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MOTIVATION: Recently, many chromatin immunoprecipitation sequencing experiments have been carried out for a diverse group of transcription factors (TFs) in many different types of human cells. These experiments manifest large-scale and dynamic changes in regulatory network connectivity (i.e. network rewiring), highlighting the different regulatory programs operating in disparate cellular states. However, due to the dense and noisy nature of current regulatory networks, directly comparing the gains and losses of targets of key TFs across cell states is often not informative. Thus, here, we seek an abstracted, low-dimensional representation to understand the main features of network change. RESULTS: We propose a method called TopicNet that applies latent Dirichlet allocation to extract functional topics for a collection of genes regulated by a given TF. We then define a rewiring score to quantify regulatory-network changes in terms of the topic changes for this TF. Using this framework, we can pinpoint particular TFs that change greatly in network connectivity between different cellular states (such as observed in oncogenesis). Also, incorporating gene expression data, we define a topic activity score that measures the degree to which a given topic is active in a particular cellular state. And we show how activity differences can indicate differential survival in various cancers. AVAILABILITY AND IMPLEMENTATION: The TopicNet framework and related analysis were implemented using R and all codes are available at https://github.com/gersteinlab/topicnet. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

There has been much effort to prioritize genomic variants with respect to their impact on function. However, function is often not precisely defined: sometimes it is the disease association of a variant; on other occasions, it reflects a molecular effect on transcription or epigenetics. Here, we coupled multiple genomic predictors to build GRAM, a GeneRAlized Model, to predict a well-defined experimental target: the expression-modulating effect of a non-coding variant on its associated gene, in a transferable, cell-specific manner. Firstly, we performed feature engineering: using LASSO, a regularized linear model, we found transcription factor (TF) binding most predictive, especially for TFs that are hubs in the regulatory network; in contrast, evolutionary conservation, a popular feature in many other variant-impact predictors, has almost no contribution. Moreover, TF binding inferred from in vitro SELEX is as effective as that from in vivo ChIP-Seq. Second, we implemented GRAM integrating only SELEX features and expression profiles; thus, the program combines a universal regulatory score with an easily obtainable modifier reflecting the particular cell type. We benchmarked GRAM on large-scale MPRA datasets, achieving AUROC scores of 0.72 in GM12878 and 0.66 in a multi-cell line dataset. We then evaluated the performance of GRAM on targeted regions using luciferase assays in the MCF7 and K562 cell lines. We noted that changing the insertion position of the construct relative to the reporter gene gave very different results, highlighting the importance of carefully defining the exact prediction target of the model. Finally, we illustrated the utility of GRAM in fine-mapping causal variants and developed a practical software pipeline to carry this out. In particular, we demonstrated in specific examples how the pipeline could pinpoint variants that directly modulate gene expression within a larger linkage-disequilibrium block associated with a phenotype of interest (e.g., for an eQTL).

The climate and land use changes caused by the natural environment and socioeconomic development have potential impacts on the green and sustainable development of agriculture. To accommodate agricultural production under multiple scenarios of future climate and land‐use change, this study proposes a "simulation–optimization" modeling approach based on a crop growth model with a synergistic "carbon emission–economic benefit" approach. This approach is based on climate change conditions and it accurately simulates future land use changes and crop growth processes, establishes a carbon emission intensity optimization model, and generates a spatial planting structure optimization and regulation scheme based on intelligent optimization algorithms under changing scenarios. The results of the model application show that the planting structure option in the future scenario can increase economic benefit by up to 14.8% compared to the current scenario while simultaneously reducing total greenhouse gas emissions by 6.77%. Correlation analysis of planting area, irrigation water volume, carbon intensity value and unilateral water use efficiency can be used to obtain the coordination level of each county under different regulation scenarios. This "simulation–optimization" modeling approach provides an effective approach to achieve synergistic and coordinated development of regional agricultural benefits and carbon reduction by fine‐tuning the planting structure, which promotes low‐carbon and high‐quality development of regional agriculture. Plain Language Summary: Understanding changes in agricultural cropping patterns under future climate change scenarios is critical for reducing carbon emissions and increasing yields in agriculture. We developed a joint approach using land use change and crop growth simulation models to investigate how cropland patterns will change under climate change scenarios and how crop yields will change when the amount of irrigation water varies. With the simulated cropland patterns and crop yields as input conditions, the optimization model is used to coordinate the acreage that should be allocated to each type of crop to achieve the highest economic efficiency and the lowest carbon emissions. This study illustrates the imperative need for farmland management to ensure that we can cope with future climate change. This approach can also be applied to other regions where agriculture is predominant. Key Points: Spatial simulation of climate and land use change scenariosCropping structure optimization coupled with spatial crop growth process simulationSynergistic optimization of economic efficiency and greenhouse gas emissions for low‐carbon and high‐efficiency development in agriculture [ABSTRACT FROM AUTHOR]

Key Points: Question: Is balloon angioplasty plus aggressive medical management superior to aggressive medical management alone for the treatment of severe symptomatic intracranial atherosclerotic stenosis (sICAS)? Finding: In this randomized clinical trial that included 501 patients, the composite outcome of any stroke or death within 30 days or an ischemic stroke or revascularization of the qualifying artery after 30 days through 12 months occurred in 4.4% of patients in the balloon angioplasty group and 13.5% of patients in the aggressive medical management group, a statistically significant difference. Meaning: The findings suggest that balloon angioplasty plus aggressive medical management may be an effective treatment for sICAS, although the risk of stroke or death within 30 days of balloon angioplasty should be considered in clinical practice. Importance: Previous randomized clinical trials did not demonstrate the superiority of endovascular stenting over aggressive medical management for patients with symptomatic intracranial atherosclerotic stenosis (sICAS). However, balloon angioplasty has not been investigated in a randomized clinical trial. Objective: To determine whether balloon angioplasty plus aggressive medical management is superior to aggressive medical management alone for patients with sICAS. Design, Setting, and Participants: A randomized, open-label, blinded end point clinical trial at 31 centers across China. Eligible patients aged 35 to 80 years with sICAS defined as recent transient ischemic attack (<90 days) or ischemic stroke (14-90 days) before enrollment attributed to a 70% to 99% atherosclerotic stenosis of a major intracranial artery receiving treatment with at least 1 antithrombotic drug and/or standard risk factor management were recruited between November 8, 2018, and April 2, 2022 (final follow-up: April 3, 2023). Interventions: Submaximal balloon angioplasty plus aggressive medical management (n = 249) or aggressive medical management alone (n = 252). Aggressive medical management included dual antiplatelet therapy for the first 90 days and risk factor control. Main Outcomes and Measures: The primary outcome was a composite of any stroke or death within 30 days after enrollment or after balloon angioplasty of the qualifying lesion or any ischemic stroke in the qualifying artery territory or revascularization of the qualifying artery after 30 days through 12 months after enrollment. Results: Among 512 randomized patients, 501 were confirmed eligible (mean age, 58.0 years; 158 [31.5%] women) and completed the trial. The incidence of the primary outcome was lower in the balloon angioplasty group than the medical management group (4.4% vs 13.5%; hazard ratio, 0.32 [95% CI, 0.16-0.63]; P <.001). The respective rates of any stroke or all-cause death within 30 days were 3.2% and 1.6%. Beyond 30 days through 1 year after enrollment, the rates of any ischemic stroke in the qualifying artery territory were 0.4% and 7.5%, respectively, and revascularization of the qualifying artery occurred in 1.2% and 8.3%, respectively. The rate of symptomatic intracranial hemorrhage in the balloon angioplasty and medical management groups was 1.2% and 0.4%, respectively. In the balloon angioplasty group, procedural complications occurred in 17.4% of patients and arterial dissection occurred in 14.5% of patients. Conclusions and Relevance: In patients with sICAS, balloon angioplasty plus aggressive medical management, compared with aggressive medical management alone, statistically significantly lowered the risk of a composite outcome of any stroke or death within 30 days or an ischemic stroke or revascularization of the qualifying artery after 30 days through 12 months. The findings suggest that balloon angioplasty plus aggressive medical management may be an effective treatment for sICAS, although the risk of stroke or death within 30 days of balloon angioplasty should be considered in clinical practice. Trial Registration: ClinicalTrials.gov Identifier: NCT03703635 This randomized clinical trial investigates the efficacy of balloon angioplasty plus aggressive medical management vs medical management alone in the treatment of patients with symptomatic intracranial atherosclerotic stenosis. [ABSTRACT FROM AUTHOR]