MultiFeatVotPIP: a voting-based ensemble learning framework for predicting proinflammatory peptides.

Inflammatory responses may lead to tissue or organ damage, and proinflammatory peptides (PIPs) are signaling peptides that can induce such responses. Many diseases have been redefined as inflammatory diseases. To identify PIPs more efficiently, we expanded the dataset and designed an ensemble learning model with manually encoded features. Specifically, we adopted a more comprehensive feature encoding method and considered the actual impact of certain features to filter them. Identification and prediction of PIPs were performed using an ensemble learning model based on five different classifiers. The results show that the model's sensitivity, specificity, accuracy, and Matthews correlation coefficient are all higher than those of the state-of-the-art models. We named this model MultiFeatVotPIP, and both the model and the data can be accessed publicly at https://github.com/ChaoruiYan019/MultiFeatVotPIP. Additionally, we have developed a user-friendly web interface for users, which can be accessed at http://www.bioai-lab.com/MultiFeatVotPIP.

The Impact of Various Organic Phosphorus Carriers on the Uptake and Use Efficiency in Barley.

Organic phosphorus (OP) is an essential component of the soil P cycle, which contributes to barley nutrition after its mineralization into inorganic phosphorus (Pi). However, the dynamics of OP utilization in the barley rhizosphere remain unclear. In this study, phytin was screened out from six OP carriers, which could reflect the difference in OP utilization between a P-inefficient genotype Baudin and a P-efficient genotype CN4027. The phosphorus utilization efficiency (PUE), root morphological traits, and expression of genes associated with P utilization were assessed under P deficiency or phytin treatments. P deficiency resulted in a greater root surface area and thicker roots. In barley fed with phytin as a P carrier, the APase activities of CN4027 were 2-3-fold lower than those of Baudin, while the phytase activities of CN4027 were 2-3-fold higher than those of Baudin. The PUE in CN4027 was mainly enhanced by activating phytase to improve the root absorption and utilization of Pi resulting from OP mineralization, while the PUE in Baudin was mainly enhanced by activating APase to improve the shoot reuse capacity. A phosphate transporter gene HvPHT1;8 regulated P transport from the roots to the shoots, while a purple acid phosphatase (PAP) family gene HvPAPhy_b contributed to the reuse of P in barley.

Integration tools for scRNA-seq data and spatial transcriptomics sequencing data.

Numerous methods have been developed to integrate spatial transcriptomics sequencing data with single-cell RNA sequencing (scRNA-seq) data. Continuous development and improvement of these methods offer multiple options for integrating and analyzing scRNA-seq and spatial transcriptomics data based on diverse research inquiries. However, each method has its own advantages, limitations and scope of application. Researchers need to select the most suitable method for their research purposes based on the actual situation. This review article presents a compilation of 19 integration methods sourced from a wide range of available approaches, serving as a comprehensive reference for researchers to select the suitable integration method for their specific research inquiries. By understanding the principles of these methods, we can identify their similarities and differences, comprehend their applicability and potential complementarity, and lay the foundation for future method development and understanding. This review article presents 19 methods that aim to integrate scRNA-seq data and spatial transcriptomics data. The methods are classified into two main groups and described accordingly. The article also emphasizes the incorporation of High Variance Genes in annotating various technologies, aiming to obtain biologically relevant information aligned with the intended purpose.

A bibliometric analysis of global research hotspots and progress on microplastics in soil‒plant systems.

Plastic pollution has become a global and persistent challenge, posing threats to ecosystems and organisms. In recent years, there has been a rapid increase in scientific research focused on understanding microplastics in the soil‒plant system. This surge is primarily driven by the direct impact of microplastics on agricultural productivity and their association with human activities. In this study, we conducted a comprehensive bibliometric analysis to provide an overview of the current research on microplastics in soil‒plant systems. We systematically analysed 192 articles and observed a significant rise in research interests since 2017. Notably, China has emerged as a leading contributor in terms of published papers, closely followed by Germany and the Netherlands. Through co-authorship network analysis, we identified 634 different institutions that participated in publishing papers in this field, with the Chinese Academy of Sciences having the most collaborations. In the co-occurrence keyword network, we identified four clusters focusing on the diversity of microplastics within the agroecosystem, transportation, and quantification of microplastics in soil, analysis of plastic contamination type and impact, and investigation of microplastic phytotoxicity. Furthermore, we identified ten research priorities, categorized into the effects of microplastics in "soil" and "plant". The research hotspots were found to be the effect of microplastics on soil physicochemical properties and the synergistic phytotoxicity of microplastics with other pollutants. Overall, this bibliometric analysis holds significant value, serving as an important reference point and offering valuable suggestions for future researchers in this rapidly advancing field.

Influence of dissolved organic matter, kaolinite, and iron oxides on aggregation and transport of biochar colloids in aqueous and soil environments.

The aggregation and transport of biochar colloids (BCs) in the soil and groundwater are critical for applying biochar in the field and assessing long-term environmental risk. This research aimed to study the influence of dissolved organic matter (DOM) with different molecular weights (including humic acid, HA; bovine serum albumin, BSA; deoxyribonucleic acid, DNA) and three minerals (including kaolinite, goethite, and hematite) on the aggregation and transport behaviors of BCs. The adsorption of DOM on the surface of BCs increased the stability, inhibited aggregation, and promoted the transport of BCs. As the molecular weight of DOM increased, the thicknesses of the adsorption layer of HA, BSA, and DNA on BCs surface were 2.2 nm, 5.3 nm, and 5.6 nm, respectively, resulting in increasing steric hindrance and improving the stability and mobility of BCs. Kaolinite also significantly enhanced the stability and mobility of BCs by increasing the electrostatic repulsion. Goethite and hematite quickly combined with BCs through electrostatic attraction, resulting in stronger aggregation and retention of BCs. Compared to hematite, goethite provided more adsorption sites for BCs due to its needle-like shape, so goethite caused a larger heteroaggregation rate. Overall, the presence of DOM with different molecular weights and the minerals with varying surface charges in the soil environment had a significant and distinct impact on the stability, aggregation, and transport of BCs, which advances the knowledge of colloidal biochar fate in the soil and groundwater.

Distinct interactions of pig and cow manure-derived colloids with TiO2 nanoparticles and their impact on stability and transport.

The application of livestock manure and aquaculture wastewater into agricultural soil introduces animal manure-derived colloids into the environment. These manure-derived colloids generally contain different organic matter components and may facilitate nanoparticle transport to the subsurface. This study investigated the interaction between manure-derived colloids (cow and pig manures) and titanium dioxide (TiO2) nanoparticles at neutral pH. The effect of this interaction on the stability, aggregation, and transport of TiO2 in a saturated porous media was studied. Our study found that cow manure-derived colloids have many humic-like substances, and pig manure-derived colloids contain many protein components and some humic-like substances. The interactions of different manure-derived colloids with TiO2 can affect the ζ-potential and aggregation status of TiO2 in the aqueous system. The results showed that cow manure-derived colloids slightly increased the TiO2 transport due to electrostatic repulsion, while pig manure-derived colloids substantially increased the TiO2 mobility in porous media because of both electrostatic repulsion and steric hindrance. Since both animal manure and TiO2 are ubiquitously present in the natural environment, manure-derived colloids can change the surface properties of TiO2 and facilitate TiO2 transport in the subsurface.

The role of Fe oxyhydroxide coating, illite clay, and peat moss in nanoscale titanium dioxide (nTiO2) retention and transport in geochemically heterogeneous media.

Natural media such as soil and sediment contain mineralogical and organic components with distinct chemical, surface, and electrostatic properties. To better understand the role of various soil and sediment components on particle transport, columns were packed with quartz sand and natural sediment with added Fe oxyhydroxide coating, illite clay, and peat moss to investigate how these added components influence nTiO2 retention and transport in geochemically heterogeneous medium. Results showed that nTiO2 transport was low at pH 5, attributable to the electrostatic attraction between positively-charged nTiO2 and negatively-charged medium. While illite did not notably affect nTiO2 transport at pH 5, Fe oxyhydroxide coating increased nTiO2 transport due to electrostatic repulsion between Fe oxyhydroxide and nTiO2. Peat moss also increased nTiO2 transport at pH 5, attributable to the increased DOC concentration, which resulted in higher DOC adsorption to nTiO2 and intensified electrostatic repulsion between nTiO2 and the medium. At pH 9, nTiO2 transport was high due to the electrostatic repulsion between negatively-charged nTiO2 and medium surfaces. Fe oxyhydroxide coating at pH 9 slightly delayed nTiO2 transport due to electrostatic attraction, while illite clay and peat moss substantially inhibited nTiO2 transport via straining/entrapment or electrostatic attraction. Overall, this study demonstrated that pH has a considerable effect on how minerals and organic components of a medium influence nTiO2 transport. At low pH, electrostatic attraction was the dominant mechanism, therefore, nTiO2 mobility was low regardless of the differences in mineralogical and organic components. Conversely, nTiO2 mobility was high at high pH and nTiO2 retention was dominated by straining/entrapment and sensitive to the mineralogical and organic composition of the medium.

Coupled effect of flow velocity and structural heterogeneity on transport and release of kaolinite colloids in saturated porous media.

Understanding the behavior and fate of clay colloids in water-saturated porous media is critical to assess its environmental impact and potential risk since clay is commonly a carrier of many contaminants. Column experiments with four-packing configurations were designed to understand the coupled effects of column structural heterogeneity and the flow velocity on the transport and fate of kaolinite colloids in the saturated porous media. The results showed that the structural heterogeneity could have facilitated the transport of kaolinite colloids in saturated porous media. For the columns with strong heterogeneity, the preferential flow paths led to an early breakthrough of kaolinite. Only few kaolinite colloids were released with slow flow rate; however, the released peak concentration and release percentage of kaolinite colloids had further increased with the high flow velocity. In the layered column, there was significant kaolinite's retention at the interface where water passed from fine to coarse quartz sand. All results indicated that both flow rates and media characteristics played an important role in controlling kaolinite's fate and transport in porous media. A thorough understanding of these processes had an important significance for pollution control in subsurface natural environment where heterogeneous soil and variation in flow pattern are usually common.

Effect of bovine serum albumin on stability and transport of kaolinite colloid.

The stability and transport of clay colloids in groundwater are strongly influenced by colloid interactions with dissolved organic matter (DOM). Protein is an important DOM component that is ubiquitous in natural water, reclaimed water, and soil solutions. To date, the interactions between clay colloids and proteins have not been fully studied. The objective of this study was to examine the effect of bovine serum albumin (BSA), a representative protein, on the stability, aggregation, and transport of kaolinite colloids under neutral pH conditions. Hydrodynamic diameter and ζ-potential measurements, stability tests, and column transport experiments were performed in salt solutions with a range of ionic strengths and different BSA concentrations at pH 7. Additionally, BSA-kaolinite colloid interactions were studied using TEM and batch adsorption experiments. The experimental results showed that BSA prevented colloid aggregation and increased the stability and transport of colloids, especially at high ionic strength, even though the charges of kaolinite colloids were less negative in the presence of BSA. Theoretical calculation of the interaction energies indicated that XDLVO theory, in which the steric force is considered due to BSA adsorption, could correctly quantify the interaction energies in the presence of BSA. This study demonstrated that the role of protein needs to be determined in order to better predict the overall effect of DOM on particle aggregation and transport in the soil environment.

Effect of physicochemical factors on transport and retention of graphene oxide in saturated media.

Fate and transport of graphene oxide (GO) have received much attention recently with the increase of GO applications. This study investigated the effect of salt concentration on the transport and retention behavior of GO particles in heterogeneous saturated porous media. Transport experiments were conducted in NaCl solutions with three concentrations (1, 20, and 50 mM) using six structurally packed columns (two homogeneous and four heterogeneous) which were made of fine and coarse grains. The results showed that GO particles had high mobility in all the homogeneous and heterogeneous columns when solution ionic strength (IS) was low. When IS was high, GO particles showed distinct transport ability in six structurally heterogeneous porous media. In homogeneous columns, decreasing ionic strength and increasing grain size increased the mobility of GO. For the column containing coarse-grained channel, the preferential flow path resulted in an early breakthrough of GO, and further larger contact area between coarse and fine grains caused a lower breakthrough peak and a stronger tailing at different IS. In the layered column, there was significant GO retention at coarse-fine grain interface where water flowed from coarse grain to fine grain. Our results indicated that the fate and transport of GO particles in the natural heterogeneous porous media was highly related to the coupled effect of medium structure and salt solution concentration.