Protein-Protein Interactions Prediction Based on Iterative Clique Extension with Gene Ontology Filtering

Cliques (maximal complete subnets) in protein-protein interaction (PPI) network are an important resource used to analyze protein complexes and functional modules. Clique-based methods of predicting PPI complement the data defection from biological experiments. However, clique-based predicting methods only depend on the topology of network. The false-positive and false-negative interactions in a network usually interfere with prediction. Therefore, we propose a method combining clique-based method of prediction and gene ontology (GO) annotations to overcome the shortcoming and improve the accuracy of predictions. According to different GO correcting rules, we generate two predicted interaction sets which guarantee the quality and quantity of predicted protein interactions. The proposed method is applied to the PPI network from the Database of Interacting Proteins (DIP) and most of the predicted interactions are verified by another biological database, BioGRID. The predicted protein interactions are appended to the original protein network, which leads to clique extension and shows the significance of biological meaning

Genetic diversity of five goat breeds in China based on microsatellite markers

The genetic diversity of five goat breeds in China was surveyed using 15 microsatellites. The five goat breeds included Tangshan dairy goat (TSD), Liaoning cashmere goat (LNC), Nanjiang yellow goat (NJY), Chengde  polled goat (CDP) and Leizhou black goat (LZB). The mean polymorphism information content value (PIC) of  the populations ranged from 0.6606 to 0.8405. The mean heterozygosity (H) of the populations ranged from  0.7936 to 0.8202. The mean number of effective allele (Ne) of the populations ranged from 5.3373 to 5.8812 and the coefficient of genetic differentiation between breeds was 0.0620. It was suggested that the five goat  populations have abundant genetic diversity and extensive genetic basis, with limited inbreeding, especially in Leizhou black goat. The unweighted pair-group method with arithmetic averages (UPGMA) dendrogram based  on the Nei's standard genetic distance indicated that Tangshan dairy goat, Chengde polled goat and Liaoning  cashmere goat breeds / populations clustered together. The Nanjiang yellow goat and Leizhou black goat  populations clustered together, consistent with the geographical distribution of goat breeds.Key words: Goat, microsatellite, genetic diversity, clustering

Phonemic Adversarial Attack against Audio Recognition in Real World

Recently, adversarial attacks for audio recognition have attracted much attention. However, most of the existing studies mainly rely on the coarse-grain audio features at the instance level to generate adversarial noises, which leads to expensive generation time costs and weak universal attacking ability. Motivated by the observations that all audio speech consists of fundamental phonemes, this paper proposes a phonemic adversarial tack (PAT) paradigm, which attacks the fine-grain audio features at the phoneme level commonly shared across audio instances, to generate phonemic adversarial noises, enjoying the more general attacking ability with fast generation speed. Specifically, for accelerating the generation, a phoneme density balanced sampling strategy is introduced to sample quantity less but phonemic features abundant audio instances as the training data via estimating the phoneme density, which substantially alleviates the heavy dependency on the large training dataset. Moreover, for promoting universal attacking ability, the phonemic noise is optimized in an asynchronous way with a sliding window, which enhances the phoneme diversity and thus well captures the critical fundamental phonemic patterns. By conducting extensive experiments, we comprehensively investigate the proposed PAT framework and demonstrate that it outperforms the SOTA baselines by large margins (i.e., at least 11X speed up and 78% attacking ability improvement)

Effect of total flavonoids from Drynaria rhizome on bone loss in ovariectomized rats

Purpose: To determine the potential effect of total flavonoids from Drynaria rhizome on bone loss in ovariectomized (OVX) rats. Methods: The rats were divided into four groups: normal control, ovariectomized (OVX) control, and two Drynaria rhizome (DR) flavonoids treatments. Post-operation, osteoporotic OVX rats were given Drynaria rhizome total flavonoids for 3 months. Thereafter, the expressions of bone-related genes and biochemical indices were investigated in samples taken from the serum and bone of the rats. Results: Treatment with total flavonoids from Drynaria rhizome prevented bone mineral loss and improved some related biochemical indices associated with osteoporosis: alkaline phosphatase (ALP), tartrate-resistant acid phosphatase (TRAP), bone gla protein (BGP) and estradiol (E2). Reverse transcription-polymerase chain reaction (RT-PCR) data showed that treatment with the total flavonoids significantly downregulated mRNA expression of Wnt10b, β-catenin, recombinant human bone morphogenetic protein-2 (BMP2) and BMP4 in OVX rats, but significantly reversed OVX-induced downregulation of dickkopf1 (Dkk1) mRNA expression. Conclusion: These results indicate that total flavonoids from Drynaria rhizome exert anti-osteoporotic effects in rats via WNT signaling and BMP-2 signaling pathways

Extraction optimization of Eucommia ulmoides Oliver and its effect on bone quality in OVX rats

Purpose: To maximize the yield of extract from Eucommia ulmoides Oliver and its effect on bone quality. Methods: Different extraction indices were optimized with response surface methodology (RSM) for maximization of extract yield from Eucommia ulmoides Oliver. Box–Behnken design (BBD) was used to identify the effects of temperature, time, and liquid to solid ratio on extract yield from Eucommia ulmoides Oliver. After 4-week acclimatization, thiry-two rats were randomly assigned to 4 groups (n = 8): group 1 (sham) given vehicle only; group 2 (OVX rats given Eucommia ulmoides Oliver extract at a dose of 4 g/kg; group 3 (OVX + vehicle); group 4 (OVX + EUOE), i.e., OVX rats given Eucommia ulmoides Oliver extract (4 g/kg). Sham rats had intact ovaries. After surgery, the rats received gentamicin intramuscularly for 3 successive days. Two months after surgery, blood and trabecular bones was taken for analysis. Results: Temperature and liquid-to-solid ratio had marked impact on extract yield from Eucommia ulmoides Oliver, with the best conditions being temperature of 88 °C, time of 137 min, and liquid to solid ratio 16:1. Using these optimized conditions, the maximum yield of extract obtained experimentally (2.53%) was very close to the predicted value of 2.49 %. There was a good fit between the mathematical model evolved and the data on extract yield. The extract significantly (p < 0.01) increased the Ca and P and Cr levels in OVX + EUOE group compared to those in OVX control. Moreover, the extract significantly (p < 0.01) increased macro-mechanical indices of trabecular bone in OVX+EUOE group, relative to those in OVX control. Conclusion: The yield of Eucommia ulmoides Oliver extract has been successfully optimized using RSM. The extract exhibited strong effects on bone quality. Keywords: Optimization, Eucommia ulmoides, Box–Behnken design, Response surface methodology, Bone loss, Gen

Observation of non-Hermitian corner states in non-reciprocal topolectrical circuits

Exploring topological phases in non-Hermitian systems has attracted significant recent attention. One intriguing question is how topological edge states compete with the non-Hermitian skin effect. Here, we report the experimental observation of corner states in a two-dimensional non-reciprocal rhombus honeycomb electric circuit. The system is non-reciprocal and non-Hermitian because the introduced capacitance between two nodes depends on the current direction. The current-inversion negative impedance converters (INIC) is employed to realize the non-reciprocal coupling in circuit. Skin effect thus emerges due to the non-reciprocity and prevails in dragging the corner state into the bulk. The non-Bloch winding number defined in generalized Brillouin zone is adopted to characterize the topological phase transition. Interestingly, we find that the non-Bloch Z2 Berry phase can serve as an invariant to describe the non-Hermitian topology. By tuning the non-reciprocal parameter, we observe unbalanced distribution of corner states emerging on two acute angles of the rhombus lattice, with the localization length of the left corner state increasing exponentially with the degree of non-reciprocity.Comment: 8 pages, 7 figure

AutoOptLib: Tailoring Metaheuristic Optimizers via Automated Algorithm Design

Metaheuristics are prominent gradient-free optimizers for solving hard problems that do not meet the rigorous mathematical assumptions of analytical solvers. The canonical manual optimizer design could be laborious, untraceable and error-prone, let alone human experts are not always available. This arises increasing interest and demand in automating the optimizer design process. In response, this paper proposes AutoOptLib, the first platform for accessible automated design of metaheuristic optimizers. AutoOptLib leverages computing resources to conceive, build up, and verify the design choices of the optimizers. It requires much less labor resources and expertise than manual design, democratizing satisfactory metaheuristic optimizers to a much broader range of researchers and practitioners. Furthermore, by fully exploring the design choices with computing resources, AutoOptLib has the potential to surpass human experience, subsequently gaining enhanced performance compared with human problem-solving. To realize the automated design, AutoOptLib provides 1) a rich library of metaheuristic components for continuous, discrete, and permutation problems; 2) a flexible algorithm representation for evolving diverse algorithm structures; 3) different design objectives and techniques for different optimization scenarios; and 4) a graphic user interface for accessibility and practicability. AutoOptLib is fully written in Matlab/Octave; its source code and documentation are available at https://github.com/qz89/AutoOpt and https://AutoOpt.readthedocs.io/, respectively