Bourns College of Engineering

A zoonotic Babesia species previously referred to as Babesia sp. MO1 is formally described and named here as Babesia hegotelforum sp. nov. This taxon is distinct from Babesia divergens based on genome-wide sequence divergence, phylogenetic placement, host associations, and clinical presentation. The parasite infects erythrocytes of humans, and eastern cottontail rabbits (Sylvilagus floridanus), and is transmitted by Ixodes dentatus. The holotype consists of a Giemsa-stained thin blood smear and cryopreserved infected erythrocytes from the cloned isolate BML-Bh-B12 at ≤10 passages in continuous in vitro culture. Paratype material includes five additional clones (BML-Bh-H1, BML-Bh-F12, BML-Bh-H6, BML-Bh-A3, and BML-Bh-F1) derived from BEI Resources strain NR-50441, along with the original mixed isolate NR-50441. This species description meets the requirements of the International Code of Zoological Nomenclature and establishes Babesia hegotelforum sp. nov. as a distinct species of clinical and epidemiological significance in North America.

PURPOSE: Conventional arterial spin labeling (ASL) reconstruction suffers from sign-flipping errors and/or noise bias under strong background suppression (BS), limiting SNR optimization. We propose reference-superimposed reconstruction (RS-recon) to enable ideal BS and robust signal recovery. METHODS: RS-recon superimposes high-SNR M0 k-space data onto ASL k-space before reconstruction, with subsequent reference subtraction. Four volunteers underwent 3T scanning with pulsed ASL, pseudo-continuous ASL, and dual-module velocity-selective ASL across varying BS levels. RS-recon integrated reconstruction pipelines were compared to standard magnitude (Mag), complex subtraction (ComplexSub), and complex (Complex) reconstruction pipelines. The performance was evaluated by metrics including ASL signal, temporal SNR (tSNR), artifacts, misalignment robustness, and generalized auto-calibrating partially parallel acquisitions (GRAPPA) compatibility. RESULTS: RS-recon eliminated subtraction artifacts due to signal sign-flipping, recovered negative ASL signals, and enabled ideal BS for maximizing SNR. It significantly improved ASL signal and tSNR in gray/white matter across all labeling methods and different BS conditions. RS-recon corrected phase errors under low-SNR conditions, preserved signal signs, maintained Gaussian noise distribution, remained robust against misalignments between the reference and the ASL images, and integrated well with GRAPPA. Mag + RS performance matched complex-based (ComplexSub and Complex) RS pipelines and is recommended for its simplicity, compatibility, and robustness overall. CONCLUSION: RS-recon offers a simple, robust strategy for ASL image reconstruction, resolving subtraction errors even with magnitude output and enabling optimal background suppression. It enhances signal fidelity, SNR, and phase accuracy while integrating seamlessly with existing reconstruction pipelines and parallel imaging.

Dissolved organic matter (DOM) is a central component of Earth’s carbon cycle and one of the planet’s most chemically diverse pools, yet the molecular structures of its constituents remain largely unresolved. This limitation has hindered our ability to link DOM composition to microbial processes and ecosystem function. Here we present ENVnet, a global molecular repository built from tandem mass spectrometry data collected across 13 terrestrial and aquatic environment types, including 419 newly generated samples that expand publicly available DOM metabolomics data and cover previously underrepresented environments. By computationally deconvolving chimeric mass spectra, a longstanding challenge in environmental metabolomics, we recover high-quality fragmentation data for >22,000 distinct molecular features (defined by a specific precursor mass and fragmentation pattern). Using ENVnet, we uncover conserved and environment-specific molecular patterns in DOM composition and underlying biogeochemical processes. We also use molecular features encoded in ENVnet to train predictive models of DOM persistence, allowing molecular-level assessment of microbial turnover in independent systems.

Rapid and sensitive detection of plant pathogens, such as the Avocado Sunblotch Viroid (ASBVd), is essential for early disease management and agricultural biosecurity. Yet, most current diagnostic methods not only require relatively large sample inputs but also often lack the ultrasensitivity required for reliable detection with scarce or minimally collected plant material. Here, we report a novel low-input but ultrasensitive diagnostic platform that integrates isothermal recombinase polymerase amplification (RPA), CRISPR-Cas12a detection, and a solid-state nanopore array for the detection of ASBVd. The system leverages CRISPR-Cas12a collateral cleavage activity to generate single-bead fluorescent signals, which are captured by a nanopore array through pressure-driven blockage. Our platform achieves a detection limit down to 1.68 copies/μL while using only 40 nL of bead-fluorophore mixture per readout, which is over 100-fold less than conventional assays based on fluorescent readout using an imaging reader, enabling detection from minimal avocado sample collection. We demonstrate robust binary classification of ASBVd-positive and -negative samples from multiple avocado tissue types and orchards in California. The assay requires just 60 min and operates entirely under isothermal conditions, avoiding the need for bulky PCR instruments and supporting on-site deployment with minimal equipment. This method provides a promising platform for field-deployable, ultrasensitive, and low-input diagnostics of viroids and other low-titer pathogens in plant or clinical settings.

Computational tools for studying the structure of protein complexes are essential for providing mechanistic insights into protein-protein interactions and therapeutic drug design. Here, we present SPICE (Structural Protein Interaction Complex Evaluator), a web-based platform that allows structural biologists to perform rapid, modular analyses of protein complexes directly from Protein Data Bank (PDB) structures. SPICE allows users to define and execute analysis workflows via an intuitive web interface, reducing analysis times from minutes to seconds. The platform offers a broad range of analytical capabilities, including (i) detection of hydrogen bonds, salt bridges, and disulfide bonds; (ii) protein-protein interface mapping; and (iii) computation of solvent accessibility, van der Waals energetics, and other key geometric descriptors. SPICE further provides interactive 3D visualization and supports comparative analyses across multiple complexes, enabling the study of mutational effects and binding variants. The tool is freely available at https://spice.cs.ucr.edu (no registration required).

OBJECTIVE: Elevated kurtosis values have been observed in subcortical grey matter structures of patients with neurodegenerative diseases. Here, we examined relationships between iron measures and kurtosis in iron-rich subcortical grey matter structures.Please check and confirm the affiliation 4 for the author "Xiaoping P. Hu".Affiliation 4 for Xiaoping P. Hu was incorrect since he is not associated with that department. We have removed this affiliation. Thanks!  MATERIALS AND METHODS: Multi-shell diffusion and multi-echo gradient echo acquisitions were used to derive mean kurtosis and iron measures (R₂* and magnetic susceptibility), respectively, in subcortical grey matter nuclei and white matter tracts in a discovery cohort (110 healthy older and 63 younger adults) and replication cohort (72 healthy older adults).Please confirm if the author names are presented accurately and in the correct sequence (Ilana J. Bennett and Xiaoping P. Hu). Also, kindly confirm the details in the metadata are correct.Thanks for asking. We've checked and the names are presented accurately and in the correct sequence. We have corrected some details in the metadata - adding an affiliation to Murphy Shao (Department of Physics) and removing the Materials Science and Engineering affiliation for Xiaoping P. Hu. Is it possible to add an orcid id for Vala Masjedizadeh? His Orcid ID is  0009-0009-3692-2553 Everything else looks okay RESULTS: Iron-rich grey matter regions exhibited higher mean kurtosis, R₂*, and magnetic susceptibility and white matter regions had lower mean kurtosis in the older adult group from the discovery cohort. In both cohorts, mean kurtosis was significantly correlated with R₂* and magnetic susceptibility in iron-rich grey matter nuclei. No association was seen between signal-to-noise ratio and mean kurtosis in any grey matter region, indicating that the increase in mean kurtosis was not due to reduced signal-to-noise. As keywords are mandatory for this journal, please provide 3-6 keywords.I'm not sure where to put the keywords so I'll reply to the query with the keywords. Our keywords are: kurtosis, iron, grey matter, aging CONCLUSION: Our findings indicate that kurtosis is associated with iron-sensitive metrics in iron-rich grey matter structures, suggesting that iron deposits may be contributing to kurtosis.

Measuring the forces of individual muscles in a muscle group around a joint is non-trivial, and researchers have suggested using surrogates for individual muscle forces instead. Traditionally, experimentalists have shown that the force output of the skeletal muscle tissue can be correlated to the intra-muscular pressure (IMP) generated by the muscle belly. However, IMP proves difficult to measure in vivo, due to variations from sensor placement and invasiveness of the procedure. Numerical biomechanical simulations offer a tool to analyze muscle contractions, enabling new insights into the correlations among non-invasive experimentally measurable quantities, such as strains and the force output. In this work, we investigate the correlations between the muscle force output, the principal, shear and volumetric strains experienced by the muscle, as well as the pressure developed within the muscle belly as the tissue undergoes isometric contractions with varying activation profiles and magnitudes. It is observed that pressure does not correlate well with force output under higher sub-maximal and maximal activation levels, especially at locations away from the center of the muscle belly due to pressure relaxation effects. This study reveals strong correlations between force output and the strains at all locations of the belly, irrespective of the type of activation considered. This observation offers evidence for further in vivo studies using experimentally measurable principal and volumetric strains in the muscle belly as proxies for the force generation by the individual muscle and consequently enables the estimation on the contribution of various muscle groups to the total force.

Neural crest stem cells (NCSCs), capable of differentiating into neurons and Schwann cells, are essential for peripheral nerve regeneration. This study investigates the role of endogenous NCSC-like cells in mechano-electrical stimulation (MES)-enhanced peripheral nerve repair. In a critical-sized nerve injury model, MES leads to complete nerve reconnection, accompanied by a significant increase in NCSC-like cells at the injury sites. In vitro, MES promotes the simultaneous differentiation of NCSC-like cells into neurons and Schwann cells, with elevated neuregulin 1 (NRG1) expression, a key factor in Schwann cell development. Mechanistically, MES activates BMP/Smad signaling, driving neuronal differentiation and subsequent NRG1 secretion, which in turn promotes Schwann cell maturation through the ErBB/NFAT pathway. These findings demonstrate that MES enhances peripheral nerve regeneration by activating and directing stem cell differentiation, supporting a novel therapeutic approach that utilizes physical stimulation for stem cell modulation for nerve repair.

OBJECTIVES: Cryogen spray cooling (CSC) is critical for protecting the epidermis during laser dermatologic procedures. The widely used cryogen, R134a, has a high global warming potential (GWP), motivating interest in environmentally favorable alternatives such as HFO-1234ze. This study evaluated whether HFO-1234ze provides epidermal protection comparable to R134a during laser exposure and investigated the mechanistic basis underlying any differences in cooling performance. METHODS: Laser-induced epidermal injury in conjunction with two cryogens was assessed in K14-SCF Mc1r^e/e mice with pharmacologically controllable interfollicular epidermal pigmentation. Laser treatment sites were assigned fluences relative to baseline skin lightness (L*) to span subthreshold to suprathreshold injury conditions, with cryogen assignment randomized. Hypopigmentation at Day 7 served as the primary injury endpoint and was scored independently by three blinded raters. Surface cooling induced by each cryogen was measured separately using thin-film thermocouples on a skin phantom, and subsurface temperature distributions were estimated using one-dimensional transient heat-transfer modeling. RESULTS: Mean hypopigmentation scores did not differ significantly between R134a- and HFO-1234ze-cooled sites across the full range of pigmentation and fluence studied (p = 0.46). Heat-map analysis and regression modeling confirmed that hypopigmentation increased with fluence and darker pigmentation but was independent of cryogen type. Surface temperature measurements using skin phantom revealed that R134a produced more aggressive transient cooling than HFO-1234ze, reaching approximately 10°C lower minimum temperatures. However, numerical modeling of skin cooling using heat flux inferred from phantom measurement showed that this surface advantage decayed rapidly with depth, resulting in ≤ 2°C-3°C differences within the viable epidermis. CONCLUSIONS: Despite differences in surface cooling magnitude, R134a and HFO-1234ze provided equivalent epidermal protection under clinically relevant conditions. These findings support HFO-1234ze as an effective, lower-GWP alternative to R134a for CSC in laser dermatologic applications.