Machine Learning Models With Prognostic Implications for Predicting Gastrointestinal Bleeding After Coronary Artery Bypass Grafting and Guiding Personalized Medicine: Multicenter Cohort Study.

Background: Gastrointestinal bleeding is a serious adverse event of coronary artery bypass grafting and lacks tailored risk assessment tools for personalized prevention.

Objective: This study aims to develop and validate predictive models to assess the risk of gastrointestinal bleeding after coronary artery bypass grafting (GIBCG) and to guide personalized prevention.

Methods: Participants were recruited from 4 medical centers, including a prospective cohort and the Medical Information Mart for Intensive Care IV (MIMIC-IV) database.

Brief Report: Methylation-Based ctDNA Serial Monitoring Correlates With Immunotherapy Response in NSCLC.

Purpose: Circulating tumor DNA (ctDNA) can reflect the genetic and epigenetic composition of malignancies and can serve as a noninvasive biomarker for cancer diagnostics and monitoring. This study aimed to evaluate the utility of a methylation-based ctDNA assay as a predictive tool in non-small cell lung cancer (NSCLC) anti-PD1 based immunotherapy monitoring.

Methods: We evaluated a cohort of 20 patients with NSCLC treated with anti-PD1 based immunotherapy that had both baseline and follow-up blood draws as well as outcome data available.

Environmental modulators of algae-bacteria interactions at scale.

Interactions between photosynthetic and heterotrophic microbes play a key role in global primary production. Understanding phototroph-heterotroph interactions remains challenging because these microbes reside in chemically complex environments. Here, we leverage a massively parallel droplet microfluidic platform that enables us to interrogate interactions between photosynthetic algae and heterotrophic bacteria in >100,000 communities across ∼525 environmental conditions with varying pH, carbon availability, and phosphorus availability.

Environmentally dependent interactions shape patterns in gene content across natural microbiomes.

Sequencing surveys of microbial communities in hosts, oceans and soils have revealed ubiquitous patterns linking community composition to environmental conditions. While metabolic capabilities restrict the environments suitable for growth, the influence of ecological interactions on patterns observed in natural microbiomes remains uncertain. Here we use denitrification as a model system to demonstrate how metagenomic patterns in soil microbiomes can emerge from pH-dependent interactions.

Spatiotemporal constrained RNA-protein heterogeneous network for protein complex identification.

The identification of protein complexes from protein interaction networks is crucial in the understanding of protein function, cellular processes and disease mechanisms. Existing methods commonly rely on the assumption that protein interaction networks are highly reliable, yet in reality, there is considerable noise in the data. In addition, these methods fail to account for the regulatory roles of biomolecules during the formation of protein complexes, which is crucial for understanding the generation of protein interactions.

Temporal Protein Complex Identification Based on Dynamic Heterogeneous Protein Information Network Representation Learning.

Protein complexes, as the fundamental units of cellular function and regulation, play a crucial role in understanding the normal physiological functions of cells. Existing methods for protein complex identification attempt to introduce other biological information on top of the protein-protein interaction (PPI) network to assist in evaluating the degree of association between proteins. However, these methods usually treat protein interaction networks as flat homogeneous static networks.

Statistical prediction of microbial metabolic traits from genomes.

The metabolic activity of microbial communities is central to their role in biogeochemical cycles, human health, and biotechnology. Despite the abundance of sequencing data characterizing these consortia, it remains a serious challenge to predict microbial metabolic traits from sequencing data alone. Here we culture 96 bacterial isolates individually and assay their ability to grow on 10 distinct compounds as a sole carbon source.

Semantic-Enhanced Graph Contrastive Learning With Adaptive Denoising for Drug Repositioning.

The traditional drug development process requires a significant investment in workforce and financial resources. Drug repositioning as an efficient alternative has attracted much attention during the last few years. Despite the wide application and success of the method, there are still many shortcomings in the existing model.

Global patterns in gene content of soil microbiomes emerge from microbial interactions.

Microbial metabolism sustains life on Earth. Sequencing surveys of communities in hosts, oceans, and soils have revealed ubiquitous patterns linking the microbes present, the genes they possess, and local environmental conditions. One prominent explanation for these patterns is environmental filtering: local conditions select strains with particular traits.

Protein Complex Identification Based on Heterogeneous Protein Information Network.

Protein complexes are the foundation of all cellular activities, and accurately identifying them is crucial for studying cellular systems. The efficient discovery of protein complexes is a focus of research in the field of bioinformatics. Most existing methods for protein complex identification are based on the structure of the protein-protein interaction (PPI) network, whereas some methods attempt to integrate biological information to enhance the features of the protein network for complex identification.

Wetland Park Planning and Management Based on the Valuation of Ecosystem Services: A Case Study of the Tieling Lotus Lake National Wetland Park (LLNWP), China.

The valuation of wetland ecosystem services and the construction of environmental landscapes are generally recognized as contributing to the sustainable development of human wellbeing. The valuation of ecosystem services plays an important role in planning for the recovery of degraded wetlands and in urban wetland park management; however, the role of the valuation of ecosystem services is always ignored. To bring more intuitive awareness to the importance of the ecological functions of wetlands and to rationally plan wetland parks, the Lotus Lake National Wetland Park (LLNWP), an urban wetland park in Northeast China, was selected as the study area.

Closed microbial communities self-organize to persistently cycle carbon.

Cycles of nutrients (N, P, etc.) and resources (C) are a defining emergent feature of ecosystems. Cycling plays a critical role in determining ecosystem structure at all scales, from microbial communities to the entire biosphere.

Enantioselective total synthesis of (-)-limaspermidine and formal synthesis of (-)-1-acetylaspidoalbidine.

Evolution of the synthetic strategy that culminated in the first asymmetric total synthesis of the Aspidosperma alkaloid limaspermidine is described. The successful enantioselective route to (-)-limaspermidine proceeds in 10 steps and with the isolation of only six intermediates using a Pd-catalyzed enantioselective decarboxylative allylation we have recently developed. This first enantioselective synthesis of (-)-limaspermidine establishes unambiguously its absolute configuration and allows the first asymmetric formal total synthesis of the Aspidoalbine alkaloid (-)-1-acetylaspidoalbidine.

Enantioselective conjugate addition of both aromatic ketones and acetone to nitroolefins catalyzed by chiral primary amines bearing multiple hydrogen-bonding donors.

A new class of chiral primary amine catalysts bearing multiple hydrogen-bonding donors have been designed and synthesized. The newly developed bifunctional organocatalysts efficiently catalyzed not only enantioselective conjugate addition of aromatic ketones to nitroolefins in good yields (up to 87%) with excellent enantioselectivities (97→99% ee) but also enantioselective conjugate addition of acetone to nitroolefins in excellent yields (90-96%) with high enantioselectivities (up to 97% ee).

Highly enantioselective one-pot synthesis of spirocyclopentaneoxindoles containing the oxime group by organocatalyzed Michael addition/ISOC/fragmentation sequence.

A highly diastereo- and enantioselective organocatalytic protocol for the synthesis of biologically important spirocyclopentaneoxindoles containing the oxime functional group from easily accessible 3-allyl-substituted oxindoles and nitroolefins has been developed by a one-pot Michael addition/ISOC/fragmentation sequence.

Catalytic asymmetric construction of spirocyclopentaneoxindoles by a combined Ru-catalyzed cross-metathesis/double Michael addition sequence.

Biologically important and synthetically challenging spirocyclopentaneoxindoles with four contiguous stereocenters including one spiroquaternary stereocenter have been constructed in good yields (72-87%) with excellent diastereoselectivity (16:1→30:1 dr) and enantioselectivity (93→99% ee) by a combined Ru-catalyzed cross-metathesis/organocatalyzed asymmetric double-Michael addition sequence.