Biomedical subjects

Lixin Gong

Publications and source records attributed to Lixin Gong.

7 recordsLinked to original sources

PubMed2026

Comparative Genomics Reveals Convergent Evolution Between Avivorous Bats (Ia io and Nyctalus aviator).

Investigating the genetic basis of dietary specialization can provide insights into the evolution of niche breadth. In this study, we employed comparative genomics to investigate the adaptive mechanisms enabling two bat species (Nyctalus aviator and Ia io) to shift from insectivory to seasonal bird consumption (avivorous bats). Our findings revealed adaptation related to immune response and lipid metabolism in avivorous bat species. Avivorous bats exhibit strong positive selection and convergent evolution in immune-related genes, which are under heightened selective pressure compared to those of non-avivorous bats. These species also display significantly fewer endogenous retroviral elements. These findings emphasized the significance of immune-driven adaptive evolution in avivory. Additionally, our results showed that the dietary evolution of avivorous bats is accompanied by convergent evolution associated with the lipid metabolism. Notably, CEPT1, the upstream gene required for the activation of the PPAR pathway, underwent positive selection and convergence, which may have affected lipid metabolism. These adaptations may enable avivorous bat species to face the challenge of immune response and nutrition during dietary niche expansion. These findings not only provide comprehensive insights into the adaptive evolution driving the unique diet of avivorous bats but also offered novel perspectives on the molecular mechanisms underlying ecological niche evolution in a dietary context.

Animals↗

PubMed2006

Automatic arm removal in PET and CT images for deformable registration.

Positron emission tomography (PET) imaging is rapidly expanding its role in clinical practice for cancer management. The high sensitivity of PET for functional abnormalities associated with cancer can be confounded by the minimal anatomical information it provides for cancer localization. Computed tomography (CT) provides detailed anatomical information but is less sensitive to pathologies than PET. Thus, combining (i.e., registering) PET and CT images would enable both accurate and sensitive cancer localization with respect to detailed patient anatomy. An additional application area of registration is to align CT-CT scans from serial studies on a patient on a PET/CT scanner to facilitate accurate assessment of therapeutic response from the co-aligned PET images. To facilitate image fusion, we are developing a deformable registration software system using mutual information and a B-spline model of the deformation. When applying deformable registration to whole body images, one of the obstacles is that the arms are present in PET images but not in CT images or are in different positions in serial CT images. This feature mismatch requires a preprocessing step to remove the arms where present and thus adds a manual step in an otherwise automatic algorithm. In this paper, we present a simple yet effective method for automatic arm removal. We demonstrate the efficiency and robustness of this algorithm on both clinical PET and CT images. By streamlining the entire registration process, we expect that the fusion technology will soon find its way into clinics, greatly benefiting cancer diagnosis, staging, therapy planning and treatment monitoring.

Algorithms↗

PubMed2006

Semiautomatic 3-D prostate segmentation from TRUS images using spherical harmonics.

Prostate brachytherapy quality assessment procedure should be performed while the patient is still on the operating table since this would enable physicians to implant additional seeds immediately into the prostate if necessary thus reducing the costs and increasing patient outcome. Seed placement procedure is readily performed under fluoroscopy and ultrasound guidance. Therefore, it has been proposed that seed locations be reconstructed from fluoroscopic images and prostate boundaries be identified in ultrasound images to perform dosimetry in the operating room. However, there is a key hurdle that needs to be overcome to perform the ultrasound and fluoroscopy-based dosimetry: it is highly time-consuming for physicians to outline prostate boundaries in ultrasound images manually, and there is no method that enables physicians to identify three-dimensional (3-D) prostate boundaries in postimplant ultrasound images in a fast and robust fashion. In this paper, we propose a new method where the segmentation is defined in an optimization framework as fitting the best surface to the underlying images under shape constraints. To derive these constraints, we modeled the shape of the prostate using spherical harmonics of degree eight and performed statistical analysis on the shape parameters. After user initialization, our algorithm identifies the prostate boundaries on the average in 2 min. For algorithm validation, we collected 30 postimplant prostate volume sets, each consisting of axial transrectal ultrasound images acquired at 1-mm increments. For each volume set, three experts outlined the prostate boundaries first manually and then using our algorithm. By treating the average of manual boundaries as the ground truth, we computed the segmentation error. The overall mean absolute distance error was 1.26 +/- 0.41 mm while the percent volume overlap was 83.5 +/- 4.2. We found the segmentation error to be slightly less than the clinically-observed interobserver variability.

Algorithms↗

PubMed2004

Parametric shape modeling using deformable superellipses for prostate segmentation.

Automatic prostate segmentation in ultrasound images is a challenging task due to speckle noise, missing boundary segments, and complex prostate anatomy. One popular approach has been the use of deformable models. For such techniques, prior knowledge of the prostate shape plays an important role in automating model initialization and constraining model evolution. In this paper, we have modeled the prostate shape using deformable superellipses. This model was fitted to 594 manual prostate contours outlined by five experts. We found that the superellipse with simple parametric deformations can efficiently model the prostate shape with the Hausdorff distance error (model versus manual outline) of 1.32 +/- 0.62 mm and mean absolute distance error of 0.54 +/- 0.20 mm. The variability between the manual outlinings and their corresponding fitted deformable superellipses was significantly less than the variability between human experts with p-value being less than 0.0001. Based on this deformable superellipse model, we have developed an efficient and robust Bayesian segmentation algorithm. This algorithm was applied to 125 prostate ultrasound images collected from 16 patients. The mean error between the computer-generated boundaries and the manual outlinings was 1.36 +/- 0.58 mm, which is significantly less than the manual interobserver distances. The algorithm was also shown to be fairly insensitive to the choice of the initial curve.

Algorithms↗

PubMed2003

A single mediaprocessor-based programmable ultrasound system.

We have developed a programmable ultrasound imaging system using a single commercially available mediaprocessor. We have efficiently mapped all of the necessary B-mode processing algorithms on the underlying processor architecture, including envelope detection, dynamic range compression, lateral and axial filtering, persistence processing, and scan conversion. Our system can handle varying specifications ranging from 128 vectors and 512 samples per vector to more than 256 vectors and 1024 samples per vector. For an image size of 330 vectors and 512 samples per vector, it can process 30 frames per second using a 300-MHz MAP-CA mediaprocessor from Hitachi/Equator Technologies. This programmable ultrasound machine will not only offer significant advantages in terms of low cost, portability, scalability, and reduced development time, but also provide a flexible platform for developing and deploying new clinical applications to aid the clinicians and improve the quality of healthcare to patients.

Algorithms↗

PubMed2002

Ultrasonography and fluoroscopic fusion for prostate brachytherapy dosimetry.

PURPOSE: To investigate the feasibility of performing postimplant and intraoperative dosimetry for prostate brachytherapy by fusing transrectal ultrasound (TRUS) and fluoroscopic data. METHODS AND MATERIALS: Registration of ultrasound (prostate boundary) and fluoroscopic (seed) data requires spatial markers that are detectable by both imaging modalities. In this study, the needle tips were considered as such fiducials. Prostate phantoms were implanted with the seeds, and four localization needles were inserted. In the TRUS frame of reference, the longitudinal coordinate of the needle tip was determined by advancing the needle until the echo from its tip just registered at a known probe depth. The tip's transverse coordinates were determined from the associated TRUS slice. The three-dimensional needle tip positions were also calculated in the fluoroscopic coordinate system using a seed reconstruction method. The transformation between the TRUS and fluoroscopy coordinate systems was established by the least-squares solution using the singular value decomposition. RESULTS: With three of four needle tips as fiducials and the one remaining needle as a test target, the mean fiducial registration error was 0.8 mm and the test target registration error was 2.5 mm. When all four points were used for registration, the errors decreased to 1.1 mm. A comparison between the proposed method and CT-based dosimetry yielded a percentage of prostate volume receiving 100% and 150% of the prescribed minimal peripheral dose and minimal dose received by 90% of the prostate gland that agreed within 0.4%, 2.7%, and 4.2%, respectively. CONCLUSION: The combination of TRUS and fluoroscopy is a feasible alternative to the currently used CT-based postimplant dosimetry. Furthermore, because of online imaging capability, the method lends itself to real-time intraoperative applications.

Brachytherapy↗

PubMed2002

Modification of prostate implants based on postimplant treatment margin assessment.

PURPOSE: To quantify the extent of additional source placement needed to perfect an implant after execution by standard techniques, assuming that uniform 5 mm treatment margins (TMs) is the criteria for perfection. MATERIALS AND METHODS: Ten consecutive, unselected patients treated with 1-125 brachytherapy were studied. Source placement is planned just inside or outside of the prostatic margin, to achieve a minimum 5 mm TM and a central dose of 150%-200% of the prescription dose. The preimplant prostate volumes ranged from 24 to 85 cc (median: 35 cc). The number of sources implanted ranged from 48 to 102 (median: 63). Axial CT images were acquired within 2 h postoperatively for postimplant dosimetry. After completion of standard dosimetric calculations, the TMs were measured and tabulated at 45 degrees intervals around the prostate periphery at 0.0, 1.0, 2.0, and 3.0 cm planes. Sources were then added to the periphery to bring the TMs to a minimum of 5 mm at each measured TM, resulting in a modified implant. All margin modifications were done manually, without the aid of automated software. RESULTS: Patients' original (unmodified) D90s ranged from 111% to 154%, with a median of 116%. The original V100s ranged from 94% to 99%, with a median of 96%. No patient required placement of additional sources to meet a minimum D90 of 90% or a minimum V100 of 80%. In contrast, patients required from 7 to 17 additional sources (median: 11) to achieve minimum 5 mm TMs around the entire prostatic periphery. Additional sources equaled from 12% to 24% of the initial number of sources placed (median: 17%). By adding sufficient peripheral sources to bring the TMs to a minimum 5 mm, patients' average V100 increased from 96% to 100%, and the average D90 increased from 124% to 160% of prescription dose. In the course of achieving a minimum 5 mm TM, the average treatment margin for all patients combined increased from 5.5 to 9.9 mm. The number of sources needed to bring the TMs to a minimum 5 mm was loosely correlated with the preimplant prostate volume and the change in prostate volume from implant-related swelling. Adding sufficient sources to achieve minimum 5 mm TMs increased the prostate volume receiving greater than 200% of the prescription dose (V200) from 39% to 58%, and increased the average urethral point dose (2.00 cm inferior to the bladder) from 154% to 171% of the 144 Gy prescription isodose. CONCLUSIONS: Minimum 5 mm TMs are not uniformly achieved with current implant techniques. It seems that doing so, even in experienced hands, will require a reappraisal of our implant techniques, or the addition of intraoperative dosimetric analysis with the capacity to substantially modify the implant with extra sources.

Brachytherapy↗