Prioritization of schizophrenia risk genes from GWAS results by integrating multi-omics data

Schizophrenia (SCZ) is a polygenic disease with a heritability approaching 80%. Over 100 SCZ-related loci have so far been identified by genome-wide association studies (GWAS). However, the risk genes associated with these loci often remain unknown. We present a new risk gene predictor, rGAT-omics, that integrates multi-omics data under a Bayesian framework by combining the Hotelling and Box–Cox transformations. The Bayesian framework was constructed using gene ontology, tissue-specific protein–protein networks, and multi-omics data including differentially expressed genes in SCZ and controls, distance from genes to the index single-nucleotide polymorphisms (SNPs), and de novo mutations. The application of rGAT-omics to the 108 loci identified by a recent GWAS study of SCZ predicted 103 high-risk genes (HRGs) that explain a high proportion of SCZ heritability (Enrichment = 43.44 and p=9.30×10−9). HRGs were shown to be significantly (padj=5.35×10−7) enriched in genes associated with neurological activities, and more likely to be expressed in brain tissues and SCZ-associated cell types than background genes. The predicted HRGs included 16 novel genes not present in any existing databases of SCZ-associated genes or previously predicted to be SCZ risk genes by any other method. More importantly, 13 of these 16 genes were not the nearest to the index SNP markers, and them would have been difficult to identify as risk genes by conventional approaches while ten out of the 16 genes are associated with neurological functions that make them prime candidates for pathological involvement in SCZ. Therefore, rGAT-omics has revealed novel insights into the molecular mechanisms underlying SCZ and could provide potential clues to future therapies

Complete plastome of the medicinally important plant, Alstonia scholaris (Apocynaceae)

Alstonia scholaris is an evergreen tropical tree with significant medicinal values. To better understand its genetic and genomic profiles, we sequenced and assembled the completed plastome of A. scholaris. The plastome is 154,699 bp in length, consisting of a large (LSC, 85,364 bp) and a small single-copy region (SSC, 18,027 bp), which are separated by a pair of inverted repeat regions (IRs, 25,654 bp). It possesses 116 unique genes (82 protein-coding genes, 30 tRNAs, and 4 rRNAs). Phylogenetic analysis suggests that A. scholaris is sister to the clade including remaining Apocynaceae species

SMRT sequencing of full-length transcriptome and gene expression analysis in two chemical types of Pogostemon cablin (Blanco) Benth.

Background Pogostemon cablin (Blanco) Benth. also called patchouli, is a traditional medicinal and aromatic plant that grows mainly in Southeast Asia and China. In China, P. cablin is divided into two chemical types: the patchouliol-type and the pogostone-type. Patchouliol-type patchouli usually grow taller, with thicker stems and bigger leaves, and produce more aromatic oil. Methods To better understand the genetic differences between the two chemical types that contribute to their differences in morphology and biosynthetic capabilities, we constructed de novo transcriptomes from both chemical types using the Pacific Biosciences (PacBio) Sequel platform and performed differential expression analysis of multiple tissues using Illumina short reads. Results In this study, using single-molecule real-time (SMRT) long-read sequencing, we obtained 22.07 GB of clean data and 134,647 nonredundant transcripts from two chemical types. Additionally, we identified 126,576 open reading frames (ORFs), 100,638 coding sequences (CDSs), 4,106 long noncoding RNAs (lncRNAs) and 6,829 transcription factors (TFs) from two chemical types of P. cablin. We adopted PacBio and Illumina sequencing to identify differentially expressed transcripts (DEGs) in three tissues of the two chemical types. More DEGs were observed in comparisons of different tissues collected from the same chemical type relative to comparisons of the same tissue collected from different chemical types. Furthormore, using KEGG enrichment analysis of DEGs, we found that the most enriched biosynthetic pathways of secondary metabolites of the two chemical types were “terpenoid backbone biosynthesis”, “phenylpropanoid biosynthesis”, “plant hormone signal transduction”, “sesquiterpenoid and triterpenoid biosynthesis”, “ubiquinone and other terpenoid-quinone biosynthesis”, “flavonoid biosynthesis”, and “flavone and flavonol biosynthesis”. However, the main pathways of the patchouliol-type also included “diterpene biosynthesis” and “monoterpene biosynthesis”. Additionally, by comparing the expression levels of the three tissues verified by qRT-PCR, more DEGs in the roots were upregulated in the mevalonate (MVA) pathway in the cytoplasm, but more DEGs in the leaves were upregulated in the methylerythritol phosphate (MEP) pathway in the plastid, both of which are important pathways for terpenoids biosynthesis. These findings promote the study of further genome annotation and transcriptome research in P. cablin

Periodical metal cylinders for improving heating uniformity of small batch materials in microwave applicators with rotating turntables

Microwave applicators with rotating turntables have been widely applied in many fields, but the heating non-uniformity still limits the further applications. Specifically, when microwave applicators are used to process small batch materials, materials have to be away from the center of rotating turntables, where the problem of heating non-uniformity is more prominent. In order to overcome this difficulty, this paper presents a novel periodical metal cylinder structure to improve the heating uniformity for microwave applicators. With the proposed periodical metal cylinders being placed beneath rotating turntables, electromagnetic fields can be well adjusted, thus improving the heating uniformity. To demonstrate the heating uniformity with the proposed structure, the heating process of the arrays of two and three potato slices in a practical microwave applicator is simulated by the finite element method, respectively. The results show that both the heating uniformity of the two and three potato slices can be improved, which is validated by experiments. Furthermore, the results show that the temperature similarity among the processed potato slices with the proposed structure is better than that without the proposed structure

Characterization of the complete plastome of medicinal plant Saururus chinensis (Saururaceae)

Saururus chinensis is an important medicinal plant in Southeast Asia. Here, we determined the first complete plastome of S. chinensis using high throughput Illumina sequencing technology. The S. chinensis plastome is 161,494 bp in length and presents a typical quadripartite structure consisting of one large single-copy region (LSC, 88,863 bp), one small single-copy region (SSC, 18,679 bp), and a pair of inverted repeat regions (IRs, 26,976 bp each). The phylogenetic analysis robustly supports that S. chinensis is sister to the group including the Saruma henryi, Asarum sieboldii, Piper kadsura, Piper cenocladum

Medical Gesture Recognition Method Based on Improved Lightweight Network

Surgery is a compelling application field for collaborative control robots. This paper proposes a gesture recognition method applied to a medical assistant robot delivering instruments to collaborate with surgeons to complete surgeries. The key to assisting the surgeon in passing instruments in the operating room is the ability to recognize the surgeon’s hand gestures accurately and quickly. Existing gesture recognition techniques suffer from poor recognition accuracy and low rate. To address the existing shortcomings, we propose an improved lightweight convolutional neural network called E-MobileNetv2. The ECA module is added to the original MobileNetv2 network model to obtain more useful features by computing the information interactions between the current channel and the adjacent channels and between the current channel and the distant channels in the feature map. We add R6-SELU activation function to enhance the network’s ability to extract features. By adjusting the shrinkable hyper-parameters, the number of parameters of the network is reduced to improve the recognition speed. The improved network model achieves excellent performance on both the self-built dataset Gesture_II and the public dataset Jester. The recognition accuracy of the improved model is 96.82%, which is 3.17 % higher than that of the original model, achieving an increase in accuracy and recognition speed

The complete plastome and phylogenetic analysis of Rhoiptelea chiliantha (Juglandaceae)

The complete plastome of Rhoiptelea chiliantha was sequenced and assembled in this study. The circular plastome of R. chiliantha is 161,702 bp in size, which contains a large single-copy region (LSC, 90,447 bp), a short single-copy region (SSC, 19,081 bp) and two inverted repeat sequences (IRs, 26,087 bp, each). It is totally comprised of 133 genes, including 88 protein-coding genes, eight ribosomal RNA, and 37 transfer RNA. The phylogenetic analysis shows that R. chiliantha is sister to the clade including remaining Juglandaceae species

Medical Gesture Recognition Method Based on Improved Lightweight Network

Surgery is a compelling application field for collaborative control robots. This paper proposes a gesture recognition method applied to a medical assistant robot delivering instruments to collaborate with surgeons to complete surgeries. The key to assisting the surgeon in passing instruments in the operating room is the ability to recognize the surgeon’s hand gestures accurately and quickly. Existing gesture recognition techniques suffer from poor recognition accuracy and low rate. To address the existing shortcomings, we propose an improved lightweight convolutional neural network called E-MobileNetv2. The ECA module is added to the original MobileNetv2 network model to obtain more useful features by computing the information interactions between the current channel and the adjacent channels and between the current channel and the distant channels in the feature map. We add R6-SELU activation function to enhance the network’s ability to extract features. By adjusting the shrinkable hyper-parameters, the number of parameters of the network is reduced to improve the recognition speed. The improved network model achieves excellent performance on both the self-built dataset Gesture_II and the public dataset Jester. The recognition accuracy of the improved model is 96.82%, which is 3.17 % higher than that of the original model, achieving an increase in accuracy and recognition speed

Complete plastome of Houttuynia cordata (Saururaceae), a medicinal and edible plant

The complete plastome of Houttuynia cordata, an important medicinal and edible plant, was identified and sequenced in this study. The circular plastome is 160,217 bp in length and consists of a pair of inverted repeats (IRs 26,854 bp each), which is separated by a large single-copy region (LSC, 88,189 bp) and a small single-copy region (SSC, 18,320 bp). It encodes 132 genes, of which 114 are unique genes (80 protein-coding genes, 30 tRNAs, and 4 rRNAs). The phylogenetic analysis strongly reveals the sister group between H. cordata and the clade including Piper kadsura, Piper cenocladum, Saruma henryi, and Asarum sieboldii

The complete plastome of Gymnotheca chinensis (Saururaceae) and its phylogenetic analysis

The complete plastome of Gymnotheca chinensis, an important medicinal herb, was firstly elucidated and analyzed in this study. The plastome is 161,621 bp in size, which comprises of one large single-copy (LSC) region and one small single-copy (SSC) region of 89,291 bp and 18,592 bp, respectively, separated by a pair of IR regions of 26,869 bp each. It encodes a total of 132 genes, including 87 protein-coding genes, 37 tRNA, and 8 rRNA. The phylogeny robustly supports that G. chinensis is sister to the clade including Piper kadsura, Piper cenocladum, Saruma henryi, Asarum sieboldii