A case of intramandibular epidermoid cyst and literature analysis.

Epidermoid cysts are generally benign neoplastic lesions, the etiology of which is unclear and is mainly related to epithelial cells left in the tissues during the embryonic period and traumatically implanted in the tissues. The most common intraosseous sites are the phalanges and the skull. Epidermoid cysts occurring in the jaws are clinically rare. In this paper, we report a case of epidermoid cyst occurring in the mandible with embedded teeth and discuss the etiology, clinical manifestations, diagnosis, and treatment of epidermoid cysts in the jaws in the context of the relevant literature.

Commissioning, clinical implementation, and initial experience with a new brain tumor treatment package on a low-field MR-linac.

To evaluate the image quality, dosimetric properties, setup reproducibility, and planar cine motion detection of a high-resolution brain coil and integrated stereotactic brain immobilization system that constitute a new brain treatment package (BTP) on a low-field magnetic resonance imaging (MRI) linear accelerator (MR-linac). Image quality of the high-resolution brain coil was evaluated with the 17 cm diameter spherical phantom and the American College of Radiology (ACR) Large MRI Phantom. Patient imaging studies approved by the institutional review board (IRB) assisted in selecting image acquisition parameters. Radiographic and dosimetric evaluation of the high-resolution brain coil and the associated immobilization devices was performed using dose calculations and ion chamber measurements. End-to-end testing was performed simulating a cranial lesion in a phantom. Inter-fraction setup variability and motion detection tests were evaluated on four healthy volunteers. Inter-fraction variability was assessed based on three repeat setups for each volunteer. Motion detection was evaluated using three-plane (axial, coronal, and sagittal) MR-cine imaging sessions, where volunteers were asked to perform a set of specific motions. The images were post-processed and evaluated using an in-house program. Contrast resolution of the high-resolution brain coil is superior to the head/neck and torso coils. The BTP receiver coils have an average HU value of 525 HU. The most significant radiation attenuation (3.14%) of the BTP, occurs through the lateral portion of the overlay board where the high-precision lateral-profile mask clips attach to the overlay. The greatest inter-fraction setup variability occurred in the pitch (average 1.08 degree) and translationally in the superior/inferior direction (average 4.88 mm). Three plane cine imaging with the BTP was able to detect large and small motions. Small voluntary motions, sub-millimeter in magnitude (maximum 0.9 mm), from motion of external limbs were detected. Imaging tests, inter-fraction setup variability, attenuation, and end-to-end measurements were quantified and performed for the BTP. Results demonstrate better contrast resolution and low contrast detectability that allows for better visualization of soft tissue anatomical changes relative to head/neck and torso coil systems.

[Analysis of clinical effects and risk factors of short implant followed up for 7-9 years].

PURPOSE: To evaluate the long-term clinical efficacy of short implants and analyze the influencing factors of the survival rate. METHODS: A total of 178 patients who received implant therapy in the Department of Stomatology, the Fourth Affiliated Hospital of Nanchang University from January 2010 to December 2014 were selected, including 334 short implants of Bicon (implant length ≤6 mm). The basic condition, restoration design, short implant survival rate and complications were observed and analyzed. SPSS 24.0 software package was used for data analysis. RESULTS: The average follow-up time of short implants was 96±17 months. During the observation period, 20 implants failed, 1 implant had mechanical complications and 6 implants had biological complications. Based on the analysis of implants and patients, the long-term cumulative survival rate of short implants was 94.0%(over 5 years survival rate was 96.4%) and 90.4% respectively. There was no significant difference between the survival rate of short implants and the patient's gender, age, whether to use special operation and the type of jaw teeth(P＜0.05). Smoking and periodontitis were risk factors for failure of short implants(P＜0.05).The difference of short implant survival rate between short implants restoration with combined crowns and single crowns was statistically significant(P＜0.05). The survival rate of short implant in mandible was higher than that in maxilla(P＜0.05). CONCLUSIONS: Under the standards clinical program and operation, short implant can be used to shorten the implant restoration cycle and avoid complicated bone augmentation which can achieve good long-term clinical effect. Short implant should be used to strictly control the risk factors that affect the survival of short implant.

Association Between Internal Organ/Liver Tumor and External Surface Motion From Cine MR Images on an MRI-Linac.

Purposes/Objectives: Historically, motion correlation between internal tumor and external surrogates have been based on limited sets of X-ray or magnetic resonance (MR) images. With the recent clinical implementation of MR-guided linear accelerators, a vast quantity of continuous planar real-time MR imaging data is acquired. In this study, information was extracted from MR cine imaging during liver cancer treatments to establish associations between internal tumor/diaphragm and external surface/skin movement. Methods and Materials: This retrospective study used 305,644 MR image frames acquired over 118 treatment/imaging sessions of the first 23 liver cancer patients treated on an MRI-linac. 9 features were automatically determined on each MR image frame: Lung_Area, the posterior (Dia_Post), dome (Dia_Dome), and anterior (Dia_Ant) points of a diaphragmatic curve and the diaphragm curve point (Dia_Max), the chest (Chest) and the belly (Belly) skin points experiencing the maximum motion ranges; the superior-interior (SI) and posterior-anterior (PA) positions of a target. For every session, correlation analyses were performed twice among the 9 features: 1) over a breath-hold (BH) set and 2) on a pseudo free-breathing (PFB) generated by removing breath-holding frames. Results: 303,123 frames of images were successfully analyzed. For BH set analysis, correlation coefficients were as follows: 0.94 ± 0.07 between any two features among Dia_Post, Dia_Dome, Dia_Max, and Lung_Area; 0.95 ± 0.06 between SI and any feature among Dia_Post, Dia_Dome, Dia_Max, or Lung_Area; 0.76 ± 0.29 between SI and Belly (with 50% of correlations ≥ 0.87). The PFB set had 142,862 frames of images. For this set, correlation coefficients were 0.96 ± 0.06 between any two features among Dia_Post, Dia_Dome, Dia_Max, and Lung_Area; 0.95 ± 0.06 between SI and any feature among Dia_Post, Dia_Dome, Dia_Max, or Lung_Area; 0.80 ± 0.26 between SI and Belly (with 50% of correlations ≥ 0.91). Conclusion: Diaphragmatic motion as assessed by cine MR imaging is highly correlated with liver tumor motion. Belly vertical motion is highly correlated with liver tumor longitudinal motion in approximately half of the cases. More detailed analyses of those cases displaying weak correlations are in progress.

PlantcircBase 7.0: Full-length transcripts and conservation of plant circRNAs.

Circular RNA (circRNA) is a special type of non-coding RNA that participates in diverse biological processes in both animals and plants. Five years ago, we developed a comprehensive plant circRNA database (PlantcircBase), which has attracted much attention from the plant circRNA community. Here, we report an updated PlantcircBase (v.7.0), which contains 171,118 circRNAs from 21 plant species. Over 31,000 of the circRNAs have full-length sequences constructed based on analysis of 749 bulk RNA sequencing (RNA-seq) datasets downloaded from the public domain and Nanopore long-read sequencing results of rice RNAs newly generated in this study. A plant multiple conservation score (PMCS), based on the conservation of both sequence and expression profiles, was calculated for each circRNA to quantify and compare the conservation of all circRNAs. A new parameter, plant circRNA confidence level (PCCL), is introduced to measure the identity reliability of each circRNA based on experimental validation results and the number of references that support the circRNA. All this information and other details of circRNAs can be browsed, searched, and downloaded from PlantcircBase 7.0, which also provides online bioinformatics tools for visualization and sequence alignment. PlantcircBase 7.0 is publicly and freely accessible at http://ibi.zju.edu.cn/plantcircbase/.

Evaluation of Auto-Contouring and Dose Distributions for Online Adaptive Radiation Therapy of Patients With Locally Advanced Lung Cancers.

PURPOSE: Retrospective studies were performed to evaluate the accuracy of automatically mapped structures and dosimetric consequences of daily online adaptive radiation therapy (ART) for lung cancer treatments. METHODS AND MATERIALS: Ten patients with locally advanced lung cancer (prescription = 2 Gy × 30) with 297 fractions of treatment were selected for this retrospective study on a research emulator (Ethos, Varian Medical Systems). All adaptive treatments were simulated twice: automatic-ART (A-ART), automatic contours were used without modification, and supervised-ART (S-ART), automatic contours were modified manually by physicians and physicists. Dosimetric results were analyzed by relating supervised scheduled (S-SCH) dose (initial baseline reference plan delivered on daily anatomy and supervised contour correction without any adaptation), A-ART and S-ART to the initial baseline reference dose. RESULTS: Two hundred ninety (of 297) fractions were analyzed. Comparing target volumes between A-ART and S-ART, dice similarity coefficient was 0.93 ± 0.05, mean contour distance was 1.5 ± 1.2 mm, and Hausdorff distance was 4.0 ± 2.3 mm. Analysis of daily results over 290 fractions of treatment showed that average target coverage improved from 0.96 ± 0.04 (S-SCH) to 1.00 ± 0.02 (A-ART) and 1.02 ± 0.04 (S-ART); average upper dose constraint was reduced from 1.01 ± 0.11 (S-SCH) to 0.94 ± 0.10 (A-ART) and 0.93 ± 0.12 (S-ART). A-ART and S-ART improved planning target volume minimum doses by 4.85 ± 3.03 Gy (P = .049) and 4.46 ± 8.99 Gy (P = .058), respectively. Statistical analysis shows that A-ART and S-ART significantly improved cumulative target dose by 0.033 ± 0.087 (P = .002) and 0.032 ± 0.086 (P = .003) and reduced upper constraints by 0.033 ± 0.072 (P < .001) and 0.032 ± 0.072 (P < .001) relative to S-SCH dose results, respectively. CONCLUSIONS: Accuracy of Ethos automatic contouring for lung cancer is considered clinically acceptable. The online adaptive radiation therapy improves target coverage and spares organs-at-risk significantly.

How does CBCT reconstruction algorithm impact on deformably mapped targets and accumulated dose distributions?

PURPOSE: We performed quantitative analysis of differences in deformable image registration (DIR) and deformable dose accumulation (DDA) computed on CBCT datasets reconstructed using the standard (Feldkamp-Davis-Kress: FDK_CBCT) and a novel iterative (iterative_CBCT) CBCT reconstruction algorithms. METHODS: Both FDK_CBCT and iterative_CBCT images were reconstructed for 323 fractions of treatment for 10 prostate cancer patients. Planning CT images were deformably registered to each CBCT image data set. After daily dose distributions were computed, they were mapped to planning CT to obtain deformed doses. Dosimetric and image registration results based CBCT images reconstructed by two algorithms were compared at three levels: (A) voxel doses over entire dose calculation volume, (B) clinical constraint results on targets and sensitive structures, and (C) contours propagated to CBCT images using DIR results based on three algorithms (SmartAdapt, Velocity, and Elastix) were compared with manually delineated contours as ground truth. RESULTS: (A) Average daily dose differences and average normalized DDA differences between FDK_CBCT and iterative_CBCT were ≤1 cGy. Maximum daily point dose differences increased from 0.22 ± 0.06 Gy (before the deformable dose mapping operation) to 1.33 ± 0.38 Gy after the deformable dose mapping. Maximum differences of normalized DDA per fraction were up to 0.80 Gy (0.42 ± 0.19 Gy). (B) Differences in target minimum doses were up to 8.31 Gy (-0.62 ± 4.60 Gy) and differences in critical structure doses were 0.70 ± 1.49 Gy. (C) For mapped prostate contours based on iterative_CBCT (relative to standard FDK_CBCT), dice similarity coefficient increased by 0.10 ± 0.09 (p < 0.0001), mass center distances decreased by 2.5 ± 3.0 mm (p < 0.00005), and Hausdorff distances decreased by 3.3 ± 4.4 mm (p < 0.00015). CONCLUSIONS: The new iterative CBCT reconstruction algorithm leads to different mapped volumes of interest, deformed and cumulative doses than results based on conventional FDK_CBCT.

Strigolactone GR24 improves cadmium tolerance by regulating cadmium uptake, nitric oxide signaling and antioxidant metabolism in barley (Hordeum vulgare L.).

Cadmium (Cd) in the food chain poses a serious hazard to human health. Therefore, a greenhouse hydroponic experiment was conducted to examine the potential of exogenously strigolactone GR24 in lessening Cd toxicity and to investigate its physiological mechanisms in the two barley genotypes, W6nk2 (Cd-sensitive) and Zhenong8 (Cd-tolerant). Exogenous application of 1 µM GR24 (strigol analogue) reduced the suppression of growth caused by 10 µM Cd, lowered plant Cd contents, increased the contents of other nutrient elements, protected chlorophyll, sustained photosynthesis, and markedly reduced Cd-induced H2O2 and malondialdehyde accumulation in barley. Furthermore, exogenous GR24 markedly increased NO contents and nitric oxide synthase activity in the Cd-sensitive genotype, W6nk2, effectively alleviating the Cd-induced repression of the activities of superoxide dismutase and peroxidase, increasing reduced glutathione (GSH) and ascorbic acid (AsA) pools and activities of AsA-GSH cycle including ascorbate peroxidase, glutathione peroxidase, glutathione reductase, dehydroascorbate reductase and monodehydroascorbate reductase. The findings of the present study indicate that GR24 could be a candidate for Cd detoxification by decreasing Cd contents, balancing nutrient elements, and protecting barley plants from toxic oxidation via indirectly eliminating reactive oxygen species (ROS), consequently contributing to reducing the potential risk of Cd pollution.

Biofertilizer-induced response to cadmium accumulation in Oryza sativa L. grains involving exogenous organic matter and soil bacterial community structure.

The accumulation of cadmium (Cd) in Oryza sativa L., the world's most significant staple crop, is a health threat to millions of people. The objective of this study was to evaluate the effectiveness of commercially available biofertilizers (with high (BF2) and low organic matter (OM) content (BF1)) on Cd accumulation in two types of soils and to determine the bacterial community responses by high-throughput sequencing. The study was conducted in the form of pot experiment in greenhouse in 2018. Four treatments were set: BF1, BF2, organic fertilizer (OF), and control (CK) and the amendments were applied before the rice cultivation. The results showed that the addition of biofertilizers immobilized or mobilized Cd in soils, depending on the soil type and the OM content in biofertilizers. The exogenous OM in biofertilizers was the driving factor for the difference in pH and Cd accumulation in rice grains. The application of biofertilizers with high OM content was effective in reducing Cd accumulation in the rice grains (19.7% lower than CK) by significantly increasing soil pH (from 6.02 to 6.67) in acid silt loam soil (TZ). The consumption of acid fermentation products by soil chemoorganotrophs and the complexation of organic anions in the biofertilizer treatment tended to buffer the pH drop in the drainage and decrease the Cd availability. However, in the weak acid silty clay loam soil (SX), the addition of biofertilizer with high OM significantly increased Cd accumulation in rice grains (21.9% higher than CK), probably owing to the release of acid substances, resulting from the significant increase of the predominant bacteria Chloroflexi. The addition of biofertilizer with low OM content did not significantly change Cd accumulation in rice grains or affect the soil microbial structures in both soils. In conclusion, the effects of biofertilizer on rice Cd accumulation were related to the OM content and soil bacterial community. Biofertilizers with high organic matter may not be suitable for amendments in the paddy soils with high clay content to reduce Cd accumulation in rice grains.

Technical Note: Comparison of the internal target volume (ITV) contours and dose calculations on 4DCT, average CBCT, and 4DCBCT imaging for lung stereotactic body radiation therapy (SBRT).

PURPOSE: To investigate the differences between internal target volumes (ITVs) contoured on the simulation 4DCT and daily 4DCBCT images for lung cancer patients treated with stereotactic body radiotherapy (SBRT) and determine the dose delivered on 4D planning technique. METHODS: For nine patients, 4DCBCTs were acquired before each fraction to assess tumor motion. An ITV was contoured on each phase of the 4DCBCT and a union of the 10 ITVs was used to create a composite ITV. Another ITV was drawn on the average 3DCBCT (avgCBCT) to compare with current clinical practice. The Dice coefficient, Hausdorff distance, and center of mass (COM) were averaged over four fractions to compare the ITVs contoured on the 4DCT, avgCBCT, and 4DCBCT for each patient. Planning was done on the average CT, and using the online registration, plans were calculated on each phase of the 4DCBCT and on the avgCBCT. Plan dose calculations were tested by measuring ion chamber dose in the CIRS lung phantom. RESULTS: The Dice coefficients were similar for all three comparisons: avgCBCT-to-4DCBCT (0.7 ± 0.1), 4DCT-to-avgCBCT (0.7 ± 0.1), and 4DCT-to-4DCBCT (0.7 ± 0.1); while the mean COM differences were also comparable (2.6 ± 2.2mm, 2.3 ± 1.4mm, and 3.1 ± 1.1mm, respectively). The Hausdorff distances for the comparisons with 4DCBCT (8.2 ± 2.9mm and 8.1 ± 3.2mm) were larger than the comparison without (6.5 ± 2.5mm). The differences in ITV D95% between the treatment plan and avgCBCT calculations were 4.3 ± 3.0% and -0.5 ± 4.6%, between treatment plan and 4DCBCT plans, respectively, while the ITV V100% coverages were 99.0 ± 1.9% and 93.1 ± 8.0% for avgCBCT and 4DCBCT, respectively. CONCLUSION: There is great potential for 4DCBCT to evaluate the extent of tumor motion before treatment, but image quality challenges the clinician to consistently delineate lung target volumes.

Hexachlorocyclohexane exposure alters the microbiome of colostrum in Chinese breastfeeding mothers.

Breast milk, especially colostrum, is not just a source of nutrients and immune factors for the newborn, but also accumulates environmental persistent pollutants and its diverse microbes affect the early colonization of the newborn's gut. Little is known about associations between environmental pollutants and the microbial composition of human colostrum. We assessed the influence of hexachlorocyclohexane (HCH), a persistent organic pollutant (POP), in colostrums on the microbial composition of human colostrum samples. HCH concentrations in 89 colostrum samples collected from a population living on the easternmost island of China were measured via gas chromatography equipped with mass spectrometer (GC-MS), HCH exposure risks for infants via dietary intake of breast milk were assessed, and for 29 colostrum samples the microbiota were profiled using 16S rRNA gene pyrosequencing to assess the association with HCH exposure levels. Our study confirmed high colostrum exposure levels of total HCHs (12.19 ±â€¯13.68 µg L-1) in this Chinese population. We predominantly identified Proteobacteria (67.6%) and Firmicutes (25.1%) in colostrum and microbial diversity at the genus level differed between samples with different HCH levels; e.g., Pseudomonas which contains several HCH degrading strains was found in significantly higher abundance in γ-HCH rich samples. Also, microbes that were statistically significantly associated with HCH levels were also highly correlated with each other (false discovery rate (FDR)＜0.01) and clustered in network analysis. Microbial diversity is associated with HCH levels in human colostrum and these associations might be attributable to their HCH degrading ability. These finding provide first insights into the role that environmental persistent pollutants may play in the microbial composition of human colostrum and the colonization of the infant gut.

Prevalence and distribution of HPV types in genital warts in Xi'an, China: a prospective study.

OBJECTIVES: To characterise the prevalence and distribution of human papillomavirus (HPV) types in genital warts in Xi'an, China. METHODS: This prospective study was conducted in Shaanxi Provincial Institute for Skin Disease and STD Control (SPISSC) between September 2014 and April 2017. Genital wart samples were obtained from 879 patients, including 512 men and 367 women. HPV genotyping was performed by using an automatic nucleic acid hybridisation system. RESULTS: Of the 879 patients with genital warts, the detectable rates of low-risk, high-risk and total HPV types were 45.4%, 34.5% and 57.8%, respectively. The detectable rate of low-risk HPV types (45.4%) was significantly higher than that of high-risk HPV types (34.5%) (χ2=21.85, p<0.01). The detectable rate of low-risk HPV types of men (52.3%) was significantly higher than that of women (35.7%) (χ2=23.90, p<0.01). The detectable rates of one HPV type infection and two and three or more HPV type coinfections were 26.1%, 17.5% and 14.2%, respectively. HPV6 (24.9%), HPV11 (17.9%), HPV52 (9.9%) and HPV16 (7.3%) were the four most common HPV types. CONCLUSIONS: The results of this study suggest that low-risk HPV types are major pathogens of genital warts, but high-risk HPV type infections and multiple HPV type coinfections are also common in genital warts. HPV6, 11, 52 and 16 are the four most common HPV types in genital wart in Xi'an, China.

Improvements in CBCT Image Quality Using a Novel Iterative Reconstruction Algorithm: A Clinical Evaluation.

PURPOSE: This study aimed to evaluate the clinical utility of a novel iterative cone beam computed tomography (CBCT) reconstruction algorithm for prostate and head and neck (HN) cancer. METHODS AND MATERIALS: A total of 10 patients with HN and 10 patients with prostate cancer were analyzed. For each patient, raw CBCT acquisition data were used to reconstruct images with a currently available algorithm (FDK_CBCT) and novel iterative algorithm (Iterative_CBCT). Quantitative contouring variation analysis was performed using structures delineated by several radiation oncologists. For prostate, observers contoured the prostate, proximal 2 cm seminal vesicles, bladder, and rectum. For HN, observers contoured the brain stem, spinal canal, right-left parotid glands, and right-left submandibular glands. Observer contours were combined to form a reference consensus contour using the simultaneous truth and performance level estimation method. All observer contours then were compared with the reference contour to calculate the Dice coefficient, Hausdorff distance, and mean contour distance (prostate contour only). Qualitative image quality analysis was performed using a 5-point scale ranging from 1 (much superior image quality for Iterative_CBCT) to 5 (much inferior image quality for Iterative_CBCT). RESULTS: The Iterative_CBCT data sets resulted in a prostate contour Dice coefficient improvement of approximately 2.4% (P = .029). The average prostate contour Dice coefficient for the Iterative_CBCT data sets was improved for all patients, with improvements up to approximately 10% for 1 patient. The mean contour distance results indicate an approximate 15% reduction in mean contouring error for all prostate regions. For the parotid contours, Iterative_CBCT data sets resulted in a Hausdorff distance improvement of approximately 2 mm (P < .01) and an approximate 2% improvement in Dice coefficient (P = .03). The Iterative_CBCT data sets were scored as equivalent or of better image quality for 97.3% (prostate) and 90.0% (HN) of the patient data sets. CONCLUSIONS: Observers noted an improvement in image uniformity, noise level, and overall image quality for Iterative_CBCT data sets. In addition, expert observers displayed an improved ability to consistently delineate soft tissue structures, such as the prostate and parotid glands. Thus, the novel iterative reconstruction algorithm analyzed in this study is capable of improving the visualization for prostate and HN cancer image guided radiation therapy.

Evaluation and Clinical Application of a Commercially Available Iterative Reconstruction Algorithm for CBCT-Based IGRT.

PURPOSE: We have quantitatively evaluated the image quality of a new commercially available iterative cone-beam computed tomography reconstruction algorithm over standard cone-beam computed tomography image reconstruction results. METHODS: This iterative cone-beam computed tomography reconstruction pipeline uses a finite element solver (AcurosCTS)-based scatter correction and a statistical (iterative) reconstruction in addition to a standard kernel-based correction followed by filtered back-projection-based Feldkamp-Davis-Kress cone-beam computed tomography reconstruction. Standard full-fan half-rotation Head, half-fan full-rotation Head, and standard Pelvis cone-beam computed tomography protocols have been investigated to scan a quality assurance phantom via the following image quality metrics: uniformity, HU constancy, spatial resolution, low contrast detection, noise level, and contrast-to-noise ratio. An anthropomorphic head phantom was scanned for verification of noise reduction. Clinical patient image data sets for 5 head/neck patients and 5 prostate patients were qualitatively evaluated. RESULTS: Quality assurance phantom study results showed that relative to filtered back-projection-based cone-beam computed tomography, noise was reduced from 28.8 ± 0.3 HU to a range between 18.3 ± 0.2 and 5.9 ± 0.2 HU for Full-Fan Head scans, from 14.4 ± 0.2 HU to a range between 12.8 ± 0.3 and 5.2 ± 0.3 HU for Half-Fan Head scans, and from 6.2 ± 0.1 HU to a range between 3.8 ± 0.1 and 2.0 ± 0.2 HU for Pelvis scans, with the iterative cone-beam computed tomography algorithm. Spatial resolution was marginally improved while results for uniformity and HU constancy were similar. For the head phantom study, noise was reduced from 43.6 HU to a range between 24.8 and 13.0 HU for a Full-Fan Head and from 35.1 HU to a range between 22.9 and 14.0 HU for a Half-Fan Head scan. The patient data study showed that artifacts due to photon starvation and streak artifacts were all reduced, and image noise in specified target regions were reduced to 62% ± 15% for 10 patients. CONCLUSION: Noise and contrast-to-noise ratio image quality characteristics were significantly improved using the iterative cone-beam computed tomography reconstruction algorithm relative to the filtered back-projection-based cone-beam computed tomography method. These improvements will enhance the accuracy of cone-beam computed tomography-based image-guided applications.

On the improvement of CBCT image quality for soft tissue-based SRS localization.

PURPOSE: We explore the optimal cone-beam CT (CBCT) acquisition parameters to improve CBCT image quality to enhance intracranial stereotactic radiosurgery (SRS) localization and also assess the imaging dose levels associated with each imaging protocol. METHODS: Twenty-six CBCT acquisition protocols were generated on an Edge® linear accelerator (Varian Medical Systems, Palo Alto, CA) with different x-ray tube current and potential settings, gantry rotation trajectories, and gantry rotation speeds. To assess image quality, images of the Catphan 504 phantom were analyzed to evaluate the following image quality metrics: uniformity, HU constancy, spatial resolution, low contrast detection, noise level, and contrast-to-noise ratio (CNR). To evaluate the imaging dose for each protocol, the cone-beam dose index (CBDI) was measured. To validate the phantom results, further analysis was performed with an anthropomorphic head phantom as well as image data acquired for a clinical SRS patient. RESULTS: The Catphan data indicates that adjusting acquisition parameters had direct effects on the image noise level, low contrast detection, and CNR, but had minimal effects on uniformity, HU constancy, and spatial resolution. The noise level was reduced from 34.5 ± 0.3 to 18.5 ± 0.2 HU with a four-fold reduction in gantry speed, and to 18.7 ± 0.2 HU with a four-fold increase in tube current. Overall, the noise level was found to be proportional to inverse square root of imaging dose, and imaging dose was proportional to the product of total tube current-time product and the cube of the x-ray potential. Analysis of the anthropomorphic head phantom data and clinical SRS imaging data also indicates that noise is reduced with imaging dose increase. CONCLUSIONS: Our results indicate that optimization of the imaging protocol, and thereby an increase in the imaging dose, is warranted for improved soft-tissue visualization for intracranial SRS.

Effect of air pollution on the total bacteria and pathogenic bacteria in different sizes of particulate matter.

In recent years, air pollution events have occurred frequently in China during the winter. Most studies have focused on the physical and chemical composition of polluted air. Some studies have examined the bacterial bioaerosols both indoors and outdoors. But few studies have focused on the relationship between air pollution and bacteria, especially pathogenic bacteria. Airborne PM samples with different diameters and different air quality index values were collected in Hangzhou, China from December 2014 to January 2015. High-throughput sequencing of 16S rRNA was used to categorize the airborne bacteria. Based on the NCBI database, the "Human Pathogen Database" was established, which is related to human health. Among all the PM samples, the diversity and concentration of total bacteria were lowest in the moderately or heavily polluted air. However, in the PM2.5 and PM10 samples, the relative abundances of pathogenic bacteria were highest in the heavily and moderately polluted air respectively. Considering the PM samples with different particle sizes, the diversities of total bacteria and the proportion of pathogenic bacteria in the PM10 samples were different from those in the PM2.5 and TSP samples. The composition of PM samples with different sizes range may be responsible for the variances. The relative humidity, carbon monoxide and ozone concentrations were the main factors, which affected the diversity of total bacteria and the proportion of pathogenic bacteria. Among the different environmental samples, the compositions of the total bacteria were very similar in all the airborne PM samples, but different from those in the water, surface soil, and ground dust samples. Which may be attributed to that the long-distance transport of the airflow may influence the composition of the airborne bacteria. This study of the pathogenic bacteria in airborne PM samples can provide a reference for environmental and public health researchers.

Online dosimetric evaluation of larynx SBRT: A pilot study to assess the necessity of adaptive replanning.

PURPOSE: We have initiated a multi-institutional phase I trial of 5-fraction stereotactic body radiotherapy (SBRT) for Stage III-IVa laryngeal cancer. We conducted this pilot dosimetric study to confirm potential utility of online adaptive replanning to preserve treatment quality. METHODS: We evaluated ten cases: five patients enrolled onto the current trial and five patients enrolled onto a separate phase I SBRT trial for early-stage glottic larynx cancer. Baseline SBRT treatment plans were generated per protocol. Daily cone-beam CT (CBCT) or diagnostic CT images were acquired prior to each treatment fraction. Simulation CT images and target volumes were deformably registered to daily volumetric images, the original SBRT plan was copied to the deformed images and contours, delivered dose distributions were re-calculated on the deformed CT images. All of these were performed on a commercial treatment planning system. In-house software was developed to propagate the delivered dose distribution back to reference CT images using the deformation information exported from the treatment planning system. Dosimetric differences were evaluated via dose-volume histograms. RESULTS: We could evaluate dose within 10 minutes in all cases. Prescribed coverage to gross tumor volume (GTV) and clinical target volume (CTV) was uniformly preserved; however, intended prescription dose coverage of planning treatment volume (PTV) was lost in 53% of daily treatments (mean: 93.9%, range: 83.9-97.9%). Maximum bystander point dose limits to arytenoids, parotids, and spinal cord remained respected in all cases, although variances in carotid artery doses were observed in a minority of cases. CONCLUSIONS: Although GTV and CTV SBRT dose coverage is preserved with in-room three-dimensional image guidance, PTV coverage can vary significantly from intended plans and dose to critical structures may exceed tolerances. Online adaptive treatment re-planning is potentially necessary and clinically applicable to fully preserve treatment quality. Confirmatory trial accrual and analysis remains ongoing.

Characterization of a disease susceptibility locus for exploring an efficient way to improve rice resistance against bacterial blight.

Bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is the most harmful bacterial disease of rice worldwide. Previously, we characterized major disease resistance (MR) gene xa25, which confers race-specific resistance to Xoo strain PXO339. The xa25 is a recessive allele of the SWEET13 locus, but SWEET13's interaction with PXO339 and how efficiently using this locus for rice breeding still need to be defined. Here we show that the SWEET13 allele from rice Zhenshan 97 is a susceptibility gene to PXO339. Using this allele's promoter to regulate xa25 resulted in disease, suggesting that the promoter is a key determinant in SWEET13 caused disease in Zhanshan 97 after PXO339 infection. PXO339 transcriptionally induces SWEET13 to cause disease. Partial suppressing SWEET13 expression leads to a high level of resistance to PXO339. Thus, the transcriptionally suppressed SWEET13 functions as xa25 in resistance to PXO339. Hybrid rice is widely grown in many countries. However, recessive MR genes have not been efficiently used for disease resistance breeding in hybrid rice production for both parents of the hybrid have to carry the same recessive gene. However, the suppressed SWEET13 functions dominantly, which will have advantage to improve the resistance of hybrid rice to xa25-incomptible Xoo.

Canny edge-based deformable image registration.

This work focuses on developing a 2D Canny edge-based deformable image registration (Canny DIR) algorithm to register in vivo white light images taken at various time points. This method uses a sparse interpolation deformation algorithm to sparsely register regions of the image with strong edge information. A stability criterion is enforced which removes regions of edges that do not deform in a smooth uniform manner. Using a synthetic mouse surface ground truth model, the accuracy of the Canny DIR algorithm was evaluated under axial rotation in the presence of deformation. The accuracy was also tested using fluorescent dye injections, which were then used for gamma analysis to establish a second ground truth. The results indicate that the Canny DIR algorithm performs better than rigid registration, intensity corrected Demons, and distinctive features for all evaluation matrices and ground truth scenarios. In conclusion Canny DIR performs well in the presence of the unique lighting and shading variations associated with white-light-based image registration.

Surface Approximation via Asymptotic Optimal Geometric Partition.

In this paper, we present a novel method on surface partition from the perspective of approximation theory. Different from previous shape proxies, the ellipsoidal variance proxy is proposed to penalize the partition results falling into disconnected parts. On its support, the Principle Component Analysis (PCA) based energy is developed for asymptotic cluster aspect ratio and size control. We provide the theoretical explanation on how the minimization of the PCA-based energy leads to the optimal asymptotic behavior for approximation. Moreover, we show the partitions on densely sampled triangular meshes converge to the theoretic expectations. To evaluate the effectiveness of surface approximation, polygonal/triangular surface remeshing results are generated. The experimental results demonstrate the high approximation quality of our method.