Efficient Construction and Utilization of k-Ordered FM-indexes with kISS for Ultra-Fast Read Mapping in Large Genomes.

MOTIVATION: The Full-text index in Minute space (FM-index) is a memory-efficient data structure widely used in bioinformatics for solving the fundamental pattern-matching task of searching for short patterns within a long reference. With the demand for short query patterns, the k-ordered concept has been proposed for FM-indexes. However, few construction algorithms in the state of the art fully exploit this idea to achieve significant speedups in the pan-genome era. RESULTS: We introduce the k-ordered Induced Suffix Sorting (kISS) for efficient construction and utilization of k-ordered FM-indexes. We present an algorithmic workflow for building k-ordered suffix arrays, incorporating two novel strategies to improve time and memory efficiency. We also demonstrate the compatibility of integrating k-ordered FM-indexes with locate operations in FMtree. Experiments show that kISS can improve the construction time, and the generated k-ordered suffix array can also be applied to FMtree without any additional in computation or memory usage. AVAILABILITY: https://github.com/jhhung/kISS. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Early inactivation of PKCε associates with late mitochondrial translocation of Bad and apoptosis in ventricle of septic rat.

BACKGROUND: Sepsis is usually accompanied by cardiomyocyte apoptosis and myocardial depression. Protein kinase C (PKC) has been reported to be important in regulating cardiac function and apoptosis; however, which PKC isoform is involved in sepsis-induced myocardial apoptosis remains unknown. MATERIALS AND METHODS: A rat model of sepsis by cecal ligation and puncture was used. Early and late sepsis refers to those rats sacrificed at 9 and 18 h after cecal ligation and puncture, respectively. Ventricular septum (Sep), left ventricle (LV), and right ventricle were fractionated into membrane, mitochondrial, and cytosolic fractions, individually. The protein levels of PKC isoforms (-α, -ß, -δ, -ε, -ζ, -ι, -λ, and -µ) and mitochondrial translocation of Bad were quantified by Western blot analysis. Apoptosis was detected by terminal deoxynucleotidyl transferase-mediated dUTP in situ nick-end labeling. The morphology of mitochondria was examined by electron microscopy. RESULTS: The membrane/cytosol ratio of PKCε was predominantly higher in the Sep, LV, and right ventricle under physiological conditions. At early sepsis, the membrane/cytosol ratio of PKCε was significantly decreased in Sep and LV. At late sepsis, cardiomyocyte apoptosis associated with severe mitochondrial swelling and crista derangement were observed in Sep and LV at late sepsis. Additionally, mitochondria/cytosol ratio of Bad was significantly increased in Sep and LV. CONCLUSIONS: The early inactivation of PKCε in the ventricle may affect the mitochondrial translocation of Bad and subsequent mitochondrial disruption and apoptosis at late sepsis. This finding opens up the prospect for a potential therapeutic strategy targeting PKCε activation to prevent myocardial depression in septic patients.

Estimation of forest canopy closure in northwest Yunnan based on multi-source remote sensing data colla-boration.

Forest canopy closure (FCC) is an important parameter to evaluate forest resources and biodiversity. Using multi-source remote sensing collaborative means to achieve regional forest canopy closure inversion with low cost and high-precision is a research hotspot. Taking ICESat-2/ATLAS data as the main information source and combined with data of 54 measured plots, we estimated FCC value by the Bayesian optimization (BO) algorithm improved random forest (RF), K-nearest neighbor (KNN), and gradient boosting regression tree (GBRT) model at footprint-scale. Combined with multi-source remote sensing image Sentinel-1/2 and terrain factors, we estimated the regional-scale FCC value of Shangri-La in the northwest Yunnan based on deep neural network (DNN) optimized by BO algorithm. The results showed that six characteristic parameters (percentage of tree canopy, standard deviation of relative height of photons at the top of the canopy, minimum canopy height, difference between 98% canopy height and median canopy height in the segment, number of top canopy photons, apparent surface reflectance) out of the 50 parameters that were extracted from ATLAS lidar footprint had higher contribution rate after RF characteristic variable optimization, which could be used as model variable for footprint-scale remote sensing estimation. Among BO-RF, BO-KNN, and BO-GBRT models, the FCC results estimated by the BO-GBRT model were the best at footprint-scale. The coefficient of determination (R2) was 0.65, the root mean square error (RMSE) was 0.10, the mean absolute residual (RS) was 0.079, and the prediction accuracy (P) was 0.792 for leave-one-out cross validation. It could be used as the FCC estimation model of 74808 ATLAS footprints for forest in the study area. We used the ATLAS footprint-scale FCC value of forest as the large sample data of the regional-scale BO-DNN model and combined with multi-source remote sensing factors to estimate FCC in the study area, the accuracy of the 10-fold cross-validation BO-DNN model was R2=0.47, RMSE=0.22, P=0.558. The mean values of FCC in the study area estimated by BO-DNN model and ordinary Kriging (OK) interpolation were 0.46 and 0.52, respectively, and the values mainly distributed in 0.3-0.6, accounting for 77.8% and 81.4%, respectively. The FCC efficiency obtained directly by the OK interpolation method was higher (R2=0.26), but the prediction accuracy was significantly lower than the BO-DNN model (R2=0.49). The FCC high value was distributed from northwest to southeast in the study area, and the northern and southeastern regions were the main distribution areas of high and low FCC values, respectively. It had certain advantages to estimate mountain area FCC based on ICESat-2/ATLAS high-density footprint, and the estimation results of small sample data at footprint-scale could be used as large sample data of deep learning model at region-scale, which would provide a reference for the low-cost and high-precision to FCC estimation on the footprint-scale up to the extrapolated regional-scale.