Noncombustion Emissions of Organic Acids at a Site near Boise, Idaho.

Gas-phase organic acids are ubiquitous in the atmosphere with mixing ratios of several species, such as formic acid and acetic acid, often as high as several parts per billion by volume (ppbv). Organic acids are produced via photochemical reactions and are also directly emitted from various sources, including combustion, microbial activity, vegetation, soils, and ruminants. We present measurements of gas-phase formic, acetic, propionic, pyruvic, and pentanoic acids from a site near Boise, Idaho, in August 2019 made by iodide-adduct chemical ionization mass spectrometry (CIMS).

Testing relationships between multiple regional features and biogeographic processes of speciation, extinction, and dispersal.

The spatial and environmental features of regions where clades are evolving are expected to impact biogeographic processes such as speciation, extinction, and dispersal. Any number of regional features (such as elevation, distance, area, etc.) may be directly or indirectly related to these processes.

Air Quality Sensor Experts Convene: Current Quality Assurance Considerations for Credible Data.

Air sensors can provide valuable non-regulatory and supplemental data as they can be affordably deployed in large numbers and stationed in remote areas far away from regulatory air monitoring stations. Air sensors have inherent limitations that are critical to understand before collecting and interpreting the data. Many of these limitations are mechanistic in nature, which will require technological advances.

Molecular composition and the impact of fuel moisture content on fresh primary organic aerosol emissions during laboratory combustion of Ponderosa pine needles.

Pine needles represent an important fuel source in coniferous forest systems in the western United States. During forest fires, they can be easily ignited and help sustain flame on the ground. In this study, a comprehensive chemical analysis was conducted to examine oxygenated organic compounds (OOCs) present in PM formed from burning dry and moist ponderosa pine needles (PPN) in the presence and absence of fine woody debris (FWD).

A Phylogenetic Model of Established and Enabled Biome Shifts.

Where each species actually lives is distinct from where it could potentially survive and persist. This suggests that it may be important to distinguish established from enabled biome affinities when considering how ancestral species moved and evolved among major habitat types. We introduce a new phylogenetic method, called RFBS, to model how anagenetic and cladogenetic events cause established and enabled biome affinities (or, more generally, other discrete realized versus fundamental niche states) to shift over evolutionary timescale.

phyddle: software for phylogenetic model exploration with deep learning.

Many realistic phylogenetic models lack tractable likelihood functions, prohibiting their use with standard inference methods. We present phyddle, a pipeline-based toolkit for performing phylogenetic modeling tasks using likelihood-free deep learning approaches. phyddle coordinates modeling tasks through five analysis steps (, , , , and ) that transform raw phylogenetic datasets as input into numerical and visualized model-based output.

PhyloJunction: A Computational Framework for Simulating, Developing, and Teaching Evolutionary Models.

We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, thanks to its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data.

HIF-2α expression and metabolic signaling require ACSS2 in clear cell renal cell carcinoma.

Clear cell renal cell carcinoma (ccRCC) is an aggressive cancer driven by VHL loss and aberrant HIF-2α signaling. Identifying means to regulate HIF-2α thus has potential therapeutic benefit. Acetyl-CoA synthetase 2 (ACSS2) converts acetate to acetyl-CoA and is associated with poor patient prognosis in ccRCC.

Obesity induces PD-1 on macrophages to suppress anti-tumour immunity.

Obesity is a leading risk factor for progression and metastasis of many cancers, yet can in some cases enhance survival and responses to immune checkpoint blockade therapies, including anti-PD-1, which targets PD-1 (encoded by PDCD1), an inhibitory receptor expressed on immune cells. Although obesity promotes chronic inflammation, the role of the immune system in the obesity-cancer connection and immunotherapy remains unclear. It has been shown that in addition to T cells, macrophages can express PD-1.

Metabolite profiling of human renal cell carcinoma reveals tissue-origin dominance in nutrient availability.

The tumor microenvironment is a determinant of cancer progression and therapeutic efficacy, with nutrient availability playing an important role. Although it is established that the local abundance of specific nutrients defines the metabolic parameters for tumor growth, the factors guiding nutrient availability in tumor compared to normal tissue and blood remain poorly understood. To define these factors in renal cell carcinoma (RCC), we performed quantitative metabolomic and comprehensive lipidomic analyses of tumor interstitial fluid (TIF), adjacent normal kidney interstitial fluid (KIF), and plasma samples collected from patients.

Controlled Biocatalytic Synthesis of a Metal Nanoparticle-Enzyme Hybrid: Demonstration for Catalytic H-driven NADH Recycling.

Here we demonstrate the preparation of enzyme-metal biohybrids of NAD reductase with biocatalytically-synthesised small gold nanoparticles (NPs, <10 nm) and core-shell gold-platinum NPs for tandem catalysis. Despite the variety of methods available for NP synthesis, there remains a need for more sustainable strategies which also give precise control over the shape and size of the metal NPs for applications in catalysis, biomedical devices, and electronics. We demonstrate facile biosynthesis of spherical, highly uniform, gold NPs under mild conditions using an isolated enzyme moiety, an NAD reductase, to reduce metal salts while oxidising a nicotinamide-containing cofactor.

VHL loss reprograms the immune landscape to promote an inflammatory myeloid microenvironment in renal tumorigenesis.

Clear cell renal cell carcinoma (ccRCC) is characterized by dysregulated hypoxia signaling and a tumor microenvironment (TME) highly enriched in myeloid and lymphoid cells. Loss of the von Hippel Lindau (VHL) gene is a critical early event in ccRCC pathogenesis and promotes stabilization of HIF. Whether VHL loss in cancer cells affects immune cells in the TME remains unclear.

A Diffusion-Based Approach for Simulating Forward-in-Time State-Dependent Speciation and Extinction Dynamics.

We establish a general framework using a diffusion approximation to simulate forward-in-time state counts or frequencies for cladogenetic state-dependent speciation-extinction (ClaSSE) models. We apply the framework to various two- and three-region geographic-state speciation-extinction (GeoSSE) models. We show that the species range state dynamics simulated under tree-based and diffusion-based processes are comparable.

Deep Learning and Likelihood Approaches for Viral Phylogeography Converge on the Same Answers Whether the Inference Model Is Right or Wrong.

Analysis of phylogenetic trees has become an essential tool in epidemiology. Likelihood-based methods fit models to phylogenies to draw inferences about the phylodynamics and history of viral transmission. However, these methods are often computationally expensive, which limits the complexity and realism of phylodynamic models and makes them ill-suited for informing policy decisions in real-time during rapidly developing outbreaks.

Metabolite profiling of human renal cell carcinoma reveals tissue-origin dominance in nutrient availability.

The tumor microenvironment is a determinant of cancer progression and therapeutic efficacy, with nutrient availability playing an important role. Although it is established that the local abundance of specific nutrients defines the metabolic parameters for tumor growth, the factors guiding nutrient availability in tumor compared to normal tissue and blood remain poorly understood. To define these factors in renal cell carcinoma (RCC), we performed quantitative metabolomic and comprehensive lipidomic analyses of tumor interstitial fluid (TIF), adjacent normal kidney interstitial fluid (KIF), and plasma samples collected from patients.

PhyloJunction: a computational framework for simulating, developing, and teaching evolutionary models.

We introduce PhyloJunction, a computational framework designed to facilitate the prototyping, testing, and characterization of evolutionary models. PhyloJunction is distributed as an open-source Python library that can be used to implement a variety of models, through its flexible graphical modeling architecture and dedicated model specification language. Model design and use are exposed to users via command-line and graphical interfaces, which integrate the steps of simulating, summarizing, and visualizing data.

Nutrient inputs and social metabolic control of T cell fate.

Cells in multicellular organisms experience diverse neighbors, signals, and evolving physical environments that drive functional and metabolic demands. To maintain proper development and homeostasis while avoiding inappropriate cell proliferation or death, individual cells interact with their neighbors via "social" cues to share and partition available nutrients. Metabolic signals also contribute to cell fate by providing biochemical links between cell-extrinsic signals and available resources.

Field intercomparison of continuous ambient FRM and FEM NO instruments in the Athabasca Oil Sands Region, Alberta, Canada and the potential impact on ambient regulatory compliance.

The Canadian Federal Government promulgated new and lower NO Ambient Air Quality Standards (CAAQS) that went into effect in 2020 with additional decreases scheduled for 2025. The new hourly and annual NO CAAQS are 60 and 17 ppb, respectively, and the 2025 hourly and annual CAAQS are 42 and 12 ppb, respectively. The province of Alberta has also promulgated Ambient Air Quality Objectives (AAAQO) for NO currently set to 159 and 24 ppb on an hourly and annual basis, respectively.

Atmospheric Dry and Wet Deposition of Total Phosphorus to the Great Lakes.

Quantifying atmospheric loadings of total phosphorus (TP) to freshwater environments is essential to improve understanding of its fate and transport, and to mitigate the effects of excessive levels in freshwater ecosystems. To date, atmospheric deposition of TP in the U.S.