Long Short-Term Memory Spatial Transformer Network

Spatial transformer network has been used in a layered form in conjunction with a convolutional network to enable the model to transform data spatially. In this paper, we propose a combined spatial transformer network (STN) and a Long Short-Term Memory network (LSTM) to classify digits in sequences formed by MINST elements. This LSTM-STN model has a top-down attention mechanism profit from LSTM layer, so that the STN layer can perform short-term independent elements for the statement in the process of spatial transformation, thus avoiding the distortion that may be caused when the entire sequence is spatially transformed. It also avoids the influence of this distortion on the subsequent classification process using convolutional neural networks and achieves a single digit error of 1.6\% compared with 2.2\% of Convolutional Neural Network with STN layer

Dynamic change of Cardiomyocytes on Shape Memory Polymer

In the previous work, it has been proven that substrate topography can influent the cell behaviors, including morphology and functions. Many research teams showed that wrinkled surfaces have been able to improve the alignment and orientation of different biological cell types. Cardiomyocytes are also influenced by the surface topography with better alignment along the winkles, comparing to the flat surface. However, there is little evidence to demonstrate how cardiomyocytes would respond to the wrinkle formation and achieve the cellular alignment change during the transition from flat surface to topographic surface. In this thesis, we have created a dynamic substrate based on shape memory polymer to change the surface topography and induce the nanoscale wrinkle formation. Using this dynamic substrate, we can observe the cardiomyocyte responses to topography changes, and investigate the dynamic reorganization progress of myofibril remodeling during the cell alignment

Controlling Mesenchyme Tissue Remodeling via Spatial Arrangement of Mechanical Constraints

Tissue morphogenetic remodeling plays an important role in tissue repair and homeostasis and is often governed by mechanical stresses. In this study, we integrated an in vitro mesenchymal tissue experimental model with a volumetric contraction-based computational model to investigate how geometrical designs of tissue mechanical constraints affect the tissue remodeling processes. Both experimental data and simulation results verified that the standing posts resisted the bulk contraction of the tissues, leading to tissue thinning around the posts as gap extension and inward remodeling at the edges as tissue compaction. We changed the geometrical designs for the engineered mesenchymal tissues with different shapes of posts arrangements (triangle vs. square), different side lengths (6 mm vs. 8 mm), and insertion of a center post. Both experimental data and simulation results showed similar trends of tissue morphological changes of significant increase of gap extension and deflection compaction with larger tissues. Additionally, insertion of center post changed the mechanical stress distribution within the tissues and stabilized the tissue remodeling. This experimental-computational integrated model can be considered as a promising initiative for future mechanistic understanding of the relationship between mechanical design and tissue remodeling, which could possibly provide design rationale for tissue stability and manufacturing

Effects of guar gum supplementation in high-fat diets on fish growth, gut histology, intestinal oxidative stress, inflammation, and apoptosis in juvenile largemouth bass (<em>Micropterus salmoides</em>)

The present study aimed to investigate the influence of guar gum supplementation in high-fat diets on the growth performance and intestinal oxidative stress, inflammation, and apoptosis of juvenile largemouth bass. Five isonitrogenous diets were prepared: a control diet (10% crude lipid, C), a high-fat diet (17% crude lipid, HF), and three high-fat diets supplemented with 0.3% guar gum (GG0.3), 1% guar gum (GG1), and 3% guar gum (GG3). Largemouth bass (3.1±0.2 g) were randomly assigned to fifteen tanks (30 fish/tank) and fed for 8 weeks. The results demonstrated that GG0.3 significantly increased specific growth rate (SGR) and increased feed conversion ratio (FCR) compared to HF (P < 0.05). For histology, high-fat diets containing guar gum significantly increased intestinal villus length, villus width, and perimeter ratio, compared with HF (P < 0.05). Compared with Control, HF significantly decreased reduced glutathione (GSH) contents and increased malondialdehyde (MDA) contents in the intestine (P < 0.05). Additionally, HF significantly increased the expression of interleukin 1β (IL-1β), tumor necrosis factor α (TNF-α), and cysteine-aspartic proteases 9 (Caspase 9) in the intestine (P < 0.05). Compared to HF, GG0.3 significantly decreased MDA contents, increased GSH contents, and downregulated the expression of IL-1β, TNF-α, and Caspase 3 than diet HF in the intestine (P < 0.05). These results suggest that guar gum can alleviate the adverse effects of high-fat diets on growth and gut health in fish

Identification of the NF-κB activating protein-like locus as a risk locus for rheumatoid arthritis

Objective: To fine-map the NF-κB activating protein-like (NKAPL) locus identified in a prior genome-wide study as a possible rheumatoid arthritis (RA) risk locus and thereby delineate additional variants with stronger and/or independent disease association. Methods: Genotypes for 101 SNPs across the NKAPL locus on chromosome 6p22.1 were obtained on 1368 Canadian RA cases and 1471 controls. Single marker associations were examined using logistic regression and the most strongly associated NKAPL locus SNPs then typed in another Canadian and a US-based RA case/control cohort. Results: Fine-mapping analyses identified six NKAPL locus variants in a single haplotype block showing association with p≤5.6×10−8 in the combined Canadian cohort. Among these SNPs, rs35656932 in the zinc finger 193 gene and rs13208096 in the NKAPL gene remained significant after conditional logistic regression, contributed independently to risk for disease, and were replicated in the US cohort (Pcomb=4.24×10−10 and 2.44×10−9, respectively). These associations remained significant after conditioning on SNPs tagging the HLA-shared epitope (SE) DRB1*0401 allele and were significantly stronger in the HLA-SE negative versus positive subgroup, with a significant negative interaction apparent between HLA-DRB1 SE and NKAPL risk alleles. Conclusions: By illuminating additional NKAPL variants with highly significant effects on risk that are distinct from, but interactive with those arising from the HLA-DRB1 locus, our data conclusively identify NKAPL as an RA susceptibility locus

The <i>Sinocyclocheilus</i> cavefish genome provides insights into cave adaptation

BACKGROUND: An emerging cavefish model, the cyprinid genus Sinocyclocheilus, is endemic to the massive southwestern karst area adjacent to the Qinghai-Tibetan Plateau of China. In order to understand whether orogeny influenced the evolution of these species, and how genomes change under isolation, especially in subterranean habitats, we performed whole-genome sequencing and comparative analyses of three species in this genus, S. grahami, S. rhinocerous and S. anshuiensis. These species are surface-dwelling, semi-cave-dwelling and cave-restricted, respectively. RESULTS: The assembled genome sizes of S. grahami, S. rhinocerous and S. anshuiensis are 1.75 Gb, 1.73 Gb and 1.68 Gb, respectively. Divergence time and population history analyses of these species reveal that their speciation and population dynamics are correlated with the different stages of uplifting of the Qinghai-Tibetan Plateau. We carried out comparative analyses of these genomes and found that many genetic changes, such as gene loss (e.g. opsin genes), pseudogenes (e.g. crystallin genes), mutations (e.g. melanogenesis-related genes), deletions (e.g. scale-related genes) and down-regulation (e.g. circadian rhythm pathway genes), are possibly associated with the regressive features (such as eye degeneration, albinism, rudimentary scales and lack of circadian rhythms), and that some gene expansion (e.g. taste-related transcription factor gene) may point to the constructive features (such as enhanced taste buds) which evolved in these cave fishes. CONCLUSION: As the first report on cavefish genomes among distinct species in Sinocyclocheilus, our work provides not only insights into genetic mechanisms of cave adaptation, but also represents a fundamental resource for a better understanding of cavefish biology. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12915-015-0223-4) contains supplementary material, which is available to authorized users

Putative DHHC-Cysteine-Rich Domain S-Acyltransferase in Plants

Protein S-acyltransferases (PATs) containing Asp-His-His-Cys within a Cys-rich domain (DHHC-CRD) are polytopic transmembrane proteins that are found in eukaryotic cells and mediate the S-acylation of target proteins. S-acylation is an important secondary and reversible modification that regulates the membrane association, trafficking and function of target proteins. However, little is known about the characteristics of PATs in plants. Here, we identified 804 PATs from 31 species with complete genomes. The analysis of the phylogenetic relationships suggested that all of the PATs fell into 8 groups. In addition, we analysed the phylogeny, genomic organization, chromosome localisation and expression pattern of PATs in Arabidopsis, Oryza sative, Zea mays and Glycine max. The microarray data revealed that PATs genes were expressed in different tissues and during different life stages. The preferential expression of the ZmPATs in specific tissues and the response of Zea mays to treatments with phytohormones and abiotic stress demonstrated that the PATs play roles in plant growth and development as well as in stress responses. Our data provide a useful reference for the identification and functional analysis of the members of this protein family

The Study on Newly Developed McAb NJ001 Specific to Non-Small Cell Lung Cancer and Its Biological Characteristics

Monoclonal antibody (McAb) is the key tool for cancer immunodiagnosis and immunotherapy. McAb-based immunotherapy that targets tumor antigens has had great achivement. In this study, a cell clone which kept secreting high-titer IgG1-type McAb named NJ001 against human non-small cell lung cancer (NSCLC) cells was obtained. The titer of purified NJ001 was 2×106. The antigen named SP70 of NSCLC specifically identified by NJ001 was proved to be a protein with the relative molecular mass (Mr) of 70 kDa. The results of immunohistochemical staining indicated that NJ001 could positively react to NSCLC, but weak positively or negatively react to human small-cell lung cancer (SCLC), pulmonary pseudotumor and other epithelial tumors. In soft agar assay, the colony formation efficiency in NJ001 groups decreased in a dose-dependent manner. For the concentration of 100 µg/ml, 200 µg/ml and 400 µg/ml, the inhibition ratio of colony formation was 23.4%, 62.5% and 100% respectively. Meanwhile, NJ001 caused significant reduction in tumor volume and tumor weight compared to control mice in lung cancer xenograft model. The tumor growth inhibition ratio in 200 µg, 400 µg and 800 µg NJ001 groups was 10.44%, 37.29% and 44.04%, respectively. NJ001 also led to cytomorphological changes and induced the apoptosis of human lung adenocarcinoma cell line SPC-A1 significantly. The newly developed NJ001 selectively reacted to NSCLC and exhibited anti-tumor activity both in vitro and in vivo. NJ001 is of great value concerning immunodiagnostics and immunotherapy for NSCLC and holds promise for further research regarding the mechanism underlying tumor progression of NSCLC