PI-BA Bundle Adjustment Acceleration on Embedded FPGAs with Co-observation Optimization

Bundle adjustment (BA) is a fundamental optimization technique used in many crucial applications, including 3D scene reconstruction, robotic localization, camera calibration, autonomous driving, space exploration, street view map generation etc. Essentially, BA is a joint non-linear optimization problem, and one which can consume a significant amount of time and power, especially for large optimization problems. Previous approaches of optimizing BA performance heavily rely on parallel processing or distributed computing, which trade higher power consumption for higher performance. In this paper we propose {\pi}-BA, the first hardware-software co-designed BA engine on an embedded FPGA-SoC that exploits custom hardware for higher performance and power efficiency. Specifically, based on our key observation that not all points appear on all images in a BA problem, we designed and implemented a Co-Observation Optimization technique to accelerate BA operations with optimized usage of memory and computation resources. Experimental results confirm that {\pi}-BA outperforms the existing software implementations in terms of performance and power consumption.Comment: in Proceedings of IEEE FCCM 201

TGFBI promoter hypermethylation correlating with paclitaxel chemoresistance in ovarian cancer

The purpose of this study is to determine the methylation status of Transforming growth factor-beta-inducible gene-h3 (TGFBI) and its correlation with paclitaxel chemoresistance in ovarian cancer. The methylation status of TGFBI was examined in ovarian cancer and control groups by methylation-specific PCR (MSP) and bisulfite sequencing PCR (BSP). The TGFBI expression and cell viability were compared by Quantitative Real-Time PCR, Western Blotting and MTT assay before and after demethylating agent 5-aza-2'-deoxycytidine (5-aza-dc) treatment in 6 cell lines (SKOV3, SKOV3/TR, SKOV3/DDP, A2780, 2780/TR, OVCAR8). In our results, TGFBI methylation was detected in 29/40 (72.5%) of ovarian cancer and 1/10 (10%) of benign ovarian tumors. No methylation was detected in normal ovarian tissues (P < 0.001). No statistical correlation between RUNX3 methylation and clinicopathological characteristics was observed. A significant correlation between TGFBI methylation and loss of TGFBI mRNA expression was found (P < 0.001). The methylation level of TGFBI was significantly higher in paclitaxel resistant cell lines (SKOV3/TR and 2780/TR) than that in the sensitive pairs (P < 0.001). After 5-aza-dc treatment, the relative expression of TGFBI mRNA and protein increased significantly in SKOV3/TR and A2780/TR cells. However, no statistical differences of relative TGFBI mRNA expression and protein were found in other cells (all P > 0.05), which showed that re-expression of TGFBI could reverse paclitaxel chemoresistance. Our results show that TGFBI is frequently methylated and associated with paclitaxel-resistance in ovarian cancer. TGFBI might be a potential therapeutic target for the enhancement of responses to chemotherapy in ovarian cancer patients

Blockage of transdifferentiation from fibroblast to myofibroblast in experimental ovarian cancer models

<p>Abstract</p> <p>Background</p> <p>Tumour stromal myofibroblasts can promote tumour invasion. As these cells are genetically more stable than cancer cells, there has been enormous interest in developing targeted molecular therapies against them. Chloride intracellular channel 4 (CLIC4) and reactive oxygen species (ROS) have been linked with promoting stromal cell transdifferentiation in various cancers, but little is known of their roles in ovarian cancer. In this study, we examined the functional roles that both CLIC4 and ROS play in the process of ovarian cancer cell-stimulated or TGF-β1 induced fibroblast-to-myofibroblast transdifferentiation. We also examine whether it is possible to reverse such a process, with the aim of developing novel therapies against ovarian cancer by targeting activated transdifferentiated myofibroblasts.</p> <p>Results</p> <p>We demonstrate that TGF-β1 induced or CM^SKOV3activate transdifferentiated myofibroblasts (fibroblasts). These fibroblasts mimic "reactive" stromal myofibroblasts and demonstrate significant up-regulation of CLIC4 expression and increased level of ROS production. Blocking the production of ROS with an antioxidant consequently reduces the expression of CLIC4, and is accompanied by disappearance of <it>α</it>-smooth-muscle actin (α-SMA), a myofibroblast marker, suggesting ROS acts as a signalling molecule that promotes and enhances CLIC4 activities in the myofibroblast transdifferentiaton process. Down-regulation of CLIC4 with a generic agent or specific siRNA both significantly reduces the expression of factors related to the phenotypes and functions of myofibroblasts, such as α-SMA, hepatocyte growth factor (HGF) and vascular endothelial growth factor (VEGF), thus reversing the myofibroblast phenotype back to fibroblasts. These results convincingly show that ROS and CLIC4 are responsible for TGF-β1 induced fibroblast-to-myofibroblast transdifferentiaton and down-regulation of both is sufficient to block transdifferentiated myofibroblasts.</p> <p>Conclusion</p> <p>Molecular targeting of ROS and CLIC4 has the potential to develop novel therapies for ovarian cancer.</p

Influence of dietary Salicornia europaea L. extract supplementation on feed efficiency of Altay sheep by modifying their gastrointestinal bacteria communities

This experiment aimed to examine the impact of Salicornia europaea L. extract on sheep growth performance, rumen fermentation variables, nutrient apparent digestibility, and gastrointestinal microbial diversity. Forty-eight male Altay sheep, weighing 32.5 ± 2.8 kg and approximately 3.5 months old, were chosen. Four dietary treatments, each consisting of four replicates and three sheep per replicate, were distributed randomly to the sheep. The pelleted total mixed ration containing Salicornia europaea L. extract at 0.0, 0.2, 0.4, and 0.6% DM was freely available to the sheep in the four treatment groups. The 56-day experiment consisted of 45 days of measurements followed by 11 days of adaptation. The growth performance was not affected by nutrition Salicornia europaea L. extract (p ≤ 0.05), but the feed-to-gain ratio was reduced when the extract was given at 0.4% DM (p ≤ 0.05). Compared to the 0 and 0.2% treatments, the apparent digestibility of DM, OM, NDF, and ADF was substantially greater in the 0.4, and 0.6% treatments. Furthermore, compared to sheep in the 0 and 0.2% groups, sheep in the 0.6% group had a noticeably higher apparent digestibility of CP. As the amount of Salicornia europaea L. extract added to the rumen fluid rose, the molar ratio of acetic acid increased. In contrast, the molar ratio of propionic acid gradually decreased, and the total volatile fatty acid content gradually reduced. Thus, adding a suitable quantity of Salicornia europaea L. extract to the sheep ration is natural and secure, which may improve the environmental sustainability of small ruminant production systems

Selection of reference genes for quantitative real-time PCR analysis in cucumber (Cucumis sativus L.), pumpkin (Cucurbita moschata Duch.) and cucumber–pumpkin grafted plants

Background Quantitative real-time PCR (qRT-PCR) is a commonly used high-throughput technique to measure mRNA transcript levels. The accuracy of this evaluation of gene expression depends on the use of optimal reference genes. Cucumber–pumpkin grafted plants, made by grafting a cucumber scion onto pumpkin rootstock, are superior to either parent plant, as grafting conveys many advantages. However, although many reliable reference genes have been identified in both cucumber and pumpkin, none have been obtained for cucumber–pumpkin grafted plants. Methods In this work, 12 candidate reference genes, including eight traditional genes and four novel genes identified from our transcriptome data, were selected to assess their expression stability. Their expression levels in 25 samples, including three cucumber and three pumpkin samples from different organs, and 19 cucumber–pumpkin grafted samples from different organs, conditions, and varieties, were analyzed by qRT-PCR, and the stability of their expression was assessed by the comparative ΔCt method, geNorm, NormFinder, BestKeeper, and RefFinder. Results The results showed that the most suitable reference gene varied dependent on the organs, conditions, and varieties. CACS and 40SRPS8 were the most stable reference genes for all samples in our research. TIP41 and CACS showed the most stable expression in different cucumber organs, TIP41 and PP2A were the optimal reference genes in pumpkin organs, and CACS and 40SRPS8 were the most stable genes in all grafted cucumber samples. However, the optimal reference gene varied under different conditions. CACS and 40SRPS8 were the best combination of genes in different organs of cucumber–pumpkin grafted plants, TUA and RPL36Aa were the most stable in the graft union under cold stress, LEA26 and ARF showed the most stable expression in the graft union during the healing process, and TIP41 and PP2A were the most stable across different varieties of cucumber–pumpkin grafted plants. The use of LEA26, ARF and LEA26+ARF as reference genes were further verified by analyzing the expression levels of csaCYCD3;1, csaRUL, cmoRUL, and cmoPIN in the graft union at different time points after grafting. Discussion This work is the first report of appropriate reference genes in grafted cucumber plants and provides useful information for the study of gene expression and molecular mechanisms in cucumber–pumpkin grafted plants

CoBacFM: Core bacteria forecast model for global grassland pH dynamics under future climate warming scenarios

Soil microbes regulate various biogeochemical cycles on Earth and respond rapidly to climate change, which is accompanied by changes in soil pH. However, the long-term patterns of these changes under future climate scenarios remain unclear. We propose a core-bacteria-forecast model (CoBacFM) to model soil pH changes by shifts of core bacterial groups under future scenarios using a curated soil microbiota dataset of global grasslands. Our model estimates that soil pH will increase in 63.8%–67.0% of grassland regions and decrease in 10.1%–12.4% of regions. Approximately 32.5%–32.9% of regions will become more alkaline by 5.6%, and these areas expand in all future scenarios. These results were supported by 14 warming simulation experiments. Using bacterial responses as bioindicators of soil pH, the CoBacFM method can accurately forecast pH changes in future scenarios, and the changing global climate is likely to result in the alkalization of grasslands.</br

Extensive Promoter-Centered Chromatin Interactions Provide a Topological Basis for Transcription Regulation

Higher-order chromosomal organization for transcription regulation is poorly understood in eukaryotes. Using genome-wide Chromatin Interaction Analysis with Paired-End-Tag sequencing (ChIAPET), we mapped long-range chromatin interactions associated with RNA polymerase II in human cells and uncovered widespread promoter-centered intragenic, extragenic, and intergenic interactions. These interactions further aggregated into higher-order clusters, wherein proximal and distal genes were engaged through promoter-promoter interactions. Most genes with promoter-promoter interactions were active and transcribed cooperatively, and some interacting promoters could influence each other implying combinatorial complexity of transcriptional controls. Comparative analyses of different cell lines showed that cell-specific chromatin interactions could provide structural frameworks for cell-specific transcription, and suggested significant enrichment of enhancer-promoter interactions for cell-specific functions. Furthermore, genetically-identified disease-associated noncoding elements were found to be spatially engaged with corresponding genes through long-range interactions. Overall, our study provides insights into transcription regulation by three-dimensional chromatin interactions for both housekeeping and cell-specific genes in human cells