Metheor: Ultrafast DNA methylation heterogeneity calculation from bisulfite read alignments.

Phased DNA methylation states within bisulfite sequencing reads are valuable source of information that can be used to estimate epigenetic diversity across cells as well as epigenomic instability in individual cells. Various measures capturing the heterogeneity of DNA methylation states have been proposed for a decade. However, in routine analyses on DNA methylation, this heterogeneity is often ignored by computing average methylation levels at CpG sites, even though such information exists in bisulfite sequencing data in the form of phased methylation states, or methylation patterns.

Learning the histone codes with large genomic windows and three-dimensional chromatin interactions using transformer.

The quantitative characterization of the transcriptional control by histone modifications has been challenged by many computational studies, but most of them only focus on narrow and linear genomic regions around promoters, leaving a room for improvement. We present Chromoformer, a transformer-based, three-dimensional chromatin conformation-aware deep learning architecture that achieves the state-of-the-art performance in the quantitative deciphering of the histone codes in gene regulation. The core essence of Chromoformer architecture lies in the three variants of attention operation, each specialized to model individual hierarchy of transcriptional regulation involving from core promoters to distal elements in contact with promoters through three-dimensional chromatin interactions.

Direct-Writable and Thermally One-Step Curable "Water-Stained" Epoxy Composite Inks.

In this study, a simple method for preparing direct-writable and thermally one-step curable epoxy composite inks was proposed. Specifically, colloidal inks containing a mixture of ordinary epoxy resin and anhydride-type hardener with the suspended alumina microplates, as exemplary fillers, are "stained" with small amounts of water. This increases the elasticity of the ink via the interparticle capillary attraction and promotes curing of the epoxy matrix in low-temperature ranges, causing the three-dimensional (3D) printed ink to avoid structural disruption during one-step thermal curing without the tedious pre-curing step.

Role of electrostatic interactions in the adsorption of dye molecules by TiC-MXenes.

MXenes, a new class of 2D materials, have recently attracted increasing attention as promising adsorbents for environmental remediation. It has been previously demonstrated that MXenes can successfully capture selected organic dyes from aqueous media; however, to date, the adsorption performance of MXenes for a wide variety of dyes in simulated real-life aquatic environments other than clean laboratory deionized (DI) water has not been systematically investigated. In this study, we systematically investigated the adsorption performance of delaminated TiC-MXenes for six different organic dyes in aquatic media at different pH levels and ionic strengths.

Bulk Nanoencapsulation of Phase Change Materials (PCMs) via Spontaneous Spreading of a UV-Curable Prepolymer.

Phase change materials (PCMs) have received considerable attention for various latent heat storage systems for efficient thermal energy utilization. Herein, a facile and fast method for the bulk nanoencapsulation of organic PCMs is proposed, based on the thermodynamically spontaneous spreading phenomenon of three immiscible liquid phases. In this approach, a complete engulfing of PCM nanodroplets (core phase) by immiscible prepolymer droplets (coating phase), both of which are bulk-dispersed in another immiscible medium (continuous phase), is thermodynamically driven by the relation between the surface energies of the core, coating, and continuous phases.

A pickering emulsion stabilized by chlorella microalgae as an eco-friendly extrusion-based 3D printing ink processable under ambient conditions.

Three-dimensional (3D) printing technology is actively utilized in various industrial fields because it facilitates effective and customizable fabrication of complex structures. An important processing route for 3D printing is the extrusion of inks in the form of colloidal suspensions or emulsions, which has recently attracted considerable attention because it allows for selection of a wide range of printing materials and is operable under ambient processing conditions. Herein, we investigate the 3D printability of complex fluids containing chlorella microalgae as an eco-friendly material for 3D printing.

Yield Stress Enhancement of a Ternary Colloidal Suspension via the Addition of Minute Amounts of Sodium Alginate to the Interparticle Capillary Bridges.

Capillary suspensions are ternary solid-liquid-liquid systems produced via the addition of a small amount of secondary fluid to the bulk fluid that contained the dispersed solid particles. The secondary fluid could exert strong capillary forces between the particles and dramatically change the rheological properties of the suspension. So far, research has focused on capillary suspensions that consist of additive-free fluids, whereas capillary suspensions with additives, particularly those of large molecular weight that are highly relevant for industrial purposes, have been relatively less studied.

Polyelectrolyte-grafted TiC-MXenes stable in extreme salinity aquatic conditions for remediation of contaminated subsurface environments.

MXenes, an emerging class of two-dimensional materials, are recently gaining significant attention for numerous environmental applications owing to their superior hydrophilicity and unique surface functionalities, which are suitable for adsorptive removal of various aqueous contaminants. However, it has recently been shown that MXenes have poor colloidal stability in both synthetic or natural waters containing small amounts of salt ions, which will limit the potential uses of MXenes in remediation of subsurface environments that might sometimes contain considerable amounts of salt ions, and other relevant environmental applications. Herein, we develop TiC-MXenes grafted with highly salt-resistant polyelectrolytes (PEs), MXene--PEs, which are colloidally stable in extreme salinity aquatic environments and have low adsorption to soil mineral substrates.

A Systematic Investigation on the Properties of Silica Nanoparticles "Multipoint"-Grafted with Poly(2-acrylamido-2-methylpropanesulfonate--acrylic Acid) in Extreme Salinity Brines and Brine-Oil Interfaces.

Nanoparticles (NPs) may have great potential for various subsurface applications, including oil and gas recovery, reservoir imaging, and environmental remediation. One of the important challenges for these downhole applications is to achieve colloidal stability in subsurface media at high salinity and high temperature. It has been previously shown that several functional NPs "multipoint"-grafted with anionic poly(2-acrylamido-2-methyl-1-propanesulfonate--acrylic acid; AMPS--AA) exhibited remarkable colloidal stabilities in specific environments mimicking the harsh subsurface aquatic media, such as the American Petroleum Institute (API) brine.