Classify Hyperdiploidy Status of Multiple Myeloma Patients Using Gene Expression Profiles

Multiple myeloma (MM) is a cancer of antibody-making plasma cells. It frequently harbors alterations in DNA and chromosome copy numbers, and can be divided into two major subtypes, hyperdiploid (HMM) and non-hyperdiploid multiple myeloma (NHMM). The two subtypes have different survival prognosis, possibly due to different but converging paths to oncogenesis. Existing methods for identifying the two subtypes are fluorescence in situ hybridization (FISH) and copy number microarrays, with increased cost and sample requirements. We hypothesize that chromosome alterations have their imprint in gene expression through dosage effect. Using five MM expression datasets that have HMM status measured by FISH and copy number microarrays, we have developed and validated a K-nearest-neighbor method to classify MM into HMM and NHMM based on gene expression profiles. Classification accuracy for test datasets ranges from 0.83 to 0.88. This classification will enable researchers to study differences and commonalities of the two MM subtypes in disease biology and prognosis using expression datasets without need for additional subtype measurements. Our study also supports the advantages of using cancer specific characteristics in feature design and pooling multiple rounds of classification results to improve accuracy. We provide R source code and processed datasets at www.ChengLiLab.org/software

Computational inference of mRNA stability from histone modification and transcriptome profiles

Histone modifications play important roles in regulating eukaryotic gene expression and have been used to model expression levels. Here, we present a regression model to systematically infer mRNA stability by comparing transcriptome profiles with ChIP-seq of H3K4me3, H3K27me3 and H3K36me3. The results from multiple human and mouse cell lines show that the inferred unstable mRNAs have significantly longer 3′Untranslated Regions (UTRs) and more microRNA binding sites within 3′UTR than the inferred stable mRNAs. Regression residuals derived from RNA-seq, but not from GRO-seq, are highly correlated with the half-lives measured by pulse-labeling experiments, supporting the rationale of our inference. Whereas, the functions enriched in the inferred stable and unstable mRNAs are consistent with those from pulse-labeling experiments, we found the unstable mRNAs have higher cell-type specificity under functional constraint. We conclude that the systematical use of histone modifications can differentiate non-expressed mRNAs from unstable mRNAs, and distinguish stable mRNAs from highly expressed ones. In summary, we represent the first computational model of mRNA stability inference that compares transcriptome and epigenome profiles, and provides an alternative strategy for directing experimental measurements

Few-shot Object Localization

Existing object localization methods are tailored to locate specific classes of objects, relying heavily on abundant labeled data for model optimization. However, acquiring large amounts of labeled data is challenging in many real-world scenarios, significantly limiting the broader application of localization models. To bridge this research gap, this paper defines a novel task named Few-Shot Object Localization (FSOL), which aims to achieve precise localization with limited samples. This task achieves generalized object localization by leveraging a small number of labeled support samples to query the positional information of objects within corresponding images. To advance this field, we design an innovative high-performance baseline model. This model integrates a dual-path feature augmentation module to enhance shape association and gradient differences between supports and query images, alongside a self query module to explore the association between feature maps and query images. Experimental results demonstrate a significant performance improvement of our approach in the FSOL task, establishing an efficient benchmark for further research. All codes and data are available at https://github.com/Ryh1218/FSOL

Lightweight Change Detection in Heterogeneous Remote Sensing Images with Online All-Integer Pruning Training

Detection of changes in heterogeneous remote sensing images is vital, especially in response to emergencies like earthquakes and floods. Current homogenous transformation-based change detection (CD) methods often suffer from high computation and memory costs, which are not friendly to edge-computation devices like onboard CD devices at satellites. To address this issue, this paper proposes a new lightweight CD method for heterogeneous remote sensing images that employs the online all-integer pruning (OAIP) training strategy to efficiently fine-tune the CD network using the current test data. The proposed CD network consists of two visual geometry group (VGG) subnetworks as the backbone architecture. In the OAIP-based training process, all the weights, gradients, and intermediate data are quantized to integers to speed up training and reduce memory usage, where the per-layer block exponentiation scaling scheme is utilized to reduce the computation errors of network parameters caused by quantization. Second, an adaptive filter-level pruning method based on the L1-norm criterion is employed to further lighten the fine-tuning process of the CD network. Experimental results show that the proposed OAIP-based method attains similar detection performance (but with significantly reduced computation complexity and memory usage) in comparison with state-of-the-art CD methods

Adaptive Environment Modeling Based Reinforcement Learning for Collision Avoidance in Complex Scenes

The major challenges of collision avoidance for robot navigation in crowded scenes lie in accurate environment modeling, fast perceptions, and trustworthy motion planning policies. This paper presents a novel adaptive environment model based collision avoidance reinforcement learning (i.e., AEMCARL) framework for an unmanned robot to achieve collision-free motions in challenging navigation scenarios. The novelty of this work is threefold: (1) developing a hierarchical network of gated-recurrent-unit (GRU) for environment modeling; (2) developing an adaptive perception mechanism with an attention module; (3) developing an adaptive reward function for the reinforcement learning (RL) framework to jointly train the environment model, perception function and motion planning policy. The proposed method is tested with the Gym-Gazebo simulator and a group of robots (Husky and Turtlebot) under various crowded scenes. Both simulation and experimental results have demonstrated the superior performance of the proposed method over baseline methods.Comment: accepted by IROS202

Otterbein Aegis May 1909

https://digitalcommons.otterbein.edu/aegis/1182/thumbnail.jp

Determination of Niobium, Tantalum, Lithium and Beryllium in Niobium Tantalum Ore by Alkali Fusion Inductively Coupled Plasma Mass Spectrometry

This is an article in the field of mineral analysis and testing. A rapid method for the simultaneous determination of Nb, Ta, Li and Be in Nb Ta ore by alkali fusion inductively coupled plasma mass spectrometry was established. The mixed alkali of sodium peroxide and sodium hydroxide=1:1 is used to decompose the sample. During extraction, niobium, tantalum and other elements are completely precipitated and separated from the liquid. The content of niobium, tantalum, lithium and beryllium in the sample is determined by inductively coupled plasma mass spectrometer after conversion and precipitation with 25 mL of 10% sulfuric acid+10% hydrogen peroxide solution. This method is used to determine the national first-class reference materials GBW 07153, GBW 07155 and GBW 07185. The measured values of each element are basically consistent with the certified values, with a relative error of 0.50%～4.77% and a relative standard deviation (n=6) of -0.009%～0.008%. It is applicable to the determination of niobium and tantalum in niobium tantalum concentrates, refractory or complex samples, and has been applied in production practice