Synergistic improvement of humus formation in compost residue by fenton-like and effective microorganism composite agents.

Improving the humification of compost through a synergistic approach of biotic and abiotic methods is of great significance. This study employed a composite reagent, comprising Fenton-like agents and effective microorganisms (EM) to improve humification. This composite reagent increased humic-acid production by 37.44 %, reaching 39.82 g kg-1, surpassing the control group. The composite reagent synergistically promoted micromolecular fulvic acid and large humic acid production. Collaborative mechanism suggests that Fenton-like agents contributed to bulk residue decomposition and stimulated the evolution of microbial communities, whereas EMs promoted highly aromatic substance synthesis and adjusted the microbial community structure. Sequencing analysis indicates the Fenton-like agent initiated compost decomposition by Firmicutes, and EM reduced the abundance of Virgibacillus, Lentibacillus, and Alcanivorax. Applied as an organic fertilizer in Brassica chinensis L. plantations, the composite reagent considerably improved growth and photosynthetic pigment content. This composite reagent with biotic and abiotic components provides a learnable method for promoting humification.

On Representation Knowledge Distillation for Graph Neural Networks.

Knowledge distillation (KD) is a learning paradigm for boosting resource-efficient graph neural networks (GNNs) using more expressive yet cumbersome teacher models. Past work on distillation for GNNs proposed the local structure preserving (LSP) loss, which matches local structural relationships defined over edges across the student and teacher's node embeddings. This article studies whether preserving the global topology of how the teacher embeds graph data can be a more effective distillation objective for GNNs, as real-world graphs often contain latent interactions and noisy edges. We propose graph contrastive representation distillation (G-CRD), which uses contrastive learning to implicitly preserve global topology by aligning the student node embeddings to those of the teacher in a shared representation space. Additionally, we introduce an expanded set of benchmarks on large-scale real-world datasets where the performance gap between teacher and student GNNs is non-negligible. Experiments across four datasets and 14 heterogeneous GNN architectures show that G-CRD consistently boosts the performance and robustness of lightweight GNNs, outperforming LSP (and a global structure preserving (GSP) variant of LSP) as well as baselines from 2-D computer vision. An analysis of the representational similarity among teacher and student embedding spaces reveals that G-CRD balances preserving local and global relationships, while structure preserving approaches are best at preserving one or the other.

Bioinformatics analysis of potential therapeutic targets for COVID-19 infection in patients with carotid atherosclerosis.

BACKGROUND: COVID-19 is a new coronavirus that constitutes a great challenge to human health. At this stage, there are still cases of COVID-19 infection in some countries and regions, in which ischemic stroke (IS) is a risk factor for new coronavirus pneumonia, and patients with COVID-19 infection have a dramatically elevated risk of stroke. At the same time, patients with long-term IS are vulnerable to COVID-19 infection and have more severe disease, and carotid atherosclerosis is an early lesion in IS. METHODS: This study used human induced pluripotent stem cell (hiPSC)-derived monolayer brain cell dataset and human carotid atherosclerosis genome-wide dataset to analyze COVID-19 infection and carotid atherosclerosis patients to determine the synergistic effect of new coronavirus infection on carotid atherosclerosis patients, to clarify the common genes of both, and to identify common pathways and potential drugs for carotid atherosclerosis in patients with COVID-19 infection RESULTS: Using several advanced bioinformatics tools, we present the causes of COVID-19 infection leading to increased mortality in carotid atherosclerosis patients and the susceptibility of carotid atherosclerosis patients to COVID-19. Potential therapeutic agents for COVID-19 -infected patients with carotid atherosclerosis are also proposed. CONCLUSIONS: With COVID-19 being a relatively new disease, associations have been proposed for its connections with several ailments and conditions, including IS and carotid atherosclerosis. More patient-based data-sets and studies are needed to fully explore and understand the relationship.

Investigation of high volume of CFBC ash on performance of basic magnesium sulfate cement.

Basic magnesium sulfate cement has the advantages of fast setting, high strength, high toughness, water resistance, corrosion resistance, etc. But the cost has become a reason for limiting its widespread application. With the widespread application of circulating fluidized bed combustion (CFBC) technology in China, the accumulation of CFBC ash is increasing. Reasonable use of CFBC ash can not only reduce cost of basic magnesium sulfate cement but also protect environment. In this paper, the effect of a high volume of CFBC ash on fluidity, flexural strength and compressive strength of basic magnesium sulfate cement is studied. Hydration products and micromorphology analyses are measured by X-ray diffraction (XRD) and scanning electron microscopy (SEM). The results reveal that the strength of basic magnesium sulfate cement with 20% CFBC ash is the highest, and its microstructure is the model that CFBC ash and MgO fill a three-dimensional network structure established by needle-shaped 5·1·7 phase. When the amount of CFBC ash is more than 40%, the formation of 5·1·7 phase is affected severely, which greatly reduces the strength.

The analysis of pharmacokinetic and pharmacogenomic impact on gefitinib efficacy in advanced non-small cell lung cancer patients: results from a prospective cohort study.

BACKGROUND: The current study is aimed to examine the impact of pharmacokinetics and gene polymorphisms of enzymes involving in absorption, distribution, metabolism and excretion (ADME) on the efficacy of gefitinib in non-small cell lung cancer (NSCLC) patients. METHODS: Eligible patients with indication of gefitinib treatment were prospectively enrolled in this study. Two peripheral blood samples at baseline and before cycle 2 day 1 were collected for the detection of single nucleotide polymorphisms (SNPs) of drug ADME enzymes and trough drug concentration (Ctrough) at steady state. Thirteen SNPs were genotyped using the Sequenom Massarray system. Ctrough was determined by validated high-performance liquid chromatographic method with tandem mass spectrometric (LC-MS/MS). RESULTS: Fifty-eight NSCLC patients were enrolled in this study. The median of Ctrough was 175ng/mL (range from 47.8 to 470 ng/mL). The trough concentration was not associated with either objective response or progression free survival (PFS). Ctrough was significantly lower in CYP3A4 rs2242480 CC + CT genotype than in TT genotype (P=0.019) and in ABCG2 rs2231142 AA genotype than in AC + CC genotype (P=0.031). ABCB1 rs2032582 dominant model was significantly correlated with overall response rate (ORR) and patients with GG phenotype respond better than patients with GT + TT phenotypes (84.6% vs. 51.2%, P=0.032). ABCB1 rs10256836 recessive model was significantly correlated with PFS and patients with GG phenotype achieved longer PFS than patients with GC + CC phenotypes (17.40 vs. 10.33 months, P=0.040). CONCLUSIONS: The Ctrough of gefitinib was significantly different between CYP3A4 and ABCG2 genotypes, but not with the efficacy of gefitinib treatment. ABCB1 rs2032582 and rs10256836 polymorphisms were correlated treatment outcome. Polymorphisms analysis of ABCB1 could be a predictive biomarker for gefitinib treatment.

Genomic Takeover by Transposable Elements in the Strawberry Poison Frog.

We sequenced the genome of the strawberry poison frog, Oophaga pumilio, at a depth of 127.5× using variable insert size libraries. The total genome size is estimated to be 6.76 Gb, of which 4.76 Gb are from high copy number repetitive elements with low differentiation across copies. These repeats encompass DNA transposons, RNA transposons, and LTR retrotransposons, including at least 0.4 and 1.0 Gb of Mariner/Tc1 and Gypsy elements, respectively. Expression data indicate high levels of gypsy and Mariner/Tc1 expression in ova of O. pumilio compared with Xenopus laevis. We further observe phylogenetic evidence for horizontal transfer (HT) of Mariner elements, possibly between fish and frogs. The elements affected by HT are present in high copy number and are highly expressed, suggesting ongoing proliferation after HT. Our results suggest that the large amphibian genome sizes, at least partially, can be explained by a process of repeated invasion of new transposable elements that are not yet suppressed in the germline. We also find changes in the spliceosome that we hypothesize are related to permissiveness of O. pumilio to increases in intron length due to transposon proliferation. Finally, we identify the complement of ion channels in the first genomic sequenced poison frog and discuss its relation to the evolution of autoresistance to toxins sequestered in the skin.

Pharmacogenomic study on anti-VEGF medicine in treatment of macular Neovascular diseases: a study protocol for a prospective observational study.

BACKGROUND: Macular neovascular diseases can cause severe vision loss. A newly approved anti-VEGF drug Conbercept has shown good efficacy and safety in rigorous random controlled trials (RCT), however, it cannot fully reflect the clinical application of Conbercept in real world clinical practice. Moreover, anti-VEGF drugs are expensive and often require multiple treatments, and some patients have poor or even no response to the drugs,this resulted enormous waste of medical resources. Therefore, how to find out those patients who have good response, and how to develop individualized therapeutic regimen in real world need to be urgently investigated in the aspect of pharmacogenomics and pharmacometabolomics. METHODS: This study is a multicenter, prospective, observational study of Conbecept treating macular neovascular diseases in China. Patients suffered from age-related macular degeneration, polypoidal choroidal vasculopathy, and pathological myopia who already planned to receive Conbercept treatment will be recruited. We aimed to enroll more than 5000 patients from 43 ophthalmic centers in China. Patients' clinical data and blood samples will be collected during the one-year follow-up period. Finally, the safety and efficacy of Conbercept, and the potential predictors of patients' response to Conbercept will be investigated by pharmacogenomics and pharmacometabolomics analysis. DISCUSSION: This study will provide important data of Conbercept in treating macular neovascular diseases in real world. Besides, finding the predictor of patients' response will help doctor make more precise individualized therapeutic regimens. TRIAL REGISTRATION: ClinicalTrials.gov, NCT03128463 . Registered on 9 March 2017.

The genome sequences of Arachis duranensis and Arachis ipaensis, the diploid ancestors of cultivated peanut.

Cultivated peanut (Arachis hypogaea) is an allotetraploid with closely related subgenomes of a total size of ∼2.7 Gb. This makes the assembly of chromosomal pseudomolecules very challenging. As a foundation to understanding the genome of cultivated peanut, we report the genome sequences of its diploid ancestors (Arachis duranensis and Arachis ipaensis). We show that these genomes are similar to cultivated peanut's A and B subgenomes and use them to identify candidate disease resistance genes, to guide tetraploid transcript assemblies and to detect genetic exchange between cultivated peanut's subgenomes. On the basis of remarkably high DNA identity of the A. ipaensis genome and the B subgenome of cultivated peanut and biogeographic evidence, we conclude that A. ipaensis may be a direct descendant of the same population that contributed the B subgenome to cultivated peanut.

Analytical and Decision Support Tools for Genomics-Assisted Breeding.

To successfully implement genomics-assisted breeding (GAB) in crop improvement programs, efficient and effective analytical and decision support tools (ADSTs) are 'must haves' to evaluate and select plants for developing next-generation crops. Here we review the applications and deployment of appropriate ADSTs for GAB, in the context of next-generation sequencing (NGS), an emerging source of massive genomic information. We discuss suitable software tools and pipelines for marker-based approaches (markers/haplotypes), including large-scale genotypic and phenotypic, data management, and molecular breeding approaches. Although phenotyping remains expensive and time consuming, prediction of allelic effects on phenotypes opens new doors to enhance genetic gain across crop cycles, building on reliable phenotyping approaches and good crop information systems, including pedigree information and target haplotypes.

Rapid, low-input, low-bias construction of shotgun fragment libraries by high-density in vitro transposition.

We characterize and extend a highly efficient method for constructing shotgun fragment libraries in which transposase catalyzes in vitro DNA fragmentation and adaptor incorporation simultaneously. We apply this method to sequencing a human genome and find that coverage biases are comparable to those of conventional protocols. We also extend its capabilities by developing protocols for sub-nanogram library construction, exome capture from 50 ng of input DNA, PCR-free and colony PCR library construction, and 96-plex sample indexing.

Aquaporin 1 expression in retinal neovascularization in a mouse model of retinopathy of prematurity.

Recently, it was found that Aquaporin 1 (AQP1) is expressed strongly in proliferating microvessels, but the role of AQP1 in retinal neovascularization remains unknown. Here, we report the distribution of AQP1 expression during neovascularization of the retina in a mouse model of retinopathy of prematurity. AQP1 was expressed in all of the samples examined in P15 mouse and P17 mouse, including experimental and control groups. Immunostaining results showed that AQP1 is located in microvessel endothelia in retinas with proliferative retinopathy and prominently in the outer retina. Expression of AQP1 was significantly increased in experimental animals at P17, compared with control mice. No significant difference was seen in the levels of AQP1 on P12 or P15, compared with control mice. These results suggest that AQP1 may play an important role in retinal neovascularization.