OsMADS1 Regulates Grain Quality, Gene Expressions, and Regulatory Networks of Starch and Storage Protein Metabolisms in Rice.

OsMADS1 plays a vital role in regulating floret development and grain shape, but whether it regulates rice grain quality still remains largely unknown. Therefore, we used comprehensive molecular genetics, plant biotechnology, and functional omics approaches, including phenotyping, mapping-by-sequencing, target gene seed-specific RNAi, transgenic experiments, and transcriptomic profiling to answer this biological and molecular question. Here, we report the characterization of the 'Oat-like rice' mutant, with poor grain quality, including chalky endosperms, abnormal morphology and loose arrangement of starch granules, and lower starch content but higher protein content in grains. The poor grain quality of Oat-like rice was found to be caused by the mutated OsMADS1Olr allele through mapping-by-sequencing analysis and transgenic experiments. OsMADS1 protein is highly expressed in florets and developing seeds. Both OsMADS1-eGFP and OsMADS1Olr-eGFP fusion proteins are localized in the nucleus. Moreover, seed-specific RNAi of OsMADS1 also caused decreased grain quality in transgenic lines, such as the Oat-like rice. Further transcriptomic profiling between Oat-like rice and Nipponbare grains revealed that OsMADS1 regulates gene expressions and regulatory networks of starch and storage protein metabolisms in rice grains, hereafter regulating rice quality. In conclusion, our results not only reveal the crucial role and preliminary mechanism of OsMADS1 in regulating rice grain quality but also highlight the application potentials of OsMADS1 and the target gene seed-specific RNAi system in improving rice grain quality by molecular breeding.

Identifying the Role of Oxidative Stress-Related Genes as Prognostic Biomarkers and Predicting the Response of Immunotherapy and Chemotherapy in Ovarian Cancer.

Background: Ovarian cancer (OC) is one of the most frequently seen and fatal gynecological malignancies, and oxidative stress (OS) plays a critical role in the development and chemoresistance of OC. Materials and Methods: OS-related genes (OSRGs) were obtained from the Molecular Signatures Database. Besides, gene expression profiles and clinical information from The Cancer Genome Atlas (TCGA) were selected to identify the prognostic OSRGs. Moreover, univariate Cox regression, LASSO, and multivariate Cox regression analyses were conducted sequentially to establish a prognostic signature, which was later validated in three independent Gene Expression Omnibus (GEO) datasets. Next, gene set enrichment analysis (GSEA) and tumor mutation burden (TMB) analysis were performed. Afterwards, immune checkpoint genes (ICGs) and the tumor immune dysfunction and exclusion (TIDE) algorithm, together with IMvigor210 and GSE78220 cohorts, were applied to comprehensively explore the role of OSRG signature in immunotherapy. Further, the CellMiner and Genomics of Drug Sensitivity in Cancer (GDSC) databases were also applied in investigating the significance of OSRG signature in chemotherapy. Results: Altogether, 34 prognostic OSRGs were identified, among which 14 were chosen to establish the most valuable prognostic signature. The Kaplan-Meier (KM) analysis suggested that patients with lower OS-related risk score had better prognosis. The area under the curve (AUC) values were 0.71, 0.76, and 0.85 in 3, 5, and 7 years separately, and the stability of this prognostic signature was confirmed in three GEO datasets. As revealed by GSEA and TMB analysis results, OC patients in low-risk group might have better immunotherapeutic response, which was consistent with ICG expression and TIDE analyses. Moreover, both IMvigor210 and GSE78220 cohorts demonstrated that patients with lower OS-related risk score were more likely to benefit from anti-PD-1/L1 immunotherapy. In addition, the association between prognostic signature and drug sensitivity was explored. Conclusion: According to our results in this work, OSRG signature can act as a powerful prognostic predictor for OC, which contributes to generating more individualized therapeutic strategies for OC patients.

Quantifying the impact of Pyramid Squeeze Attention mechanism and filtering approaches on Alzheimer's disease classification.

Brain medical imaging and deep learning are important foundations for diagnosing and predicting Alzheimer's disease. In this study, we explored the impact of different image filtering approaches and Pyramid Squeeze Attention (PSA) mechanism on the image classification of Alzheimer's disease. First, during the image preprocessing, we register MRI images and remove skulls, then apply median filtering, Gaussian blur filtering, and anisotropic diffusion filtering to obtain different experimental images. After that, we add the Squeeze and Excitation (SE) mechanism and Pyramid Squeeze Attention (PSA) mechanism to the Fully Convolutional Network (FCN) model respectively, to obtain each MRI image's corresponding feature information of disease probability map. Besides, we also construct Multi-Layer Perceptron (MLP) model's framework, combining feature information of disease probability map with age, gender, and Mini-Mental State Examination (MMSE) of each sample, to get the final classification performance of model. Among them, the accuracy of the MLP-C model combining anisotropic diffusion filtering with the Pyramid Squeeze Attention mechanism can reach 98.85%. The corresponding quantitative experimental results show that different image filtering approaches and attention mechanisms provide effective assistance for the diagnosis and classification of Alzheimer's disease.

Systemic characterization of alternative splicing related to prognosis, immune infiltration, and drug sensitivity analysis in ovarian cancer.

Background: Alternative splicing (AS) plays an essential role in tumorigenesis and progression. This study intended to construct an innovative prognostic model based on AS events to gain more precise survival prediction and search for potential therapeutic targets in ovarian cancer. Methods: Seven types of AS events in ovarian serous cystadenocarcinoma (OV) patients with RNA-seq were obtained using The Cancer Genome Atlas (TCGA) SpliceSeq tool and database. Cox and Kaplan-Meier curve analyses were employed to establish the prognostic models. Relying on drug sensitivity data from the CellMiner database, Genomics of Drug Sensitivity (GDS) was adopted to estimate the platinum-sensitive analysis. Furthermore, a prognostic splicing factor (SF)-AS network was constructed using Cytoscape. Finally, in order to explore the influence of the tumor microenvironment on the prognosis of OV patients, we first combined a similar network fusion and consensus clustering (SNF-CC) algorithm to identify three OV subtypes based on survival-related AS events and then utilized single-sample Gene Set Enrichment Analysis (ssGSEA) method to perform immune cell infiltration analysis. Results: A total of 48,049 AS events and 21,841 related genes were selected from 318 OV samples, and 2,206 AS events associated with disease-free survival (DFS) were identified. Multivariate Cox and Kaplan-Meier curve analyses were then employed to establish the prognostic models. Receiver operating characteristic (ROC) analysis from 0.59 to 0.75 showed that these models were highly efficient in distinguishing patient survival. GDS was adopted with the CellMiner database to provide some insights for platinum-sensitive analysis of OV. Furthermore, a prognostic SF-AS network, which discovered a significant connection between SFs and prognostic AS genes, was constructed using Cytoscape. The combined SNF-CC algorithm revealed three distinct OV subtypes based on the prognostic AS events, and the associations between this novel molecular classification and immune cell infiltration were further explored. Conclusions: We developed a powerful prognostic AS signature for OV and provided a deeper understanding of SF-AS network regulatory mechanisms, as well as platinum-sensitive and cancer immune microenvironments. These results revealed various candidate biomarkers and potential targets for OV treatment strategies.

Ferroptosis-related genes identify tumor immune microenvironment characterization for the prediction of prognosis in cervical cancer.

Background: Cervical cancer (CC) is a disease that affects female health; therefore, timely prevention and diagnosis of CC are crucial to decrease its mortality. Ferroptosis, an iron-dependent form of non-apoptotic cell death, is involved in tumor progression. However, the role of ferroptosis-related genes (FRGs) in the immune microenvironment of cervical squamous cell carcinoma and endocervical adenocarcinoma (CESC) remains unclear. Methods: The data sets of CESC patients, including RNA sequencing (RNA-seq) data and clinical information, were obtained from The Cancer Genome Atlas (TCGA). The ESTIMATE algorithm was used to determine the stromal score, immune score, estimate score, and tumor purity in the CESC patients' data. Additionally, FRGs were identified and used to construct a signature marker for the diagnosis and prognosis of CESC. Patients were assigned to a high- or low-risk group based on their median risk score. The tumor microenvironment (TME), immune infiltration, and functional enrichment were compared between the low- and high-risk groups. Functional analyses, including Gene Ontology (GO) analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis, and single-sample Gene Set Enrichment Analysis (ssGSEA), were conducted to explore the underlying mechanisms in the development and prognosis of CESC. Results: The results showed that the estimate score was suitable for predicting the prognosis of CESC patients. Additionally, a prediction model involving four FRGs [phosphatidylethanolamine-binding protein 1 (PEBP1), dual oxidase 1 (DUOX1), iron-sulfur cluster assembly enzyme (ISCU), and cytochrome b (-245) beta subunit (CYBB)] was constructed. The performance of the prognostic model and significant clinical characteristics in predicting CESC prognosis was subsequently validated. Our results showed that the expression of CYBB affected immune cells. Gene functional enrichment analyses showed that these differentially expressed FRGs were mainly enriched in the immunity-related signaling pathways, which indicated that FRGs might affect the development and prognosis of CC by regulating the immune microenvironment. Conclusions: The expression profiles of FRGs are closely related to the TME and the prognostic survival of CESC patients. The interaction between ferroptosis and immunity in the development of CC provides new insight into the molecular mechanisms of CC.

Highly enriched BEND3 prevents the premature activation of bivalent genes during differentiation.

Bivalent genes are ready for activation upon the arrival of developmental cues. Here, we report that BEND3 is a CpG island (CGI)-binding protein that is enriched at regulatory elements. The cocrystal structure of BEND3 in complex with its target DNA reveals the structural basis for its DNA methylation-sensitive binding property. Mouse embryos ablated of Bend3 died at the pregastrulation stage. Bend3 null embryonic stem cells (ESCs) exhibited severe defects in differentiation, during which hundreds of CGI-containing bivalent genes were prematurely activated. BEND3 is required for the stable association of polycomb repressive complex 2 (PRC2) at bivalent genes that are highly occupied by BEND3, which suggests a reining function of BEND3 in maintaining high levels of H3K27me3 at these bivalent genes in ESCs to prevent their premature activation in the forthcoming developmental stage.

Systemic Inflammatory Markers for Predicting Overall Survival in Patients with Osteosarcoma: A Systematic Review and Meta-Analysis.

BACKGROUND: Inflammatory markers are associated with tumor genesis and progression, but their prognostic significance in osteosarcoma remains unclear. Therefore, we discussed the prognostic value of related inflammatory markers in osteosarcoma through a meta-analysis and systematic review. These inflammatory markers include C-reactive protein (CRP), neutrophil to lymphocyte ratio (NLR), lymphocyte to monocyte ratio (LMR), platelet to lymphocyte ratio (PLR), and Glasgow prognostic score (GPS). METHODS: The Chinese National Knowledge Infrastructure (CNKI), Wanfang, Chinese Scientific Journals (VIP), PubMed, Embase, and Cochrane libraries were searched. The design of meta-analysis was made based on the PICOS (population, intervention/exposure, control, outcomes, and study design) principles, and STATA 15.1 was used to analyze the data. The Newcastle-Ottawa scale (NOS) was used to assess the quality of included studies. Hazard ratios (HRs) for overall survival (OS) and disease-specific survival (DPS) were extracted for the investigation of the prognostic value of inflammatory markers. RESULTS: Twelve researches with 2162 osteosarcoma patients were included in total. The pooled results showed that elevated NLR, CRP, and GPS are all greatly related to shortening of OS among patients with osteosarcoma (HR = 1.68, P = 0.007, 95% CI: 1.15-2.45; HR = 1.96, P = 0.002, 95% CI: 1.28-3.00; HR = 2.54, P < 0.0001, 95% CI: 1.95-3.31, respectively), and CRP level is significantly associated with shortening of DPS among patients with osteosarcoma (HR = 2.76, 95% CI:2.01-3.80, P < 0.0001), additionally. However, the correlation between LMR or PLR and the prognosis of osteosarcoma is not statistically significant (HR = 0.60, 95% CI: 0.30-1.18, P = 0.138; HR = 1.13, 95% CI: 0.85-1.49, P = 0.405, respectively). The outcomes of subgroup analysis to NLR and CRP suggested that histology, ethnicity, metastasis, and sample size all have an impact on its prognosis of patients with osteosarcoma. CONCLUSION: Worsened prognosis may be related to high levels of NLR, CRP, and GPS before treatment rather than LMR or PLR, which can provide the basis for clinicians to judge the outcomes of prognosis. Trial Registration. PROSPERO (CRD42021249954), https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=249954.

FA-GAN: Fused attentive generative adversarial networks for MRI image super-resolution.

High-resolution magnetic resonance images can provide fine-grained anatomical information, but acquiring such data requires a long scanning time. In this paper, a framework called the Fused Attentive Generative Adversarial Networks(FA-GAN) is proposed to generate the super- resolution MR image from low-resolution magnetic resonance images, which can reduce the scanning time effectively but with high resolution MR images. In the framework of the FA-GAN, the local fusion feature block, consisting of different three-pass networks by using different convolution kernels, is proposed to extract image features at different scales. And the global feature fusion module, including the channel attention module, the self-attention module, and the fusion operation, is designed to enhance the important features of the MR image. Moreover, the spectral normalization process is introduced to make the discriminator network stable. 40 sets of 3D magnetic resonance images (each set of images contains 256 slices) are used to train the network, and 10 sets of images are used to test the proposed method. The experimental results show that the PSNR and SSIM values of the super-resolution magnetic resonance image generated by the proposed FA-GAN method are higher than the state-of-the-art reconstruction methods.

Screening of cervical cancer-related hub genes based on comprehensive bioinformatics analysis.

BACKGROUND: Since the molecular mechanisms of cervical cancer (CC) have not been completely discovered, it is of great significance to identify the hub genes and pathways of this disease to reveal the molecular mechanisms of cervical cancer. OBJECTIVE: The study aimed to identify the biological functions and prognostic value of hub genes in cervical cancer. METHODS: The gene expression data of CC patients were downloaded from the Gene Expression Omnibus (GEO) database and The Cancer Genome Atlas (TCGA) database. The core genes were screened out by differential gene expression analysis and weighted gene co-expression network analysis (WGCNA). R software, the STRING online tool and Cytoscape software were used to screen out the hub genes. The GEPIA public database was used to further verify the expression levels of the hub genes in normal tissues and tumour tissues and determine the disease-free survival (DFS) rates of the hub genes. The protein expression of the survival-related hub genes was identified with the Human Protein Atlas (HPA) database. RESULTS: A total of 64 core genes were screened, and 10 genes, including RFC5, POLE3, RAD51, RMI1, PALB2, HDAC1, MCM4, ESR1, FOS and E2F1, were identified as hub genes. Compared with that in normal tissues, RFC5, POLE3, RAD51,RMI1, PALB2, MCM4 and E2F1 were all significantly upregulated in cervical cancer, ESR1 was significantly downregulated in cervical cancer, and RFC5 expression in CC patients was significantly related to OS. In the DFS analysis, no significant difference was observed in the expression level of RFC5 in cervical cancer patients. Finally, RFC5 protein levels verified by the HPA database were consistently upregulated with mRNA levels in CC samples. CONCLUSIONS: RFC5 may play important roles in the occurrence and prognosis of CC. It could be further explored and validated as a potential predictor and therapeutic target for CC.

ELF5 inhibits the proliferation and invasion of breast cancer cells by regulating CD24.

E74-like factor five (ELF5) is a basic transcription factor that plays a key role in breast tissue and gland development. However, the molecular mechanism of ELF5 in breast cancer cells has not been elucidated. In this study, we examined the effect of ELF5 on the human breast cancer cell lines MCF-7 and T47D and confirmed that ELF5 can inhibit cell proliferation, migration and invasion. In further research, the relationship between ELF5 and CD24 was characterized in breast cancer cells. We found that CD24 was a target gene of ELF5 through chromatin immunoprecipitation (ChIP) -Sequence assays, and proved that ELF5 could bind to the ETS cis-element on the proximal promoter of the CD24 gene and regulate the expression of CD24. Moreover, overexpression of ELF5 in MCF-7 cells significantly increased both the mRNA and protein levels of CD24, while knockdown of CD24 expression restored cell proliferation, migration and invasion through adaptive ELF5 expression in MCF-7 cells. Therefore, these data suggest that ELF5 inhibits migration and invasion of breast cancer cells by regulating CD24 expression, which make provides a molecular mechanism for ELF5 to inhibit breast cancer from a new perspective and provides further theoretical support for the treatment and prevention of breast cancer.

Improved robust tensor principal component analysis for accelerating dynamic MR imaging reconstruction.

Dynamic magnetic resonance imaging (dMRI) strikes a balance between reconstruction speed and image accuracy in medical imaging field. In this paper, an improved robust tensor principal component analysis (RTPCA) method is proposed to reconstruct the dynamic magnetic resonance imaging (MRI) from highly under-sampled K-space data. The MR reconstruction problem is formulated as a high-order low-rank tenor plus sparse tensor recovery problem, which is solved by robust tensor principal component analysis (RTPCA) with a new tensor nuclear norm (TNN). To further exploit the low-rank structures in multi-way data, the core matrix nuclear norm, extracted from the diagonal elements of the core tensor under tensor singular value decomposition (t-SVD) framework, is also integrated into TNN for enforcing the low-rank structure in MRI datasets. The experimental results show that the proposed method outperforms state-of-the-art methods in terms of both MR image reconstruction accuracy and computational efficiency on 3D and 4D experiment datasets, especially for 4D MR image reconstruction. Graphical abstract The flowchart of the proposed method to reconstruct the dynamic magnetic resonance imaging (MRI) from highly under-sampled K-space data in the kth iteration. To further exploit the low-rank structures in multi-way data, the core matrix nuclear norm, extracted from the diagonal elements of the core tensor under tensor singular value decomposition (t-SVD) framework, is also integrated into tensor nuclear norm (TNN) for enforcing the low-rank structure in MRI datasets. In each iteration, the first step is to get low-rank tensor ℓk - 1 by using soft thresholding on the singular values of ℓk - 1 = χk - 1 - ξk - 1, and an improved tensor nuclear norm method is proposed to process the low-rank tensor ℓk - 1 firstly. Then, the shrinkage operator is applied to ξk - 1 = χk - 1 - ℓk - 1 for sparse part ξk - 1. The final reconstructed d-MRI χk is obtained by enforcing data consistency that the residual in K-space is subtracted by the sum of the reconstructed low-rank tensor and sparse tensor.

The complete chloroplast genome of Aster hypoleucus (Asteraceae: Astereae): an endemic species from China.

This study was the first report about complete chloroplast genome of Aster hypoleucus (Asteraceae, Astereae), an endemic species in Xizang (China). The circular whole cp genome of A. hypoleucus was 152,300 bp in length, contained a large single-copy (LSC) region of 84,031 bp and a small single-copy (SSC) region of 18,269 bp. These two regions were separated by a pair of inverted repeat regions (IRa and IRb), each of them 25,000 bp in length. A total of 134 functional genes were encoded, consisted of 89 protein-coding genes, 37 tRNA genes, and eight rRNA genes. The overall GC content of the chloroplast genome sequence was 37.3%, and the GC contents of the LSC, SSC, and IR regions were 35.2%, 31.2%, and 43.0%, respectively.

[Randomized Controlled Clinical Trials of Treatment of Knee Osteoarthritis of Yang-deficiency Pattern by Acupuncture Plus Moxibustion].

OBJECTIVE: To compare the therapeutic effect of acupuncture plus moxibustion and simple acupuncture in the treatment of patients with knee osteoarthritis (KOA) of yang-deficiency syndrome. METHODS: Fifty-eight KOA patients with yang-deficiency syndrome were chosen and randomly divided into acupuncture plus moxibustion group (n＝30) and acupuncture group (n＝28). Neixiyan (EX-LE 4), Dubi (ST 35), Liangqiu (ST 34), Heding (EX-LE 2), Xuehai (SP 10), Yanglingquan (GB 34) on the affected side of the body were punctured with filiform needles or/and stimulated with moxibustion using seed-sized moxa cones. The treatment was conducted once daily for 10 days, followed with another 10 days after 2 days interval. The pain severity was evaluated by using visual analogue scale (VAS), and the Western Ontario and McMaster Universities Osteoarthritis Index (WOMAC) scores were used to measure the KOA pain, stiffness and function before and after the treatment, and 1 month after the treatment. The therapeutic effect was also evaluated according to the "Standards for Diagnosis and Therapeutic Effect Evaluation of Diseases/Syndromes of Traditional Chinese Medicine" (issued by the State Administration of Traditional Chinese Medicine of China in 1994). RESULTS: Twenty days and 1 month after the treatment, the scores of VAS, and KOA pain, stiffness and motor function of WOMAC were significantly decreased in both groups in comparison with their own pre-treatment (P<0.01), and were obviously lower in the acupuncture plus moxibustion group than in the acupuncture group (P<0.05, P<0.01). Of the 28 and 30 cases in the acupuncture and acupuncture plus moxibustion groups, 7 and 12 experienced marked improvement, 12 and 16 were effective, 9 and 2 ineffective, with the therapeutic effect being 67.86% and 93.33%, respectively. The therapeutic effect of acupuncture plus moxibustion was apparently superior to that of simple acupuncture (P<0.05). CONCLUSION: Acupuncture plus moxibustion is significantly superior to simple acupuncture therapy in relieving symptoms of KOA patients, and also has a better post-effect.

Differential responses of body growth to artificial warming between parasitoids and hosts and the consequences for plant seed damage.

Temperature increase may disrupt trophic interactions by differentially changing body growth of the species involved. In this study, we tested whether the response of body growth to artificial warming (~2.2 °C) of a solitary koinobiont endo-parasitoid wasp (Pteromalus albipennis, Hymenoptera: Pteromalidae) differed from its main host tephritid fly (Tephritis femoralis, Diptera: Tephritidae; pre-dispersal seed predator), and whether the plant seed damage caused by wasp-parasitized and unparasitized maggots (larval flies) were altered by warming. In contrast to the significant and season-dependent effects of warming on body growth of the host tephritid fly reported in one of our previous studies, the effect of artificial warming on body growth was non-significant on the studied wasp. Moreover, the warming effect on seed damage due to unparasitized maggots was significant and varied with season, but the damage by parasitized maggots was not altered by warming. Distinct responses of body growth to warming between parasitoids studied here and hosts assessed in a previous study indicate that temperature increase may differentially affect life history traits of animals along food chains, which is likely to affect trophic interactions.

Planning 4D intensity-modulated arc therapy for tumor tracking with a multileaf collimator.

This study introduces a practical four-dimensional (4D) planning scheme of IMAT using 4D computed tomography (4D CT) for planning tumor tracking with dynamic multileaf beam collimation. We assume that patients can breathe regularly, i.e. the same way as during 4D CT with an unchanged period and amplitude, and that the start of 4D-IMAT delivery can be synchronized with a designated respiratory phase. Each control point of the IMAT-delivery process can be associated with an image set of 4D CT at a specified respiratory phase. Target is contoured at each respiratory phase without a motion-induced margin. A 3D-IMAT plan is first optimized on a reference-phase image set of 4D CT. Then, based on the projections of the planning target volume in the beam's eye view at different respiratory phases, a 4D-IMAT plan is generated by transforming the segments of the optimized 3D plan by using a direct aperture deformation method. Compensation for both translational and deformable tumor motion is accomplished, and the smooth delivery of the transformed plan is ensured by forcing connectivity between adjacent angles (control points). It is envisioned that the resultant plans can be delivered accurately using the dose rate regulated tracking method which handles breathing irregularities (Yi et al 2008 Med. Phys. 35 3955-62).This planning process is straightforward and only adds a small step to current clinical 3D planning practice. Our 4D planning scheme was tested on three cases to evaluate dosimetric benefits. The created 4D-IMAT plans showed similar dose distributions as compared with the 3D-IMAT plans on a single static phase, indicating that our method is capable of eliminating the dosimetric effects of breathing induced target motion. Compared to the 3D-IMAT plans with large treatment margins encompassing respiratory motion, our 4D-IMAT plans reduced radiation doses to surrounding normal organs and tissues.

Clinical implementation of an electron monitor unit dosimetry system based on task group 71 report and a commercial calculation program.

Many clinics still use monitor unit (MU) calculations for electron treatment planning and/or quality assurance (QA). This work (1) investigates the clinical implementation of a dosimetry system including a modified American Association of Physicists in Medicine-task group-71 (TG-71)-based electron MU calculation protocol (modified TG-71 electron [mTG-71E] and an independent commercial calculation program and (2) provides the practice recommendations for clinical usage. Following the recently published TG-71 guidance, an organized mTG-71E databook was developed to facilitate data access and subsequent MU computation according to our clinical need. A recently released commercial secondary calculation program - Mobius3D (version 1.5.1) Electron Quick Calc (EQC) (Mobius Medical System, LP, Houston, TX, USA), with inherent pencil beam algorithm and independent beam data, was used to corroborate the calculation results. For various setups, the calculation consistency and accuracy of mTG-71E and EQC were validated by their cross-comparison and the ion chamber measurements in a solid water phantom. Our results show good agreement between mTG-71E and EQC calculations, with average 2% difference. Both mTG-71E and EQC calculations match with measurements within 3%. In general, these differences increase with decreased cutout size, increased extended source to surface distance, and lower energy. It is feasible to use TG71 and Mobius3D clinically as primary and secondary electron MU calculations or vice versa. We recommend a practice that only requires patient-specific measurements in rare cases when mTG-71E and EQC calculations differ by 5% or more.

Optimizing the MLC model parameters for IMRT in the RayStation treatment planning system.

Unlike other commercial treatment planning systems (TPS) which model the rounded leaf end differently (such as the MLC dosimetric leaf gap (DLG) or rounded leaf-tip radius), the RayStation TPS (RaySearch Laboratories, Stockholm, Sweden) models transmission through the rounded leaf end of the MLC with a step function, in which the radiation transmission through the leaf end is the square root of the average MLC transmission factor. We report on the optimization of MLC model parameters for the RayStation planning system. This (TPS) models the rounded leaf end of the MLC with the following parameters: eaf-tip offset, leaf-tip width, average transmission factor, and tongue and groove. We optimized the MLC model parameters for IMRT in the RayStation v. 4.0 planning system and for a Varian C-series linac with a 120-leaf Millennium MLC, and validated the model using measured data. The leaf-tip offset is the geometric offset due to the rounded leaf-end design and resulting divergence of the light/radiation field. The offset value is a function of the leaf-tip position, and tabulated data are available from the vendor. The leaf-tip width was iteratively evaluated by comparing computed and measured transverse dose profiles of MLC defined fields at dmax in water. In-water profile comparisons were also used to verify the MLC leaf position (leaf-tip offset). The average transmission factor and leaf tongue-and-groove width were derived iteratively by maximizing the agreement between measurements and RayStation TPS calculations for five clinical IMRT QA plans. Plan verifications were performed by comparing MapCHECK2 measurements and Monte Carlo calculations. The MLC model was validated using five test IMRT cases from the AAPM Task Group 119 report. Absolute gamma analyses (3 mm/3% and 2 mm/2%) were applied. In addition, computed output factors for MLC-defined small fields (2 × 2, 3 × 3, 4 × 4, 6× 6cm2) of both 6 MV and 18 MV photons were compared to those independently measured by the Imaging and Radiation Oncology Core (IROC), Houston, TX. 6MV and 18 MV models were both determined to have the same MLC parameters: leaf-tip offset = 0.3 cm, 2.5% transmission, and leaf tongue-and-groove width = 0.05 cm. IMRT QA analysis for five test cases in TG-119 resulted in a 100% passing rate with 3 mm/3% gamma analysis for 6 MV, and > 97.5% for 18 MV. The passing rate was > 94.6% for 6 MV and > 90.9% for 18 MV when the 2 mm/2% gamma analysis criteria was applied. These results compared favorably with those published in AAPM Task Group 119. The reported MLC model parameters serve as a reference for other users.

Four-dimensional dose distributions of step-and-shoot IMRT delivered with real-time tumor tracking for patients with irregular breathing: constant dose rate vs dose rate regulation.

PURPOSE: Dose-rate-regulated tracking (DRRT) is a tumor tracking strategy that programs the MLC to track the tumor under regular breathing and adapts to breathing irregularities during delivery using dose rate regulation. Constant-dose-rate tracking (CDRT) is a strategy that dynamically repositions the beam to account for intrafractional 3D target motion according to real-time information of target location obtained from an independent position monitoring system. The purpose of this study is to illustrate the differences in the effectiveness and delivery accuracy between these two tracking methods in the presence of breathing irregularities. METHODS: Step-and-shoot IMRT plans optimized at a reference phase were extended to remaining phases to generate 10-phased 4D-IMRT plans using segment aperture morphing (SAM) algorithm, where both tumor displacement and deformation were considered. A SAM-based 4D plan has been demonstrated to provide better plan quality than plans not considering target deformation. However, delivering such a plan requires preprogramming of the MLC aperture sequence. Deliveries of the 4D plans using DRRT and CDRT tracking approaches were simulated assuming the breathing period is either shorter or longer than the planning day, for 4 IMRT cases: two lung and two pancreatic cases with maximum GTV centroid motion greater than 1 cm were selected. In DRRT, dose rate was regulated to speed up or slow down delivery as needed such that each planned segment is delivered at the planned breathing phase. In CDRT, MLC is separately controlled to follow the tumor motion, but dose rate was kept constant. In addition to breathing period change, effect of breathing amplitude variation on target and critical tissue dose distribution is also evaluated. RESULTS: Delivery of preprogrammed 4D plans by the CDRT method resulted in an average of 5% increase in target dose and noticeable increase in organs at risk (OAR) dose when patient breathing is either 10% faster or slower than the planning day. In contrast, DRRT method showed less than 1% reduction in target dose and no noticeable change in OAR dose under the same breathing period irregularities. When ±20% variation of target motion amplitude was present as breathing irregularity, the two delivery methods show compatible plan quality if the dose distribution of CDRT delivery is renormalized. CONCLUSIONS: Delivery of 4D-IMRT treatment plans, stemmed from 3D step-and-shoot IMRT and preprogrammed using SAM algorithm, is simulated for two dynamic MLC-based real-time tumor tracking strategies: with and without dose-rate regulation. Comparison of cumulative dose distribution indicates that the preprogrammed 4D plan is more accurately and efficiently conformed using the DRRT strategy, as it compensates the interplay between patient breathing irregularity and tracking delivery without compromising the segment-weight modulation.

Direct observation of inhomogeneous solid electrolyte interphase on MnO anode with atomic force microscopy and spectroscopy.

Solid electrolyte interphase (SEI) is an in situ formed thin coating on lithium ion battery (LIB) electrodes. The mechanical property of SEI largely defines the cycling performance and the safety of LIBs but has been rarely investigated. Here, we report quantitatively the Young's modulus of SEI films on MnO anodes. The inhomogeneity of SEI film in morphology, structure, and mechanical properties provides new insights to the evolution of SEI on electrodes. Furthermore, the quantitative methodology established in this study opens a new approach to direct investigation of SEI properties in various electrode materials systems.