Conformer: Local Features Coupling Global Representations for Recognition and Detection.

With convolution operations, Convolutional Neural Networks (CNNs) are good at extracting local features but experience difficulty to capture global representations. With cascaded self-attention modules, vision transformers can capture long-distance feature dependencies but unfortunately deteriorate local feature details. In this paper, we propose a hybrid network structure, termed Conformer, to take both advantages of convolution operations and self-attention mechanisms for enhanced representation learning. Conformer roots in feature coupling of CNN local features and transformer global representations under different resolutions in an interactive fashion. Conformer adopts a dual structure so that local details and global dependencies are retained to the maximum extent. We also propose a Conformer-based detector (ConformerDet), which learns to predict and refine object proposals, by performing region-level feature coupling in an augmented cross-attention fashion. Experiments on ImageNet and MS COCO datasets validate Conformer's superiority for visual recognition and object detection, demonstrating its potential to be a general backbone network.

[Effects of biochar and biochar compound fertilizer on the communities of nitrifier and denitrifier in a reclaimed soil from coal-mining area]. / ç”Ÿç‰©ç‚­ä¸Žç‚­åŸºè‚¥å¯¹é‡‡ç ¤å¡Œé™·å¤åž¦åŒºåœŸå£¤ç¡åŒ–å’Œåç¡åŒ–å¾®ç”Ÿç‰©ç¾¤è½çš„å½±å“.

As a new soil amendment strategy, the effects of biochar application on soil microbial community have been reported in literature, but little information is available on the response of nitrogen-related microbial communities to biochar application in the reclaimed soil from coal-mining area. Through an outdoor pot experiment with reclaimed soil from coal-mining area of Huaibei, the effects of biochar and biochar compound fertilizer on nitrifier and denitrifier communities were investigated by real time PCR (qPCR) and terminal-restricted fragment length polymorphism (T-RFLP). There were five treatments: control (CK), NPK fertilizer (CF), biochar compound fertili-zer (BF), 2% biochar and NPK fertilizer (LB), 4% biochar and NPK fertilizer (HB). Results showed that compared with the CK, the treatments CF, BF, LB and HB significantly increased the abundance of ammonia oxidizing archaea (AOA), ammonia oxidizing bacteria (AOB), nirK and nirS genes of denitrifier. Compared with the CF treatment, BF, LB and HB significantly increased the abundance of AOB and nirK genes by 42.9%-82.1% and 33.5%-62.7%, respectively. Results of redundancy analysis showed that soil organic carbon, pH, NH4+-N and available potassium significantly affected AOB community structure, while soil organic carbon concentration, pH and NO3--N concentration significantly altered nirK-denitrifier community structure. Therefore, the application of biochar and biochar compound fertilizer could improve soil quality of the reclaimed soil from coal-mining area, and increase the abundances of nitrifier and denitrifier and alter community structure of AOB and nirK-denitrifier.

Overgrowth of Lactobacillus in gastric cancer.

Dysbiosis of the gastric microbiome is involved in the development of gastric cancer (GC). A number of studies have demonstrated an increase in the relative abundance of Lactobacillus in GC. In this review, we present data that support the overgrowth of Lactobacillus in GC from studies on molecular and bacterial culture of the gastric microbiome, discuss the heterogenic effects of Lactobacillus on the health of human stomach, and explore the potential roles of the overgrowth of Lactobacillus in gastric carcinogenesis. Further studies are required to examine the association between Lactobacillus and GC at strain and species levels, which would facilitate to elucidate its role in the carcinogenic process.

Different Responses of Soil Bacterial and Fungal Communities to 3 Years of Biochar Amendment in an Alkaline Soybean Soil.

Biochar as a soil amendment has been regarded as a promising way to improve soil fertility. However, the response of microbial community after biochar and biochar compound fertilizer (BCF) application has not been thoroughly elucidated. This study evaluated the changes in abundance and composition of bacterial and fungal communities using quantitative real-time PCR (qPCR) and Illumina MiSeq amplicon sequencing. The field experiment ran for 3 years and comprised five treatments: chemical fertilizer as control (CK), straw-returning combined with chemical fertilizer (CS), low biochar application combined with chemical fertilizer (LB), high biochar application combined with chemical fertilizer (HB) and BCF. The results showed that biochar amendment results no changes in the abundance and diversity of bacteria in the bulk and rhizosphere soils. However, the abundance of soil fungi was significantly increased by biochar amendment (LB and HB). LB treatment significantly increased the fungal alpha diversity, while there was no significant change under HB. Furthermore, the dominant bacterial phyla found in the samples were Proteobacteria, Actinobacteria, and Acidobacteria. Biochar addition increased the relative abundance of Actinobacteria in both bulk and rhizosphere soils. The dominant fungal phyla were Ascomycota, Mortierellomycota, and Basidiomycota. The relative abundance of Ascomycota significantly decreased, but Mortierellomycota significantly increased in LB and HB. In addition, redundancy analysis indicated that the changes in bacterial and fungal communities are associated with soil properties such as SOC and TN, which are crucial contributors in regulating the community composition. This study is expected to provide significant theoretical and practical knowledge for the application of biochar in agricultural ecosystem.

Impact of biochar amendment on the abundance and structure of diazotrophic community in an alkaline soil.

Biological nitrogen (N) fixation contributes to the pool of plant-available N in soil and helps to minimize the use of inorganic N fertilizer in agricultural ecosystems. Although diazotrophs play an important role in the biological fixation of atmospheric N2 in a range of soil types, the knowledge of their response to biochar amendment is still limited. Here, using the nifH gene as a molecular marker, we investigated the short-term effect of biochar application on the abundance, community composition and activity of diazotroph in an alkaline soil. A field trial was established before soybean sowing in 2017 and five treatments were included: inorganic NPK fertilizer (CK); inorganic NPK fertilizer + wheat straw (CS); inorganic NPK fertilizer + low rate of biochar (B4); inorganic NPK fertilizer + high rate of biochar (B20); biochar compound fertilizer (BCF). The field trial was lasted for one crop season and samples were collected by soybean harvest. The results showed that biochar addition generally increased the concentration of soil organic carbon (SOC) and available phosphorous (AP), while B20 treatment significantly increased the total nitrogen (TN) and available potassium (AK). Biochar addition treatments increased the nifH gene abundance and altered the community structure of soil diazotrophs. The abundance of nifH gene was positively correlated with SOC, indicating that increasing SOC potentially affected diazotrophic population in the alkaline soil. Community structure of diazotrophs in the CS treatment was similar with the CK treatment; thus, there was no effect of crop straw on diazotroph community structure. In contrast, the application of biochar and biochar compound fertilizer altered the diazotroph community structure with shifts in the dominant genus, with higher Sinorhizobium in the biochar-amended treatments. SOC, C/N and AP were the key factors correlated with change in diazotroph community structure. Overall, our results suggest that the addition of biochar or biochar compound fertilizer could increase the abundance and alter the community structure of diazotrophs, which may benefit N fixation in alkaline agricultural soil. Conversely, the direct straw return had no effect on the abundance and community structure of diazotrophs.

Effects of biochar amendment on bacterial and fungal communities in the reclaimed soil from a mining subsidence area.

Biochar amendment of soil is well known to improve soil fertility and microbial function. However, little is known about the effect of biochar addition to reclaimed soil in coal mining subsidence area on microbial community. A plant soil cultivation experiment was conducted with wheat grown and four treatments were included: P and K fertilizer (CK); NPK inorganic fertilizer (NPK); NPK inorganic fertilizer and straw (NPKS); and NPK inorganic fertilizer and biochar (NPKB). The results indicated that biochar amendment significantly increased the concentrations of NH4+-N, total N, and available P and K compared with the NPK. Biochar addition also significantly increased the grain yield and total biomass of wheat. Furthermore, biochar amendment treatment increased the absolute abundance and altered the community structure of soil bacteria and fungi in the reclaimed soil. Illumina MiSeq sequencing showed that the addition of biochar increased α-diversity of bacteria and relative abundances of Proteobacteria, Actinobacteria, and Bacteroidetes, whereas the relative abundance of Firmicutes were decreased by 61%. However, biochar addition did not change the relative abundance of dominant fungal phyla. Redundancy analysis (RDA) suggested that total N, available P, and K contents were the key factors correlated with changes in microbial community structure. Overall, our results suggest that biochar amendment in reclaimed soil in coal mine subsidence area could increase wheat yield and abundance and alter microbial community compositions.

Corrigendum: Using Integrative Analysis of DNA Methylation and Gene Expression Data in Multiple Tissue Types to Prioritize Candidate Genes for Drug Development in Obesity.

[This corrects the article DOI: 10.3389/fgene.2018.00663.].

Using Integrative Analysis of DNA Methylation and Gene Expression Data in Multiple Tissue Types to Prioritize Candidate Genes for Drug Development in Obesity.

Obesity has become a major public health issue which is caused by a combination of genetic and environmental factors. Genome-wide DNA methylation studies have identified that DNA methylation at Cytosine-phosphate-Guanine (CpG) sites are associated with obesity. However, subsequent functional validation of the results from these studies has been challenging given the high number of reported associations. In this study, we applied an integrative analysis approach, aiming to prioritize the drug development candidate genes from many associated CpGs. Association data was collected from previous genome-wide DNA methylation studies and combined using a sample-size-weighted strategy. Gene expression data in adipose tissues and enriched pathways of the affiliated genes were overlapped, to shortlist the associated CpGs. The CpGs with the most overlapping evidence were indicated as the most appropriate CpGs for future studies. Our results revealed that 119 CpGs were associated with obesity (p ≤ 1.03 × 10-7). Of the affiliated genes, SOCS3 was the only gene involved in all enriched pathways and was differentially expressed in both visceral adipose tissue (VAT) and subcutaneous adipose tissue (SAT). In conclusion, our integrative analysis is an effective approach in highlighting the DNA methylation with the highest drug development relevance. SOCS3 may serve as a target for drug development of obesity and its complications.

Model checking optimal finite-horizon control for probabilistic gene regulatory networks.

BACKGROUND: Probabilistic Boolean networks (PBNs) have been proposed for analyzing external control in gene regulatory networks with incorporation of uncertainty. A context-sensitive PBN with perturbation (CS-PBNp), extending a PBN with context-sensitivity to reflect the inherent biological stability and random perturbations to express the impact of external stimuli, is considered to be more suitable for modeling small biological systems intervened by conditions from the outside. In this paper, we apply probabilistic model checking, a formal verification technique, to optimal control for a CS-PBNp that minimizes the expected cost over a finite control horizon. RESULTS: We first describe a procedure of modeling a CS-PBNp using the language provided by a widely used probabilistic model checker PRISM. We then analyze the reward-based temporal properties and the computation in probabilistic model checking; based on the analysis, we provide a method to formulate the optimal control problem as minimum reachability reward properties. Furthermore, we incorporate control and state cost information into the PRISM code of a CS-PBNp such that automated model checking a minimum reachability reward property on the code gives the solution to the optimal control problem. We conduct experiments on two examples, an apoptosis network and a WNT5A network. Preliminary experiment results show the feasibility and effectiveness of our approach. CONCLUSIONS: The approach based on probabilistic model checking for optimal control avoids explicit computation of large-size state transition relations associated with PBNs. It enables a natural depiction of the dynamics of gene regulatory networks, and provides a canonical form to formulate optimal control problems using temporal properties that can be automated solved by leveraging the analysis power of underlying model checking engines. This work will be helpful for further utilization of the advances in formal verification techniques in system biology.

Luminescent dinuclear copper(I) complexes bearing 1,4-bis(diphenylphosphino)butane and functionalized 3-(2'-pyridyl)pyrazole mixed ligands.

A family of new dinuclear Cu(i) complexes with 1,4-bis(diphenylphosphino)butane (dppb) and functionalized 3-(2'-pyridyl)pyrazole mixed ligands has been synthesized and characterized. It is revealed that all these Cu(i) complexes include a [Cu2(dppb)2](2+) framework with the two Cu(i) atoms doubly bridged by a pair of dppb to generate a fourteen-membered Cu2P4C8 ring, and functionalized 3-(2'-pyridyl)pyrazole adopts a neutral chelating coordination mode without the N-H bond cleavage of the pyrazolyl ring. All these dinuclear Cu(i) complexes display a relatively weak low-energy absorption in CH2Cl2 solution, which is closely related to the variation of the Cu-N and Cu-P bonds caused by the substituent on the pyrazolyl ring. These dinuclear Cu(i) complexes are all emissive in solution and solid states at ambient temperature, which can be well modulated through structural modification of 3-(2'-pyridyl)pyrazole. It is shown that introduction of the trifluoromethyl group into the pyrazolyl ring is helpful for enhancing the luminescence properties of Cu(i) pyrazole phosphine complexes.