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Yimin Hu

Publications and source records attributed to Yimin Hu.

7 recordsLinked to original sources
PubMed2025

Evolutionary legacy of the "living fossil" genus Parrotia (Hamamelidaceae): genomic insights into species divergence and polygenic adaptation.

Despite their long evolutionary history, the genomic basis of adaptation and speciation in "living fossil" plants remain largely unexplored. Parrotia, a Tertiary relict tree genus with two extant species, P. subaequalis and P. persica, exhibits a disjunct distribution between East Asia and West Asia. Here, we present the first chromosome-level assemblies for both species, confirmed their sibling relationship, and dated the speciation event to the early Miocene. The recent proliferation of long-terminal repeat retrotransposons has driven the genome expansion in P. subaequalis. We detected widespread heterogeneous genomic differentiation between species. Extensive signals of divergent selection, local adaptation, and elevated Ka/Ks ratios in Parrotia indicate that this genus has undergone adaptive evolution in distinct refugia, challenging the notion of it as an "evolutionary dead end". Our findings provide new insights into the genomic evolution, environmental adaptation, and speciation of this "living fossil" tree genus.

Genome, Plant↗
PubMed2006

Beam orientation optimization for intensity-modulated radiation therapy using mixed integer programming.

The purpose of this study is to extend an algorithm proposed for beam orientation optimization in classical conformal radiotherapy to intensity-modulated radiation therapy (IMRT) and to evaluate the algorithm's performance in IMRT scenarios. In addition, the effect of the candidate pool of beam orientations, in terms of beam orientation resolution and starting orientation, on the optimized beam configuration, plan quality and optimization time is also explored. The algorithm is based on the technique of mixed integer linear programming in which binary and positive float variables are employed to represent candidates for beam orientation and beamlet weights in beam intensity maps. Both beam orientations and beam intensity maps are simultaneously optimized in the algorithm with a deterministic method. Several different clinical cases were used to test the algorithm and the results show that both target coverage and critical structures sparing were significantly improved for the plans with optimized beam orientations compared to those with equi-spaced beam orientations. The calculation time was less than an hour for the cases with 36 binary variables on a PC with a Pentium IV 2.66 GHz processor. It is also found that decreasing beam orientation resolution to 10 degrees greatly reduced the size of the candidate pool of beam orientations without significant influence on the optimized beam configuration and plan quality, while selecting different starting orientations had large influence. Our study demonstrates that the algorithm can be applied to IMRT scenarios, and better beam orientation configurations can be obtained using this algorithm. Furthermore, the optimization efficiency can be greatly increased through proper selection of beam orientation resolution and starting beam orientation while guaranteeing the optimized beam configurations and plan quality.

Algorithms↗
PubMed2004

Delivery time comparison for intensity-modulated radiation therapy with/without flattening filter: a planning study.

The treatment delivery time of intensity-modulated radiation therapy (IMRT) with a multileaf collimator (MLC) is generally longer than that of conventional radiotherapy. In theory, removing the flattening filter from the treatment head may reduce the beam-on time by enhancing the output dose rate, and then reduce the treatment delivery time. And in practice, there is a possibility of delivering the required fluence distribution by modulating the unflattened non-uniform fluence distribution. However, the reduction of beam-on time may be discounted by the increase of leaf-travel time and (or) verification-and-recording (V&R) time. Here we investigate the overall effect of flattening filter on the treatment delivery time of IMRT with MLCs implemented in the step and shoot method, as well as with compensators on six hybrid machines. We compared the treatment delivery time with/without flattening filter for ten nasopharynx cases and ten prostate cases by observing the variations of the ratio of the beam-on time, segment number, leaf-travel time and the treatment delivery time with dose rate, leaf speed and V&R time. The results show that, without the flattening filter, the beam-on time reduces for both static MLC and compensator-based techniques: the number of segments and the leaf-travel time increase slightly for the static MLC technique; the relative IMRT treatment delivery time decreases more with lower dose rate, higher leaf speed and shorter V&R overhead time. The absolute treatment delivery time reduction depends on the fraction dose. It is not clinically significant at a fraction dose of 2 Gy for the technique of removing the flattening filter, but becomes significant when the fraction dose is as high as that for radiosurgery.

Algorithms↗
PubMed2004

The influence of lateral electronic disequilibrium on the radiation treatment planning for lung cancer irradiation.

Using higher energy photons can obtain better target dose uniformity and skin sparing for treating deep lesions, but the effect of lacking lateral scattering in the low-density lung may degrade the target coverage. To analyze the influence of lateral electronic disequilibrium on the radiation treatment planning for lung cancer, three dimension conformal treatment (3D-CRT) plans of using 6 MV and 18 MV X-ray respectively for a lung cancer case have been worked out by using pencil beam algorithm and collapsed cone algorithm provided by Helax-TMS treatment planning system for the same radiation field arrangement for both energies. Dose volume histogram (DVH) in target and organs at risk (OARs) are used for comparison of different plans. The study shows that using pencil beam algorithm, the target DVH are similar for 6 MV and 18 MV plan. However, using collapsed cone algorithm that can make account of lateral electron scattering, the target is underdosed. The change is even more pronounced for 18 MV plan. The doses for lung and spinal cord are similar for these two energies and two algorithms. Therefore, for lung cancer, dose calculation algorithm should have the ability of handling accurately the effect of the tissue density heterogeneity. It is better to use the lower-energy photons (6 MV) than to use the higher-energy photons (18 MV).

Humans↗
PubMed2003

Optimization of beam orientations and beam weights for conformal radiotherapy using mixed integer programming.

An algorithm for optimizing beam orientations and beam weights for conformal radiotherapy has been developed. The algorithm models the optimization of beam orientations and beam weights as a problem of mixed integer linear programming (MILP), and optimizes the beam orientations and beam weights simultaneously. The application process of the algorithm has four steps: (a) prepare a pool of beam orientation candidates with the consideration of avoiding any patient-gantry collision and avoiding direct irradiation of organs at risk with quite low tolerances (e.g., eyes). (b) Represent each beam orientation candidate with a binary variable, and each beam weight with a continuous variable. (c) Set up an optimization problem according to dose prescriptions and the maximum allowed number of beam orientations. (d) Solve the optimization problem with a ready-to-use MILP solver. After optimization, the candidates with unity binary variables remain in the final beam configuration. The performance of the algorithm was tested with clinical cases. Compared with standard treatment plans, the beam-orientation-optimized plans had better dose distributions in terms of target coverage and avoidance of critical structures. The optimization processes took less than 1 h on a PC with a Pentium IV 2.4 GHz processor.

Algorithms↗
PubMed2002

A three-source model for the calculation of head scatter factors.

Accurate determination of the head scatter factor Sc is an important issue, especially for intensity modulated radiation therapy, where the segmented fields are often very irregular and much less than the collimator jaw settings. In this work, we report an Sc calculation algorithm for symmetric, asymmetric, and irregular open fields shaped by the tertiary collimator (a multileaf collimator or blocks) at different source-to-chamber distance. The algorithm was based on a three-source model, in which the photon radiation to the point of calculation was treated as if it originated from three effective sources: one source for the primary photons from the target and two extra-focal photon sources for the scattered photons from the primary collimator and the flattening filter, respectively. The field mapping method proposed by Kim et al. [Phys. Med. Biol. 43, 1593-1604 (1998)] was extended to two extra-focal source planes and the scatter contributions were integrated over the projected areas (determined by the detector's eye view) in the three source planes considering the source intensity distributions. The algorithm was implemented using Microsoft Visual C/C++ in the MS Windows environment. The only input data required were head scatter factors for symmetric square fields, which are normally acquired during machine commissioning. A large number of different fields were used to evaluate the algorithm and the results were compared with measurements. We found that most of the calculated Sc's agreed with the measured values to within 0.4%. The algorithm can also be easily applied to deal with irregular fields shaped by a multileaf collimator that replaces the upper or lower collimator jaws.

Algorithms↗