TBestDB: a taxonomically broad database of expressed sequence tags (ESTs)

The TBestDB database contains ∼370 000 clustered expressed sequence tag (EST) sequences from 49 organisms, covering a taxonomically broad range of poorly studied, mainly unicellular eukaryotes, and includes experimental information, consensus sequences, gene annotations and metabolic pathway predictions. Most of these ESTs have been generated by the Protist EST Program, a collaboration among six Canadian research groups. EST sequences are read from trace files up to a minimum quality cut-off, vector and linker sequence is masked, and the ESTs are clustered using phrap. The resulting consensus sequences are automatically annotated by using the AutoFACT program. The datasets are automatically checked for clustering errors due to chimerism and potential cross-contamination between organisms, and suspect data are flagged in or removed from the database. Access to data deposited in TBestDB by individual users can be restricted to those users for a limited period. With this first report on TBestDB, we open the database to the research community for free processing, annotation, interspecies comparisons and GenBank submission of EST data generated in individual laboratories. For instructions on submission to TBestDB, contact [email protected]. The database can be queried at

A design of a BLAST server with Jini technology

The explosion of biological data, particularly the nucleic acid and protein sequences, has been proved to be both an opportunity and challenge for biologists as well as computer experts. The burgeoning of huge-sized sequence databases necessitates the invention and renovation of powerful computational tools to efficiently manage and utilize these sequence data. Among the various bioinformatics tools, BLAST Local Alignment Search Tool) is the most commonly used one for DNA sequence database searching. To enhance its working efficiency, in this thesis, we have tried to design a new distributed system for BLAST service with the recently developed Jini technology. Since the service is involved in sequence databases query, the RMI (Remote Method Invocation) proxy was chosen in its architecture. The structures on both the client and the server sides were designed mainly based on Java technology and demonstrated with class diagrams of Unified Modeling Language (UML)

Researching the CNN Collaborative Inference Mechanism for Heterogeneous Edge Devices

Convolutional Neural Networks (CNNs) have been widely applied in various edge computing devices based on intelligent sensors. However, due to the high computational demands of CNN tasks, the limited computing resources of edge intelligent terminal devices, and significant architectural differences among these devices, it is challenging for edge devices to independently execute inference tasks locally. Collaborative inference among edge terminal devices can effectively utilize idle computing and storage resources and optimize latency characteristics, thus significantly addressing the challenges posed by the computational intensity of CNNs. This paper targets efficient collaborative execution of CNN inference tasks among heterogeneous and resource-constrained edge terminal devices. We propose a pre-partitioning deployment method for CNNs based on critical operator layers, and optimize the system bottleneck latency during pipeline parallelism using data compression, queuing, and “micro-shifting” techniques. Experimental results demonstrate that our method achieves significant acceleration in CNN inference within heterogeneous environments, improving performance by 71.6% compared to existing popular frameworks

The Polymorphisms in LNK Gene Correlated to the Clinical Type of Myeloproliferative Neoplasms.

LNK is an adapter protein negatively regulating the JAK/STAT cell signaling pathway. In this study, we observed the correlation between variation in LNK gene and the clinical type of myeloproliferative neoplasms (MPN).A total of 285 MPN cases were recruited, including essential thrombocythemia (ET) 154 cases, polycythemia vera (PV) 76 cases, primary myelofibrosis (PMF) 19 cases, and chronic myeloid leukemia (CML) 36 cases. Ninety-three healthy individuals were used as normal controls. V617F mutation in JAK2 was identified by allele-specific PCR method, RT-PCR was used for the detection of BCR/ABL1 fusion gene, and mutations and variations in coding exons and their flanking sequences of LNK gene were examined by PCR-sequencing.Missense mutations of A300V, V402M, and R415H in LNK were found in 8 patients including ET (4 cases, all combined with JAK2-V617F mutation), PV (2 cases, one combined with JAK2-V617F mutation), PMF (one case, combined with JAK2-V617F mutation) and CML (one case, combined with BCR/ABL1 fusion gene). The genotype and allele frequencies of the three SNPs (rs3184504, rs111340708 and rs78894077) in LNK were significantly different between MPN patients and controls. For rs3184504 (T/C, in exon2), the T allele (p.262W) and TT genotype were frequently seen in ET, PV and PMF (P<0.01), and C allele (p.262R) and CC genotype were frequently seen in CML (P<0.01). For rs78894077 (T/C, in exon1), the T allele (p.242S) was frequently found in ET (P<0.05). For rs111340708 (TGGGGx5/TGGGGx4, in intron 5), the TGGGG x4 allele was infrequently found in ET, PMF and CML(P<0.01).Mutations in LNK could be found in some of MPN patients in the presence or absence of JAK2-V617F mutation. Several polymorphisms in LNK gene may affect the clinical type or the genetic predisposition of MPN

GOBASE—a database of organelle and bacterial genome information

The organelle genome database GOBASE is now in its twelfth release, and includes 350 000 mitochondrial sequences and 118 000 chloroplast sequences, roughly a 3-fold expansion since previously documented. GOBASE also includes a fully reannotated genome sequence of Rickettsia prowazekii, one of the closest bacterial relatives of mitochondria, and will shortly expand to contain more data from bacteria from which organelles originated. All these sequences are now accessible through a single unified interface. Enhancements to the functionality of GOBASE include addition of pages for RNA structures and a page compiling data about the taxonomic distribution of organelle-encoded genes; incorporation of Gene Ontology terms; addition of features deduced from incomplete annotations to sequences in GenBank; marking of type examples in cases where single genes in single species are oversampled within GenBank; and addition of graphics illustrating gene structure and the position of neighbouring genes on a sequence. The database has been reimplemented in PostgreSQL to facilitate development and maintenance, and structural modifications have been made to speed up queries, particularly those related to taxonomy. The GOBASE database can be queried a

Semiparametric Deep Learning Manipulator Inverse Dynamics Modeling Method for Smart City and Industrial Applications

In smart cities and factories, robotic applications require high accuracy and security, which depends on precise inverse dynamics modeling. However, the physical modeling methods cannot include the nondeterministic factors of the manipulator, such as flexibility, joint clearance, and friction. In this paper, the Semiparametric Deep Learning (SDL) method is proposed to model robot inverse dynamics. SDL is a type of deep learning framework, designed for optimal inference, combining the Rigid Body Dynamics (RBD) model and Nonparametric Deep Learning (NDL) model. The SDL model takes advantage of the global characteristics of classic RBD and the powerful fitting capabilities of the deep learning approach. Moreover, the parametric and nonparametric parts of the SDL model can be optimized at the same time instead of being optimized separately. The proposed method is validated using experiments, performed on a UR5 robotic platform. The results show that the performance of SDL model is better than that of RBD model and NDL model. SDL can always provide relatively accurate joint torque prediction, even when the RBD or NDL model is not accurate

Identification of Important Factors Causing Developmental Arrest in Cloned Pig Embryos by Embryo Biopsy Combined with Microproteomics

The technique of pig cloning holds great promise for the livestock industry, life science, and biomedicine. However, the prenatal death rate of cloned pig embryos is extremely high, resulting in a very low cloning efficiency. This limits the development and application of pig cloning. In this study, we utilized embryo biopsy combined with microproteomics to identify potential factors causing the developmental arrest in cloned pig embryos. We verified the roles of two potential regulators, PDCD6 and PLK1, in cloned pig embryo development. We found that siRNA-mediated knockdown of PDCD6 reduced mRNA and protein expression levels of the pro-apoptotic gene, CASP3, in cloned pig embryos. PDCD6 knockdown also increased the cleavage rate and blastocyst rate of cloned porcine embryos. Overexpression of PLK1 via mRNA microinjection also improved the cleavage rate of cloned pig embryos. This study provided a new strategy to identify key factors responsible for the developmental defects in cloned pig embryos. It also helped establish new methods to improve pig cloning efficiency, specifically by correcting the expression pattern of PDCD6 and PLK1 in cloned pig embryos

Coordinated Dispatch of Integrated Energy Systems Considering the Differences of Multiple Functional Areas

A large amount of wind turbine power and photovoltaic power is abandoned in many areas with abundant renewable energy due to thermal-electric coupling, inadequate local consumption capacity, and limited capacity of transmission lines, etc. To solve the above problems, a coordinated dispatching method for integrated energy systems is proposed in this paper. Firstly, the spatiotemporal characteristics of diversified loads in multiple functional areas are introduced, including the inertia and elasticity of heating/cooling loads, the spatiotemporal distribution of electric vehicles, and the optimum transmission distance of diversified loads, etc. Secondly, a coordinated dispatching model of integrated energy systems is proposed, which considers the differences of multiple functional areas and various forms of energy systems. Finally, an actual distribution system in Jianshan District, Haining, Zhejiang Province of China is investigated for demonstrating the effectiveness of the proposed model. The results illustrate that the proposed model could effectively improve the consumption rate of renewable energy and reduce the volatility of renewable energy by considering the coordination of electric vehicles, tie lines, and heating/cooling systems in multiple functional areas

Knockdown of YY1 Inhibits <i>XIST</i> Expression and Enhances Cloned Pig Embryo Development

The technique of cloning has wide applications in animal husbandry and human biomedicine. However, the very low developmental efficiency of cloned embryos limits the application of cloning. Ectopic XIST-expression-induced abnormal X chromosome inactivation (XCI) is a primary cause of the low developmental competence of cloned mouse and pig embryos. Knockout or knockdown of XIST improves cloning efficiency in both pigs and mice. The transcription factor Yin yang 1(YY1) plays a critical role in XCI by triggering the transcription of X-inactive specific transcript (XIST) and facilitating the localization of XIST RNA on the X chromosome. This study aimed to investigate whether RNA interference to suppress the expression of YY1 can inhibit erroneous XIST expression, rescue abnormal XCI, and improve the developmental ability of cloned pig embryos. The results showed that YY1 binds to the 5′ regulatory region of the porcine XIST gene in pig cells. The microinjection of YY1 siRNA into cloned pig embryos reduced the transcript abundance of XIST and upregulated the mRNA level of X-linked genes at the 4-cell and blastocyst stages. The siRNA-mediated knockdown of YY1 altered the transcriptome and enhanced the in vitro and in vivo developmental efficiency of cloned porcine embryos. These results suggested that YY1 participates in regulating XIST expression and XCI in cloned pig embryos and that the suppression of YY1 expression can increase the developmental rate of cloned pig embryos. The present study established a new method for improving the efficiency of pig cloning