Sepsis

Phylogeny-agnostic strain-level prediction of phage-host interactions from genomes

Bacteriophages offer promising alternatives to antibiotics for treating drug-resistant infections and engineering microbiomes, but applications are limited by inability to select phages infecting specific strains. Selecting suitable phages requires either one-to-one experimental assays or strain-level predictions of phage-host interactions. Existing computational approaches either predict host tax...

ADHD Medications and Preadolescent Brain Structure: Patterns of Cortical Attenuation from the ABCD Study

Attention-deficit/hyperactivity disorder (ADHD) is the most common neurodevelopmental disorder in the U.S., and the stimulant and nonstimulant medications used to treat ADHD are among the most widely prescribed treatments in youth. Stimulants—including amphetamine-based (AMP) and methylphenidate-based (MPH) medications—act primarily on dopaminergic and noradrenergic systems, while nonstimulants (N...

What kind of birds are more susceptible to avian malaria? A global analysis based on interpretable machine learning approach

Avian malaria (genus Plasmodium) is a mosquito-transmitted parasitic disease of birds. It has a wide distribution across the world, infecting more tha...

Design of multimodal antibiotics using deep learning

The rise of antimicrobial resistance has rendered many treatments ineffective, posing serious public health challenges. Intracellular infections are p...

SARS-CoV-2 Variant-Dependent Alterations in Nasopharyngeal Microbiota and Host Inflammatory Response

The SARS-CoV-2 pandemic saw multiple outbreaks occur over short periods. This was linked to the virus’s high infectivity and rapid mutation rate, whic...

Reinforcement learning for adaptive control of phenotypically heterogeneous bacterial populations

Bacterial populations display extraordinary resilience to antibiotic stress, driven by diverse physiological states that allow some cells to persist a...

Confidence-based Prediction of Antibiotic Resistance at the Patient Level

Rapid and accurate diagnostics of bacterial infections are necessary for efficient treatment of antibiotic-resistant pathogens. Cultivation-based meth...

Predicting Future SARS-CoV-2 Mutations using Deep Learning

SARS-CoV-2 continues to spread over the world steadily as opposed to many earlier estimations that it would disappear in less than two years. Even tho...

Extending digital biology: bacterial survival and morphological heterogeneity under antibiotic stress

The morphology of bacteria is modified by antibiotic stress while also serving to survive the antibiotic. However associating morphological descriptor...

Harnessing Interpretable Deep Learning to Predict Meropenem Resistance in Klebsiella pneumoniae

Antimicrobial resistance represents an escalating global healthcare threat, complicating treatment and increasing both morbidity and mortality. Deep l...

Topological basal ganglia model with dopamine-modulated spike-timing-dependent plasticity reproduces reinforcement learning, discriminatory learning, and neuropsychiatric disorders

The basal ganglia (BG) are central to action selection and reinforcement learning, yet how the topological organization of the BG circuit with dopamin...

Composing the value signal for dopamine-mediated learning

The seminal reward prediction error theory of dopamine function faces several key challenges. Most notable is the difficulty learning multiple rewards...

Development of a metabolic signature of post-weaning diarrhoea in pigs

In the agricultural sector, antibiotics have been used to improve swine growth performance. This application is banned nowadays, due to increased risk...

Scoring gene importance by interpreting single-cell foundation models

Determining a gene’s functional significance within a cellular context has long been a challenge, as absolute expression level is an unreliable indica...

A foundation model for microbial growth dynamics

Microbial growth dynamics contain rich information about microbial populations, which support applications from antibiotic testing to microbiome engin...

Image-based morphological profiling of autophagy phenotypes in Zika virus infected cells

Autophagy is a dynamic intracellular process that is essential in maintaining cellular homeostasis. Its potential as a therapeutic target is exemplifi...

Non-invasive vagus nerve stimulation modulates Pavlovian bias in a state-dependent manner

The vagus nerve transmits vital signals between organ systems of the body and the brain. Despite growing interest in non-invasive transcutaneous vagus...

Dopamine drives a positive reward bias on human reinforcement learning

Formal theories of reinforcement learning (RL) prescribe a clearly defined function for dopamine, namely modulating learning via reward prediction err...

Large scale prospective evaluation of co-folding across 557 Mac1-ligand complexes and three virtual screens

Accurate prediction of ligand-bound protein complexes and ranking them by affinity are central problems in drug discovery. While deep learning co-fold...

Ω-Loop mutations control dynamics of the active site by modulating the hydrogen-bonding network in PDC-3 β-lactamase

The expression of antibiotic-inactivating enzymes, such as Pseudomonas-derived cephalosporinase-3 (PDC-3), is a major mechanism of intrinsic resistanc...