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Chen, J

Publications and source records attributed to Chen, J.

At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2025

Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti.

The genus Aspergillus is diverse, including species of industrial importance, human pathogens, plant pests, and model organisms. Aspergillus includes species from sections Usti and Cavernicolus, which until recently were joined in section Usti, but have now been proposed to be non-monophyletic and were split by section Nidulantes, Aenei and Raperi. To learn more about these sections, we have sequenced the genomes of 13 Aspergillus species from section Cavernicolus (A. cavernicola, A. californicus, and A. egyptiacus), section Usti (A. carlsbadensis, A. germanicus, A. granulosus, A. heterothallicus, A. insuetus, A. keveii, A. lucknowensis, A. pseudodeflectus and A. pseudoustus), and section Nidulantes (A. quadrilineatus, previously A. tetrazonus). We compared these genomes with 16 additional species from Aspergillus to explore their genetic diversity, based on their genome content, repeat-induced point mutations (RIPs), transposable elements, carbohydrate-active enzyme (CAZyme) profile, growth on plant polysaccharides, and secondary metabolite gene clusters (SMGCs). All analyses support the split of section Usti and provide additional insights: Analyses of genes found only in single species show that these constitute genes which appear to be involved in adaptation to new carbon sources, regulation to fit new niches, and bioactive compounds for competitive advantages, suggesting that these support species differentiation in Aspergillus species. Sections Usti and Cavernicolus have mainly unique SMGCs. Section Usti contains very large and information-rich genomes, an expansion partially driven by CAZymes, as section Usti contains the most CAZyme-rich species seen in genus Aspergillus. Section Usti is clearly an underutilized source of plant biomass degraders and shows great potential as industrial enzyme producers. Citation: Nybo JL, Vesth TC, Theobald S, Frisvad JC, Larsen TO, Kjaerboelling I, Rothschild-Mancinelli K, Lyhne EK, Barry K, Clum A, Yoshinaga Y, Ledsgaard L, Daum C, Lipzen A, Kuo A, Riley R, Mondo S, LaButti K, Haridas S, Pangalinan J, Salamov AA, Simmons BA, Magnuson JK, Chen J, Drula E, Henrissat B, Wiebenga A, Lubbers RJM, Müller A, dos Santos Gomes AC, Mäkelä MR, Stajich JE, Grigoriev IV, Mortensen UH, de Vries RP, Baker SE, Andersen MR (2025). Section-level genome sequencing and comparative genomics of Aspergillus sections Cavernicolus and Usti. Studies in Mycology 111: 101-114. doi: 10.3114/sim.2025.111.03.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Configuration mixing in 28 Mg and the 26 Mg (t,p) 28 Mg reaction

We have studied the 26 Mg(t,p) 28 Mg reaction. The nucleus 28 Mg lies between 24 Mg and 32 Mg, the latter of which is central to the “island of inversion” characterized by low-lying neutron fp-shell configurations. The present results show that the second-excited 0 + state in 28 Mg contains large fp-shell occupation for the neutrons. The experiment was performed in inverse kinematics using the HELIcal Orbit Spectrometer (HELIOS) at Argonne National Laboratory. Shell-model calculations using the SDPF-MU interaction yielded level energies and two-neutron transfer amplitudes that were used in one-step distorted-wave Furthermore, born approximation calculations to provide theoretical predictions of the proton angular distributions. In many, but not all cases, the data were in good agreement with theoretical predictions.

20 ≤ A ≤ 38↗
DOE OSTI2016

SU-F-I-14: 3D Breast Digital Phantom for XACT Imaging

Purpose: The X-ray induced acoustic computed tomography (XACT) is a new imaging modality which combines X-ray contrast and high ultrasonic resolution in a single modality. Using XACT in breast imaging, a 3D breast volume can be imaged by only one pulsed X-ray radiation, which could dramatically reduce the imaging dose for patients undergoing breast cancer screening and diagnosis. A 3D digital phantom that contains both X-ray properties and acoustic properties of different tissue types is indeed needed for developing and optimizing the XACT system. The purpose of this study is to offer a realistic breast digital phantom as a valuable tool for improving breast XACT imaging techniques and potentially leading to better diagnostic outcomes. Methods: A series of breast CT images along the coronal plane from a patient who has breast calcifications are used as the source images. A HU value based segmentation algorithm is employed to identify breast tissues in five categories, namely the skin tissue, fat tissue, glandular tissue, chest bone and calcifications. For each pixel, the dose related parameters, such as material components and density, and acoustic related parameters, such as frequency-dependent acoustic attenuation coefficient and bandwidth, are assigned based on tissue types. Meanwhile, other parameters which are used in sound propagation, including the sound speed, thermal expansion coefficient, and heat capacity are also assigned to each tissue. Results: A series of 2D tissue type image is acquired first and the 3D digital breast phantom is obtained by using commercial 3D reconstruction software. When giving specific settings including dose depositions and ultrasound center frequency, the X-ray induced initial pressure rise can be calculated accordingly. Conclusion: The proposed 3D breast digital phantom represents a realistic breast anatomic structure and provides a valuable tool for developing and evaluating the system performance for XACT.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-J-221: Adjusted Dose and Its Relation to Radiation Induced Liver Disease During Hepatocellular Carcinoma Radiotherapy

Purpose: Many patients with hepatocellular carcinoma (HCC) had hepatic anatomy variations as a result of inter-fraction deformation during fractionated radiotherapy, which may result in difference from the planned dose. This study aimed to investigate the relationship between adjusted dose and radiation induced liver disease (RILD) in HCC patients receiving three dimensional conformal radiotherapy (3DCRT). Methods: Twenty-three HCC patients received conventional fractionated 3DCRT were enrolled in this retrospective investigation. Among them, seven patients had been diagnosed of RILD post-radiotherapy, including 4 cases of grade 2, 3 cases of grade 3 according to the CTCAE Version 3.0. Daily cone-beam CT (CBCT) scans were acquired throughout the whole treatment course for each patient. To reconstruct the daily dose to a patient considering the interfraction anatomy variations, the planned beams from each patient’s treatment plan were firstly applied to each daily modified CBCT (mCBCT). The daily doses were then summed together with the help of deformable image registration (DIR) to obtain the adjusted dose (Dadjusted) of the patient. Finally, the dose changes in normal liver between planned dose (Dplan) and Dadjusted were evaluated by V20, V30, V40 and the mean dose to normal liver (MDTNL). Univariate analysis was performed to identify the significant dose changes. Results: Among the twenty-three patients, the adjusted liver V20, V30, V40 and MDTNL showed significant changes from the planned ones (p<0.05) and averagely increased by 4.1%, 4.7%, 4.5% and 3.9Gy, respectively. And the adjusted liver dose in twenty-one patients (91%) were higher than planned value, the adjusted dose of patients with RILD (6/7) exceeds to the hepatic radiation tolerance. Conclusion: The adjusted dose of all the studied patients significantly differs from planned dose, and mCBCT-based dose reconstruction can aid in evaluating the robustness of the planning solutions, and adjusted dose has the potential to reduce the risk of RILD. The author would like to express great thanks to Lei Xing, Daniel S Kapp and Yong Yang in the Stanford University School of Medicine for their valuable suggestions to this work.This work is supported by NSFC(61471226),China Postdoctoral Science Foundation (2015T80739, 2014M551949) and research funding from Shandong Province(JQ201516).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-245: The Investigation of Failure Mode and Effects Analysis and PDCA for the Radiotherapy Risk Reduction

Purpose: To optimize the clinical processes of radiotherapy and to reduce the radiotherapy risks by implementing the powerful risk management tools of failure mode and effects analysis(FMEA) and PDCA(plan-do-check-act). Methods: A multidiciplinary QA(Quality Assurance) team from our department consisting of oncologists, physicists, dosimetrists, therapists and administrator was established and an entire workflow QA process management using FMEA and PDCA tools was implemented for the whole treatment process. After the primary process tree was created, the failure modes and Risk priority numbers(RPNs) were determined by each member, and then the RPNs were averaged after team discussion. Results: 3 of 9 failure modes with RPN above 100 in the practice were identified in the first PDCA cycle, which were further analyzed to investigate the RPNs: including of patient registration error, prescription error and treating wrong patient. New process controls reduced the occurrence, or detectability scores from the top 3 failure modes. Two important corrective actions reduced the highest RPNs from 300 to 50, and the error rate of radiotherapy decreased remarkably. Conclusion: FMEA and PDCA are helpful in identifying potential problems in the radiotherapy process, which was proven to improve the safety, quality and efficiency of radiation therapy in our department. The implementation of the FMEA approach may improve the understanding of the overall process of radiotherapy while may identify potential flaws in the whole process. Further more, repeating the PDCA cycle can bring us closer to the goal: higher safety and accuracy radiotherapy.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-251: The Quality Assurance for the Heavy Patient Load Department in the Developing Country: The Primary Experience of An Entire Workflow QA Process Management in Radiotherapy

Purpose: To implement an entire workflow quality assurance (QA) process in the radiotherapy department and to reduce the error rates of radiotherapy based on the entire workflow management in the developing country. Methods: The entire workflow QA process management starts from patient registration to the end of last treatment including all steps through the entire radiotherapy process. Error rate of chartcheck is used to evaluate the the entire workflow QA process. Two to three qualified senior medical physicists checked the documents before the first treatment fraction of every patient. Random check of the treatment history during treatment was also performed. A total of around 6000 patients treatment data before and after implementing the entire workflow QA process were compared from May, 2014 to December, 2015. Results: A systemic checklist was established. It mainly includes patient’s registration, treatment plan QA, information exporting to OIS(Oncology Information System), documents of treatment QAand QA of the treatment history. The error rate derived from the chart check decreases from 1.7% to 0.9% after our the entire workflow QA process. All checked errors before the first treatment fraction were corrected as soon as oncologist re-confirmed them and reinforce staff training was accordingly followed to prevent those errors. Conclusion: The entire workflow QA process improved the safety, quality of radiotherapy in our department and we consider that our QA experience can be applicable for the heavily-loaded radiotherapy departments in developing country.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-421: Dosimetry Change During Radiotherapy and Dosimetry Difference for Rigid and Deformed Registration in the Mid-Thoracic Esophageal Carcinoma

Purpose: This study aimed to analyze dosimetry changes during radiotherapy for the mid-thoracic esophageal carcinoma, and investigate dosimetry difference between rigid and deformed registration. Methods: Twelve patients with primary middle thoracic esophageal carcinoma were selected randomly. Based on first CT scanning of each patient, plans-o were generated by experience physicists. After 20 fractions treatment, the corresponding plans-re were created with second CT scanning. And then, these two CT images were rigid and deformed registration respectively, and the dose was accumulated plan-o with plan-re. The dosimetry variation of these plans (plan-o: with 30 fractions, plan-rig: the accumulated dose with rigid registration and plan-def: the accumulated dose with deformed registration) were evaluated by paired T-test. Results: The V20 value of total lung were 32.68%, 30.3% and 29.71% for plan-o, plan-rig and plan-def respectively. The mean dose of total lung was 17.19 Gy, 16.67 Gy and 16.51 Gy for plan-o plan-rig and plan-def respectively. There were significant differences between plan-o and plan-rig or plan-def for both V20 and mean dose of total lung (with p= 0.003, p= 0.000 for V20 and p=0.008, p= 0.000 for mean dose respectively). There was no significant difference between plan-rig and plan-def (with p=0.118 for V20 and p=0.384 for mean dose). The max dose of spinal-cord was 41.95 Gy, 41.48 Gy and 41.4 Gy for plan-o, plan-rig and plan-def respectively. There were no significant differences for the max dose of spinal-cord between these plans. Conclusion: The target volume changes and anatomic position displacement of mid-thoracic esophageal carcinoma should not be neglected in clinics. These changes would cause overdose in normal tissue. Therefore, it is necessary to have another CT scanning and re-plan during the mid-thoracic esophageal carcinoma radiotherapy. And the dosimetry difference between rigid and deformed fusions was not found in this study.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-F-T-435: Helical Tomotherapy for Craniospinal Irradiation: What We Have Learned from a Multi-Institutional Study

Purpose: To report cranio-spinal irradiation (CSI) planning experience, compare dosimetric quality and delivery efficiency with Tomotherapy from different institutions, and to investigate effect of planning parameters on plan quality and treatment time. Methods: Clinical helical tomotherapy IMRT plans for thirty-nine CSI cases from three academic institutions were retrospectively evaluated. The planning parameters: field width (FW), pitch, modulation factor (MF), and achieved dosimetric endpoints were cross-compared. A fraction-dose-delivery-timing index (FDTI), defined as treatment time per fraction dose per PTV length, was utilized to evaluate plan delivery efficiency. A lower FDTI indicates higher delivery efficiency. We studied the correlation between planning quality, treatment time and planning parameters by grouping the plans under specific planning parameters. Additionally, we created new plans using 5cm jaw for a subset of plans that used 2.5cm jaw to exam if treatment efficiency can be improved without sacrificing plan quality. Results: There were significant dosimetric differences for organ at risks (OARs) among different institutions (A,B,C). Using the lowest average MF (1.9±0.4) and 5cm field width, C had the highest lung, heart, kidney, liver mean doses and maximum doses for lens. Using the same field width of 5cm, but higher MF (2.6±0.6), B had lower doses to the OARs in the thorax and abdomen area. Most of A’s plans were planned with 2.5cm jaw, the plans yielded better PTV coverage, higher OAR doses and slightly shorter FDTI compared to institution B. The replanned 5cm jaw plans achieved comparable PTV coverage and OARs sparing, while saving up to 44.7% treatment time. Conclusion: Plan quality and delivery efficiency could vary significantly in CSI planning on Tomotheapy due to choice of different planning parameters. CSI plans using a 5cm jaw, with proper selection of pitch and MF, can achieve comparable/ better plan quality with shorter delivery time compared to 2.5cm jaw plans.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

SU-G-206-16: Investigation of Dosimetric Consequence Via Cone-Beam CT Based Dose Reconstruction in Hepatocellular Carcinoma Radiotherapy

Purpose: Many patients with technically unresectable or medically inoperable hepatocellular carcinoma (HCC) had hepatic dosimetric variations as a result of inter-fraction anatomical deformation. This study was conducted to assess the hepatic dosimetric consequences via reconstructing weekly dose in HCC patients receiving three dimensional conformal radiation therapy. Methods: Twenty-one HCC patients with 21 planning CT (pCT) scans and 63 weekly Cone-beam CT (CBCT) scans were enrolled in this investigation. Among them, six patients had been diagnosed of radiation induced liver disease (RILD) and the other fifteen patients had good prognosis after treatment. And each patient had three weekly CBCT before re-planning. In reconstructing CBCT-based weekly dose, we registered pCT to CBCT to provide the correct Hounsfield units for the CBCT using gradient-based deformable image registration (DIR), and this modified CBCT (mCBCT) were introduced to enable dose calculation.To obtain the weekly dosimetric consequences, the initial plan beam configurations and dose constraints were re-applied to mCBCT for performing dose calculation, and the mCBCT were extrapolated to 25 fractions. Besides, the manually delineated contour was propagated automatically onto the mCBCT of the new patient by exploiting the deformation vectors field, and the reconstructed weekly dose was mapped back to pCT to understand the dose distribution difference. Also, weekly dosimetric variations were compared with the hepatic radiation tolerance in terms of D50 and Dmean. Results: Among the twenty-one patients, the three weekly D50 increased by 0.7Gy, 5.1Gy and 6.1Gy, respectively, and Dmean increased by 0.9%, 4.7% and 5.5%, respectively. For patients with RILD, the average values of the third weekly D50 and Dmean were both high than hepatic radiation tolerance, while the values of patients without RILD were below. Conclusion: The planned dose on pCT was not a real dose to the liver, and the liver overdose increased the risk of RILD. The author would like to express great thanks to Lei Xing, Daniel S Kapp and Yong Yang in the Stanford University School of Medicine for their valuable suggestions to this work. This work is supported by NSFC(61471226), China Postdoctoral Science Foundation (2015T80739,2014M551949) and research funding from Shandong Province (JQ201516).

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

MO-DE-207A-10: One-Step CT Reconstruction for Metal Artifact Reduction by a Modification of Penalized Weighted Least-Squares (PWLS)

Purpose: Metal objects create severe artifacts in kilo-voltage (kV) CT image reconstructions due to the high attenuation coefficients of high atomic number objects. Most of the techniques devised to reduce this artifact utilize a two-step approach, which do not reliably yield the qualified reconstructed images. Thus, for accuracy and simplicity, this work presents a one-step reconstruction method based on a modified penalized weighted least-squares (PWLS) technique. Methods: Existing techniques for metal artifact reduction mostly adopt a two-step approach, which conduct additional reconstruction with the modified projection data from the initial reconstruction. This procedure does not consistently perform well due to the uncertainties in manipulating the metal-contaminated projection data by thresholding and linear interpolation. This study proposes a one-step reconstruction process using a new PWLS operation with total-variation (TV) minimization, while not manipulating the projection. The PWLS for CT reconstruction has been investigated using a pre-defined weight, based on the variance of the projection datum at each detector bin. It works well when reconstructing CT images from metal-free projection data, which does not appropriately penalize metal-contaminated projection data. The proposed work defines the weight at each projection element under the assumption of a Poisson random variable. This small modification using element-wise penalization has a large impact in reducing metal artifacts. For evaluation, the proposed technique was assessed with two noisy, metal-contaminated digital phantoms, against the existing PWLS with TV minimization and the two-step approach. Result: The proposed PWLS with TV minimization greatly improved the metal artifact reduction, relative to the other techniques, by watching the results. Numerically, the new approach lowered the normalized root-mean-square error about 30 and 60% for the two cases, respectively, compared to the two-step method. Conclusion: A new PWLS operation shows promise for improving metal artifact reduction in CT imaging, as well as simplifying the reconstructing procedure.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TU-AB-202-03: Prediction of PET Transfer Uncertainty by DIR Error Estimating Software, AUTODIRECT

Purpose: Deformable image registration (DIR) is a powerful tool, but DIR errors can adversely affect its clinical applications. To estimate voxel-specific DIR uncertainty, a software tool, called AUTODIRECT (automated DIR evaluation of confidence tool), has been developed and validated. This work tests the ability of this software to predict uncertainty for the transfer of standard uptake values (SUV) from positron-emission tomography (PET) with DIR. Methods: Virtual phantoms are used for this study. Each phantom has a planning computed tomography (CT) image and a diagnostic PET-CT image set. A deformation was digitally applied to the diagnostic CT to create the planning CT image and establish a known deformation between the images. One lung and three rectum patient datasets were employed to create the virtual phantoms. Both of these sites have difficult deformation scenarios associated with them, which can affect DIR accuracy (lung tissue sliding and changes in rectal filling). The virtual phantoms were created to simulate these scenarios by introducing discontinuities in the deformation field at the lung rectum border. The DIR algorithm from Plastimatch software was applied to these phantoms. The SUV mapping errors from the DIR were then compared to that predicted by AUTODIRECT. Results: The SUV error distributions closely followed the AUTODIRECT predicted error distribution for the 4 test cases. The minimum and maximum PET SUVs were produced from AUTODIRECT at 95% confidence interval before applying gradient-based SUV segmentation for each of these volumes. Notably, 93.5% of the target volume warped by the true deformation was included within the AUTODIRECT-predicted maximum SUV volume after the segmentation, while 78.9% of the target volume was within the target volume warped by Plastimatch. Conclusion: The AUTODIRECT framework is able to predict PET transfer uncertainty caused by DIR, which enables an understanding of the associated target volume uncertainty.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-AB-209-08: Next Generation Dedicated 3D Breast Imaging with XACT

Purpose: Exposure to radiation increases the risk of cancer. We have designed a new imaging paradigm, X-ray induced acoustic computed tomography (XACT). Applying this innovative technology to breast imaging, an X-ray exposure can generate a 3D acoustic image, which dramatically reduces the radiation dose to patients when compared to conventional breast CT. Methods: Theoretical calculations are done to determine the appropriate X-ray energy and ultrasound frequency in breast XACT imaging. A series of breast CT image along the coronal plane from a patient with calcifications in the breast tissue are used as the source image. HU value based segmentation is done to distinguish the skin, adipose tissue, glandular tissue, breast calcification, and chest bone from each CT image. X-ray dose deposition in each pixel is calculated based on the tissue type by using GEANT4 Monte Carlo toolkits. The initial pressure rise caused by X-ray energy deposition is calculated according to tissue properties. Then, the X-ray induced acoustic wave propagation is simulated by K-WAVE toolkit. Breast XACT images are reconstructed from the recorded time-dependent ultrasound waves. Results: For imaging a breast with large size (16cm in diameter at chest wall), the photon energy of X-ray source and the central frequency of ultrasound detector is determined as 20keV and 5.5MHz. Approximately 10 times contrast between a calcification and the breast tissue can be acquire from XACT image. The calcification can be clearly identified from the reconstructed XACT image. Conclusion: XACT technique takes the advantages of X-ray absorption contrast and high ultrasonic resolution. With the proposed innovative technology, one can potentially reduce radiation dose to patient in 3D breast imaging as compared with current x-ray modalities, while still maintaining high imaging contrast and spatial resolution.

60 APPLIED LIFE SCIENCES↗
DOE OSTI2016

TH-CD-206-08: An Anthropopathic Deformable Phantom for Geometric and Dose Accumulation Accuracy Validation of Deformable Image Registration

Purpose: To design and construct a three-dimensional (3D) anthropopathic abdominal phantom for evaluating deformable image registration (DIR) accuracy on images and dose deformation in adaptive radiation therapy (ART). Method: Organ moulds, including liver, kidney, spleen, stomach, vertebra and two metastasis tumors, are 3D printed using the contours from an ovarian cancer patient. The organ moulds are molded with deformable gels that made of different mixtures of polyvinyl chloride (PVC) and the softener dioctyl terephthalate. Gels with different densities are obtained by a polynomial fitting curve which describes the relation between the CT number and PVC-softener blending ratio. The rigid vertebras are constructed by moulding with white cement. The final abdominal phantom is assembled by arranging all the fabricated organs inside a hollow dummy according to their anatomies and sealed with deformable gel with averaged CT number of muscle and fat. Geometric and dosimetric landmarks are embedded inside the phantom for spatial accuracy and dose accumulation accuracy studies. Three DIR algorithms available in the open source DIR toolkit-DIRART, including the Demons, the Horn-Schunck and Lucas-Kanade method and the Level-Set Motion method, are tested using the constructed phantom. Results: Viscoelastic behavior is observed in the constructed deformable gel, which serves as an ideal material for the deformable phantom. The constructed abdominal phantom consists of highly realistic anatomy and the fabricated organs inside have close CT number to its reference patient. DIR accuracy studies conducted on the constructed phantom using three DIR approaches indicate that geometric accuracy of a DIR algorithm has achieved does not guarantee accuracy in dose accumulation. Conclusions: We have designed and constructed an anthropopathic abdominal deformable phantom with satisfactory elastic property, realistic organ density and anatomy. This physical phantom is recyclable and can be used for routine validations of DIR geometric accuracy and dose accumulation accuracy in ART. This work is supported in part by grant from VARIAN MEDICAL SYSTEMS INC, the National Natural Science Foundation of China (no 81428019 and no 81301940), the Guangdong Natural Science Foundation (2015A030313302) and the 2015 Pearl River S&T Nova Program of Guangzhou (201506010096).

60 APPLIED LIFE SCIENCES↗