

Signet ring cell (SRC) gastric cancer at advanced stage has poor prognosis. While a recent study reported nearly one-third of SRC cases contain tumors with deficient mismatch repair (MMR) genes, other studies in SRC have been inconclusive. To re-analyze the results, we performed immunohistochemical staining of MLH1, MSH2, MSH6 and PMS2 proteins in 38 SRC gastric tumors compared with 109 non-SRC (NSRC) tumors from 94 patients. In contrast to the previous study, all SRC gastric tumors normally expressed MMR proteins, whereas 22 of 109 of NSRC (20%) showed deficient MMR proteins. To reinforce our results, we referred to the Cancer Genome Atlas (TCGA) genomic database and found that only 6 (6%) of 99 samples with diffuse gastric tumors showed deficient MMR, whereas 64 (21%) of 304 in intestinal gastric tumors showed deficient MMR. Our results as well as the TCGA database indicated that MMR genes are infrequently inactivated in SRC gastric cancer. These findings indicate that SRC patients may not be the best candidates for immuno-oncology therapy.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2018

Quantum Calculations on Plant Cell Wall Component Interactions

In this paper, density functional theory calculations were performed to assess the relative interaction energies of plant cell wall components: cellulose, xylan, lignin and pectin. Monomeric and tetramer linear molecules were allowed to interact in four different configurations for each pair of compounds. The M0 5 -2X exchange-correlation functional which implicitly accounts for short- and mid-range dispersion was compared against MP2 and RI-MP2 to assess the reliability of the former for modeling van der Waals forces between these PCW components. Solvation effects were examined by modeling the interactions in the gas phase, in explicit H 2 O, and in polarized continuum models (PCM) of solvation. PCMs were used to represent water, methanol, and chloroform. The results predict the relative ranges of each type of interaction and when specific configurations will be strongly preferred. Finally, structures and energies are useful as a basis for testing classical force fields and as guidance for coarse-grained models of PCWs.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2018

Orai1 is involved in leptin-sensitive cell maturation in mouse dendritic cells

Store operated calcium entry(SOCE) is known to play a pivotal role in DCs functions including migration, maturation and antigen-presenting ability. Orai1, the major component of SOCE which mainly pairs with Stim1, is surely involved in the regulation of DCs functions. Leptin is recently found to mature DCs, we aim to evaluate the role of Orai1 in leptin-induced dendritic cells(DCs) maturation process and elucidate the mechanism. To this end, Flow cytometry and ELISA were utilized to detect the costimulatory molecule CD86 expression and IL-12 secretion, respectively. Transwell assay was used to examine DCs migration capacity. To evaluate the activity of SOCE, calcium(Ca{sup 2+}) imaging was performed. Firstly, we confirmed the positive effects of leptin upon SOCE and Orai1 expression in DCs isolated from mouse bone marrow. Secondly, we showed that the effects of leptin on DCs migration and maturation are Orai1 dependent. Moreover, Janus kinase 2(Jak2) silencing inhibited leptin-induced Orai1 expression and influenced DCs functions including migration and maturation as well as IL-12 secretion. In conclusion, our results imply that leptin regulates Orai1 by activating Jak2 signaling pathway, hence facilitating DCs migration and maturation.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2018

Evaluating the PD-1 Axis and Immune Effector Cell Infiltration in Oropharyngeal Squamous Cell Carcinoma

Programmed death-1 (PD-1) inhibitors are approved for the treatment of patients with recurrent and metastatic squamous cell carcinoma of the head and neck (SCCHN). Ongoing and planned randomized phase 3 trials are testing the benefit of combining PD-1/programmed death-ligand 1 (PD-L1) inhibitors with chemoradiation for patients with locoregionally confined SCCHN. Few studies have investigated relationships among potential predictive pathologic biomarkers such as PD-L1, PD-L2, and PD-1 in this population and associations between these markers and clinical characteristics.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2021

Patterns and Predictors of Failure in Recurrent or Refractory Large B-Cell Lymphomas After Chimeric Antigen Receptor T-Cell Therapy

Chimeric antigen receptor T-cell (CAR T) therapy is capable of eliciting durable responses in patients with relapsed/refractory (R/R) lymphomas. However, most treated patients relapse. Patterns of failure after CAR T have not been previously characterized, and may provide insights into the mechanisms of resistance guiding future treatment strategies.

62 RADIOLOGY AND NUCLEAR MEDICINE↗
DOE OSTI2023

Reverse-Bias Resilience of Monolithic Perovskite/Silicon Tandem Solar Cells

Metal halide perovskites have rapidly enabled a range of high-performance photovoltaic technologies. However, catastrophic failure under reverse voltage bias poses a roadblock for their commercialization. In this work, we conduct a series of stress tests to compare the reverse-bias stability of perovskite single-junction, silicon single-junction, and monolithic perovskite/silicon tandem solar cells. We demonstrate that the tested perovskite/silicon tandem devices are considerably more resilient against reverse bias compared with perovskite single-junction devices. The origin of such improved stability stems from the low reverse-bias diode current of the silicon subcell. This translates to dropping most of the voltage over the silicon subcell, where such a favorable voltage distribution protects the perovskite subcell from reverse-bias-induced degradation. These results highlight that, compared with other perovskite technologies, monolithic perovskite/silicon tandems are at a higher technology readiness level in terms of tackling the reverse bias and partial shading challenges, which is a considerable advantage toward commercialization.

halide perovskite↗
DOE OSTI2022

Numerical Simulation of Vibrational Sum Frequency Generation Intensity for Non-Centrosymmetric Domains Interspersed in an Amorphous Matrix: A Case Study for Cellulose in Plant Cell Wall

Vibrational sum frequency generation (SFG) spectroscopy can specifically probe molecular species non-centrosymmetrically arranged in a centrosymmetric or isotropic medium. This capability has been extensively utilized to detect and study molecular species present at the two-dimensional (2D) interface at which the centrosymmetry or isotropy of bulk phases is naturally broken. The same principle has been demonstrated to be very effective for the selective detection of non-centrosymmetric crystalline nanodomains interspersed in three-dimensional (3D) amorphous phases. However, the full spectral interpretation of SFG features has been difficult due to the complexity associated with the theoretical calculation of SFG responses of such 3D systems. This paper describes a numerical method to predict the relative SFG intensities of non-centrosymmetric nanodomains in 3D systems as functions of their size and concentration as well as their assembly patterns, i.e., the distributions of tilt, azimuth, and rotation angles with respect to the lab coordinate. We applied the developed method to predict changes in the CH and OH stretch modes characteristic to crystalline cellulose microfibrils distributed with various orders, which are relevant to plant cell wall structures. As a result, the same algorithm can also be applied to any SFG-active nanodomains interspersed in 3D amorphous matrices.

36 MATERIALS SCIENCE↗
DOE OSTI2017

Simultaneous Increase in Open-Circuit Voltage and Efficiency of Fullerene-Free Solar Cells through Chlorinated Thieno[3,4- b ]thiophene Polymer Donor

The chlorinated polymer, PBTCl, has been found to be an efficient donor in nonfullerene polymer solar cells (PSCs), which showed a blue-shifted absorbance compared to that of its fluorine analogue (PTB7-th) and resulted in more complementary light absorption with a nonfullerene acceptor, such as ITIC. Meanwhile, chlorine substitution lowered the HOMO level of PBTCl, which increased the open-circuit voltage of the corresponding polymer-based devices. The 2D GIWAXS analysis illustrated that the PBTCl/ITIC blend film exhibited a “face-on” orientation and scattering features of both PBTCl and ITIC, suggesting that the blend of PBTCl and ITIC was phase-separated and formed individual crystalline domains of the donor and acceptor, which promoted charge transfer in the bicontinuous film and eventually elevated the solar energy conversion efficiency. The PBTCl-based nonfullerene PSC exhibited a maximum PCE of 7.57% with a Voc of 0.91 V, which was an approximately 13% increasing in the PCE compared to that of the fluorine-analogue-based device.

36 MATERIALS SCIENCE↗
DOE OSTI2020

Phase Transitions in Metal–Organic Frameworks Directly Monitored through In Situ Variable Temperature Liquid-Cell Transmission Electron Microscopy and In Situ X-ray Diffraction

Zr 6 -based metal–organic frameworks (MOFs) with tetratopic organic linkers have been extensively investigated owing to their versatile structural tunability. While diverse topologies and polymorphism in the resulting MOFs are often encountered with tetratopic linkers and Zr 6 nodes, reports on phase transitions within these systems are rare. Thus, we have a limited understanding of polymorph transformations, hindering the rational development of pure phase materials. In this study, a phase transition from a microporous MOF, scu-NU-906, to a mesoporous MOF, csq-NU-1008, was discovered and monitored through in situ variable temperature liquid-cell transmission electron microscopy (VT-LCTEM), high-resolution transmission electron microscopy (HRTEM), and in situ variable temperature powder X-ray diffraction (VT-PXRD). Furthermore, it was found that the microporous- to-mesoporous transformation in the presence of formic acid occurs via a concomitant dissolution–reprecipitation process.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗