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  1. Nature serves as a rich source of molecules with immense chemical diversity. Aptly named, these ‘natural products’ boast a wide variety of environmental, medicinal and industrial applications. Type II polyketides, in particular, confer substantial medicinal benefits, including antibacterial, antifungal, anticancer and anti-inflammatory properties. These molecules are produced by enzyme assemblies known as type II polyketide synthases (PKSs), which use domains such as the ketosynthase chain-length factor and acyl carrier protein to produce polyketides with varying lengths, cyclization patterns and oxidation states. In this work, we use a novel bioinformatic workflow to identify biosynthetic gene clusters (BGCs) that code for the core type II PKS enzymes. This method does not rely on annotation and thus was able to unearth previously ‘hidden’ type II PKS BGCs. This work led us to identify over 6000 putative type II PKS BGCs spanning a diverse set of microbial phyla, nearly double those found in most recent studies. Notably, many of these newly identified BGCs were found in non-actinobacteria, which are relatively underexplored as sources of type II polyketides. Results from this work lay an important foundation for future bioprospecting and engineering efforts that will enable sustainable access to diverse and structurally complex molecules with medicinallymore »relevant properties.« less
    Free, publicly-accessible full text available March 23, 2024
  2. Few fires are known to have burned the tundra of the Arctic Slope north of the Brooks Range in Alaska, USA. A total of 90 fires between 1969 and 2022 are known. Because fire has been rare, old burns can be detected by the traces of thermokarst and distinct vegetation they leave in otherwise uniform tundra, which are visible in aerial photograph archives. Several prehistoric tundra burns have been found in this way. Detection of tundra fires in this sparsely populated and remote area has been historically inconsistent and opportunistic, relying on reports by aircraft pilots. Fire reports have been logged into an administrative database which, out of necessity, has been used to scientifically evaluate changes in the fire regime. To improve the consistency of the record, we completed a systematic search of Landsat Collection 2 for the Brooks Range Foothills ecoregion over the period 1972–2022. We found 57 unrecorded tundra burns, about 41% of the total, which now numbers 138. Only 15% and 33% of all fires appear in MODIS and VIIRS satellite-borne thermal anomaly products, respectively. The fire frequency in the first 37 years of the record is 0.89 y−1 for natural ignitions that spread ≥10 ha. Frequencymore »in the last 13 years is 2.5 y−1, indicating a nearly three-fold increase in fire frequency.« less
    Free, publicly-accessible full text available March 1, 2024
  3. Abstract

    Measured intensity in high-energy monochromatic X-ray diffraction (HEXD) experiments provides information regarding the microstructure of the crystalline material under study. The location of intensity on an areal detector is determined by the lattice spacing and orientation of crystals so that changes in theheterogeneityof these quantities are reflected in the spreading of diffraction peaks over time. High temporal resolution of such dynamics can now be experimentally observed using technologies such as the mixed-mode pixel array detector (MM-PAD) which facilitates in situ dynamic HEXD experiments to study plasticity and its underlying mechanisms. In this paper, we define and demonstrate a feature computed directly from such diffraction time series data quantifying signal spread in a manner that is correlated with plastic deformation of the sample. A distinguishing characteristic of the analysis is the capability to describe the evolution from the distinct diffraction peaks of an undeformed alloy sample through to the non-uniform Debye–Scherrer rings developed upon significant plastic deformation. We build on our previous work modeling data using an overcomplete dictionary by treating temporal measurements jointly to improve signal spread recovery. We demonstrate our approach in simulations and on experimental HEXD measurements captured using the MM-PAD. Our method for characterizing the temporalmore »evolution of signal spread is shown to provide an informative means of data analysis that adds to the capabilities of existing methods. Our work draws on ideas from convolutional sparse coding and requires solving a coupled convex optimization problem based on the alternating direction method of multipliers.

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  4. Optical coherence tomography (OCT) and scanning laser ophthalmoscopy (SLO) are imaging technologies invented in the 1980s that have revolutionized the field ofin vivoretinal diagnostics and are now commonly used in ophthalmology clinics as well as in vision science research. Adaptive optics (AO) technology enables high-fidelity correction of ocular aberrations, resulting in improved resolution and sensitivity for both SLO and OCT systems. The potential of gathering multi-modal cellular-resolution information in a single instrument is of great interest to the ophthalmic imaging community. Although similar instruments have been developed for imaging the human retina, developing such a system for mice will benefit basic science research and should help with further dissemination of AO technology. Here, we present our work integrating OCT into an existing mouse retinal AO-SLO system, resulting in a multi-modal AO-enhanced imaging system of the living mouse eye. The new system allows either independent or simultaneous data acquisition of AO-SLO and AO-OCT, depending on the requirements of specific scientific experiments. The system allows a data acquisition speed of 200 kHz A-scans/pixel rate for OCT and SLO, respectively. It offers ∼6 µm axial resolution for AO-OCT and a ∼1 µm lateral resolution for AO-SLO-OCT imaging.

  5. Abstract Human machine interfaces that can track head motion will result in advances in physical rehabilitation, improved augmented reality/virtual reality systems, and aid in the study of human behavior. This paper presents a head position monitoring and classification system using thin flexible strain sensing threads placed on the neck of an individual. A wireless circuit module consisting of impedance readout circuitry and a Bluetooth module records and transmits strain information to a computer. A data processing algorithm for motion recognition provides near real-time quantification of head position. Incoming data is filtered, normalized and divided into data segments. A set of features is extracted from each data segment and employed as input to nine classifiers including Support Vector Machine, Naive Bayes and KNN for position prediction. A testing accuracy of around 92% was achieved for a set of nine head orientations. Results indicate that this human machine interface platform is accurate, flexible, easy to use, and cost effective.
  6. The sharing of research data is essential to ensure reproducibility and maximize the impact of public investments in scientific research. Here, we describe OpenNeuro, a BRAIN Initiative data archive that provides the ability to openly share data from a broad range of brain imaging data types following the FAIR principles for data sharing. We highlight the importance of the Brain Imaging Data Structure standard for enabling effective curation, sharing, and reuse of data. The archive presently shares more than 600 datasets including data from more than 20,000 participants, comprising multiple species and measurement modalities and a broad range of phenotypes. The impact of the shared data is evident in a growing number of published reuses, currently totalling more than 150 publications. We conclude by describing plans for future development and integration with other ongoing open science efforts.