Improved resolution of avian influenza virus using Oxford Nanopore R10 sequencing chemistry.

Unlabelled: Highly pathogenic avian influenza viruses continue to pose global risks to One Health, including agriculture, public, and animal health. Rapid and accurate genomic surveillance is critical for monitoring viral mutations, tracing transmission, and guiding interventions in near real-time. Oxford Nanopore sequencing holds promise for real-time influenza genotyping, but data quality from R9 chemistry has limited its adoption due to challenges resolving low-complexity regions such as the biologically critical hemagglutinin cleavage site, a homopolymer of basic amino acids that distinguish highly pathogenic strains.

Dephasingless two-color terahertz generation.

A laser pulse composed of a fundamental and an appropriately phased second harmonic can drive a time-dependent current of photoionized electrons that generates broadband THz radiation. Over the propagation distances relevant to many experiments, dispersion causes the relative phase between the harmonics to evolve. This "dephasing" slows the accumulation of THz energy and results in a multi-cycle THz pulse with significant angular dispersion.

Organoid intelligence for developmental neurotoxicity testing.

The increasing prevalence of neurodevelopmental disorders has highlighted the need for improved testing methods to determine developmental neurotoxicity (DNT) hazard for thousands of chemicals. This paper proposes the integration of organoid intelligence (OI); leveraging brain organoids to study neuroplasticity into the DNT testing paradigm. OI brings a new approach to measure the impacts of xenobiotics on plasticity mechanisms - a critical biological process that is not adequately covered in current DNT assays.

A click-based electrocorticographic brain-computer interface enables long-term high-performance switch scan spelling.

Background: Brain-computer interfaces (BCIs) can restore communication for movement- and/or speech-impaired individuals by enabling neural control of computer typing applications. Single command click detectors provide a basic yet highly functional capability.

Methods: We sought to test the performance and long-term stability of click decoding using a chronically implanted high density electrocorticographic (ECoG) BCI with coverage of the sensorimotor cortex in a human clinical trial participant (ClinicalTrials.

Quantifying the impact of prevalence-dependent adaptive behavior on COVID-19 transmission: A modeling case study in Maryland.

The COVID-19 pandemic highlighted the need for robust epidemic forecasts, projecting health burden over short- and medium-term time horizons. Many COVID-19 forecasting models incorporate information on infection transmission, disease progression, and the effects of interventions, but few combine information on how individuals change their behavior based on altruism, fear, risk perception, or personal economic circumstances. Moreover, early models of COVID-19 produced under- and over-estimates, failing to consider the complexity of human responses to disease threat and prevention measures.

Material Characterization Study of Magnetite Nanocrystals for RF Sensing.

Magnetite nanocrystals show promise for electrically small gigahertz frequency applications, which could lead to miniaturizing transformer cores and new sensing technologies. This work presents a rigorous radiofrequency characterization of these nanocrystals using vector network analyzer (VNA) ferromagnetic resonance (FMR) measurements. For the first time, two different average diameters of FeO nanocrystals are investigated (7.

Estimating rate of lung function change using clinical spirometry data.

Rationale: In chronic obstructive pulmonary disease (COPD), accurately estimating lung function from electronic health record (EHR) data would be beneficial but requires addressing complexities in clinically obtained testing. This study compared analytic methods for estimating rate of forced expiratory volume in one second (FEV) change from EHR data.

Methods: We estimated rate of FEV change in patients with COPD from a single centre who had ≥3 outpatient tests spanning at least 1 year.

Human Neural Organoid Microphysiological Systems Show the Building Blocks Necessary for Basic Learning and Memory.

Brain Microphysiological Systems including neural organoids derived from human induced pluripotent stem cells offer a unique lens to study the intricate workings of the human brain. This paper investigates the foundational elements of learning and memory in neural organoids, also known as Organoid Intelligence by quantifying immediate early gene expression, synaptic plasticity, neuronal network dynamics, and criticality to demonstrate the utility of these organoids in basic science research. Neural organoids showed synapse formation, glutamatergic and GABAergic receptor expression, immediate early gene expression basally and evoked, functional connectivity, criticality, and synaptic plasticity in response to theta-burst stimulation.

Quantifying physical degradation alongside recording and stimulation performance of 980 intracortical microelectrodes chronically implanted in three humans for 956-2246 days.

Motivation: The clinical success of brain-machine interfaces depends on overcoming both biological and material challenges to ensure a long-term stable connection for neural recording and stimulation. Therefore, there is a need to quantify any damage that microelectrodes sustain when they are chronically implanted in the human cortex.

Methods: Using scanning electron microscopy (SEM), we imaged 980 microelectrodes from Neuroport arrays chronically implanted in the cortex of three people with tetraplegia for 956-2246 days.

Uncertainty Estimation for Dual View X-ray Mammographic Image Registration Using Deep Ensembles.

Techniques are developed for generating uncertainty estimates for convolutional neural network (CNN)-based methods for registering the locations of lesions between the craniocaudal (CC) and mediolateral oblique (MLO) mammographic X-ray image views. Multi-view lesion correspondence is an important task that clinicians perform for characterizing lesions during routine mammographic exams. Automated registration tools can aid in this task, yet if the tools also provide confidence estimates, they can be of greater value to clinicians, especially in cases involving dense tissue where lesions may be difficult to see.

Transformer model generated bacteriophage genomes are compositionally distinct from natural sequences.

Novel applications of language models in genomics promise to have a large impact on the field. The megaDNA model is the first publicly available generative model for creating synthetic viral genomes. To evaluate megaDNA's ability to recapitulate the nonrandom genome composition of viruses and assess whether synthetic genomes can be algorithmically detected, compositional metrics for 4969 natural bacteriophage genomes and 1002 synthetic bacteriophage genomes were compared.

Silicon photonic microresonator-based high-resolution line-by-line pulse shaping.

Optical pulse shaping stands as a formidable technique in ultrafast optics, radio-frequency photonics, and quantum communications. While existing systems rely on bulk optics or integrated platforms with planar waveguide sections for spatial dispersion, they face limitations in achieving finer (few- or sub-GHz) spectrum control. These methods either demand considerable space or suffer from pronounced phase errors and optical losses when assembled to achieve fine resolution.

Iterative alignment discovery of speech-associated neural activity.

. Brain-computer interfaces (BCIs) have the potential to preserve or restore speech in patients with neurological disorders that weaken the muscles involved in speech production. However, successful training of low-latency speech synthesis and recognition models requires alignment of neural activity with intended phonetic or acoustic output with high temporal precision.

Complete genome sequences of two new strains of the shipworm endosymbiont, .

We present the complete genome sequences of two strains of , SR01903 and SR02026, shipworm endosymbionts isolated from the gills of and , respectively, and derived from Oxford Nanopore sequencing. These sequences will aid in the comparative genomics of shipworm endosymbionts and understanding of host-symbiont selection.

Enhancing the Management of Deployment-Limiting Medical Conditions in the U.S. Department of Navy Leveraging Electronic Health Records and Predictive Analytics Methods.

Introduction: Deployment-limiting medical conditions (DLMCs) such as debilitating injuries and conditions may interfere with the ability of military service members (SMs) to deploy. SMs in the United States (U.S.

Biosignature Molecules Accumulate and Persist in Evaporitic Brines: Implications for Planetary Exploration.

The abundance of potentially habitable hypersaline environments in our solar system compels us to understand the impacts of high-salt matrices and brine dynamics on biosignature detection efforts. We identified and quantified organic compounds in brines from South Bay Salt Works (SBSW), where evapoconcentration of ocean water enables exploration of the impact of NaCl- and MgCl-dominated brines on the detection of potential biosignature molecules. In SBSW, organic biosignature abundance and distribution are likely influenced by evapoconcentration, osmolyte accumulation, and preservation effects.

Closing the genome of T7902 by long-read nanopore sequencing.

We present the complete closed circular genome sequence derived from Oxford Nanopore sequencing of the shipworm endosymbiont T7902 (DSM 15152, ATCC 39867), originally isolated from the shipworm (1). This sequence will aid in the comparative genomics of shipworm endosymbionts and the understanding of host-symbiont evolution.

Neurodynamical Computing at the Information Boundaries of Intelligent Systems.

Artificial intelligence has not achieved defining features of biological intelligence despite models boasting more parameters than neurons in the human brain. In this perspective article, we synthesize historical approaches to understanding intelligent systems and argue that methodological and epistemic biases in these fields can be resolved by shifting away from cognitivist brain-as-computer theories and recognizing that brains exist within large, interdependent living systems. Integrating the dynamical systems view of cognition with the massive distributed feedback of perceptual control theory highlights a theoretical gap in our understanding of nonreductive neural mechanisms.

A database of multi-principal element alloy phase-specific mechanical properties measured with nano-indentation.

Multi-principal element alloys (MPEAs) have been the focus of study and computationally-guided design for two reasons. MPEAs have shown high strengths and, the vast potential compositional space is more efficiently navigated with machine learning. In this article, we present data from 7385 indentation tests performed on 19 different MPEAs.

Fast boulder fracturing by thermal fatigue detected on stony asteroids.

Spacecraft observations revealed that rocks on carbonaceous asteroids, which constitute the most numerous class by composition, can develop millimeter-to-meter-scale fractures due to thermal stresses. However, signatures of this process on the second-most populous group of asteroids, the S-complex, have been poorly constrained. Here, we report observations of boulders' fractures on Dimorphos, which is the moonlet of the S-complex asteroid (65803) Didymos, the target of NASA's Double Asteroid Redirection Test (DART) planetary defense mission.