The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

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Goal: The gold standard for detecting the presence of apneic events is a time and effort-consuming manual evaluation of type I polysomnographic recordings by experts, often not error-free. Such acquisition protocol requires dedicated facilities resulting i ...

Controlled assembly of a protein shell around a viral genome is a key step in the life cycle of many viruses. Here we report a strategy for regulating the co-assembly of nonviral proteins and nucleic acids into highly ordered nucleocapsids in vitro. By fus ...

Cutting plane methods are a fundamental approach for solving integer linear programs (ILPs). In each iteration of such methods, additional linear constraints (cuts) are introduced to the constraint set with the aim of excluding the previous fractional opti ...

Analysis of single-cell datasets generated from diverse organisms offers unprecedented opportunities to unravel fundamental evolutionary processes of conservation and diversification of cell types. However, interspecies genomic differences limit the joint ...

This paper offers a new algorithm to efficiently optimize scheduling decisions for dial-a-ride problems (DARPs), including problem variants considering electric and autonomous vehicles (e-ADARPs). The scheduling heuristic, based on linear programming theor ...

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

Materials for high -temperature environments are actively being investigated for deployment in aerospace and nuclear applications. This study uses computational approaches to unravel the crystallography and thermodynamics of a promising class of refractory ...

In light of the challenges posed by climate change and the goals of the Paris Agreement, electricity generation is shifting to a more renewable and decentralized pattern, while the operation of systems like buildings is increasingly electrified. This calls ...

We prove that the Cohn-Elkies linear programming bound for sphere packing is not sharp in dimension 6. The proof uses duality and optimization over a space of modular forms, generalizing a construction of Cohn- Triantafillou [Math. Comp. 91 (2021), pp. 491 ...

We develop a very general version of the hyperbola method which extends the known method by Blomer and Brudern for products of projective spaces to complete smooth split toric varieties. We use it to count Campana points of bounded log-anticanonical height ...

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Messenger RNA (mRNA) vaccines have made remarkable public health contributions during the pandemic and initiated a new era for nucleic acid–based therapeutics. With the unique strength of nucleic acids, including not only mRNA but also DNA, microRNA, small ...

Experimental measurements of the turbulence amplitude utilizing a short pulse reflectometry method are presented. Two discharges with shaped plasma possessing opposite signs of triangularity are considered and a higher turbulence amplitude is found in the ...

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

Aquatic ecosystems continue to be threatened by chemical pollution. To what extent organisms are able to cope with chemical exposure depends on their ability to display mechanisms of defense across different organs. Among these mechanisms, biotransformatio ...

Cis-genetic effects are key determinants of transcriptional divergence in discrete tissues and cell types. However, how cis- and trans-effects act across continuous trajectories of cellular differentiation in vivo is poorly understood. Here, we quantify al ...

Borrowing some quotes from Harper Lee's novel "To Kill A Mockingbird" to help frame our manuscript, we discuss methods to profile local proteomes. We initially focus on chemical biology regimens that function in live organisms and use reactive biotin speci ...

RNA-binding proteins are instrumental for post-transcriptional gene regulation, controlling all aspects throughout the lifecycle of RNA molecules. However, transcriptome-wide methods to profile RNA-protein interactions in vivo remain technically challengin ...

Telomeres are the nucleoprotein structures at the ends of linear chromosomes. Telomeres are transcribed into long non-coding Telomeric Repeat-Containing RNA (TERRA), whose functions rely on its ability to associate with telomeric chromatin. The conserved T ...

One of the main challenges hampering the development of kinetic models is the lack of kinetic parameters for many enzymatic reactions. Here, the authors introduce a framework to explore the catalytically optimal operating conditions of any complex enzyme m ...

The ETFL formulation allows multi-omics integration in thermodynamics-compliant metabolism and expression models

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Sleep Apnea Events Recognition Based on Polysomnographic Recordings: A Large-Scale Multi-Channel Machine Learning approach

Stimulus-responsive assembly of nonviral nucleocapsids

Learning to Remove Cuts in Integer Linear Programming

Toward universal cell embeddings: integrating single-cell RNA-seq datasets across species with SATURN

A ride time-oriented scheduling algorithm for dial-a-ride problems

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

First-principles thermodynamics of precipitation in aluminum-containing refractory alloys

Quantifying the Unknown: Data-Driven Approaches and Applications in Energy Systems

Six-dimensional sphere packing and linear programming

HYPERBOLA METHOD ON TORIC VARIETIES

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Delivery approaches of immunomodulatory nucleic acids for cancer therapy

Validation of short-pulse reflectometry turbulence measurements with a synthetic diagnostic

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

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The dynamic genetic determinants of increased transcriptional divergence in spermatids

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Efficient and sensitive profiling of RNA–protein interactions using TLC-CLIP

The THO complex counteracts TERRA R-loop-mediated telomere fragility in telomerase(+) cells and telomeric recombination in ALT(+) cells

Optimal enzyme utilization suggests that concentrations and thermodynamics determine binding mechanisms and enzyme saturations