Biology subjects

Dominguez, J.

Publications and source records attributed to Dominguez, J..

12 recordsLinked to original sources

bioRxiv2026

Visibly Transparent, Near-Infrared Absorbing Nanofluids Enable High-Efficiency and Safe Laser Lithotripsy

Laser lithotripsy (LL) is the gold standard for urinary stone management yet maximizing ablation efficiency while maintaining procedural safety remains clinically challenging. Here, we present a visibly transparent, near-infrared (NIR)-absorbing ITO@SiO2 nanofluid irrigation strategy that significantly enhances LL efficiency without compromising endoscopic visibility. By spectrally matching the absorption profile of ITO@SiO2 with the clinical Holmium:YAG laser wavelength, ablation efficiency improved by >200% in the bench-top spot treatments and >100% in the hydrogel kidney model. Mechanistic investigations revealed that the enhanced optical absorption of the nanofluid modifies bubble dynamics and synergistically amplifies photothermal/microexplosion effects and cavitation damage. Importantly, both in-vitro hydrogel and in-vivo porcine kidney models demonstrated a substantial thermal safety margin (maximum temperatures <35 {degrees}C) and excellent acute biocompatibility, with no evidence of thermal tissue injury. Integrating seamlessly into established clinical workflows without requiring stone pretreatment, this strategy offers a highly translatable, safe, and efficient platform for next-generation endoscopic lithotripsy.

bioengineering↗

bioRxiv2026

Effects of antibiotics on the abundance of antibiotic resistance determinants during and after antibiotic administration to beef cattle: A systematic review and meta-analysis of longitudinal studies

BackgroundBeef feedlots are increasing concerns that antibiotic use in beef cattle selects for antibiotic resistance, but limitations of primary studies and previous syntheses make it difficult to confirm a consistent effect. We conducted a rigorous systematic review and meta-analysis to summarise: 1) the effect during and after antibiotic administration; 2) its moderation by time since administration started/ended. MethodsEligible studies longitudinally compared beef cattle administered antibiotics to those that were not, measuring resistance determinants in faeces and/or environments. Information sources included Web of Science, CAB Abstracts, and Medline (last searches: 05/03/25). Risk of bias was assessed using RoB 2 and ROBINS-I. Meta-analysis was conducted where feasible, using individual participant data where necessary. ResultsThe 33 included studies were mostly small trials of North American feedlot cattle, all with high risks of bias. Meta-analysis of 11 studies of tylosin, ceftiofur, and chlortetracycline indicated positive effects on absolute abundance of resistance both during (SMDH = 0.4; 95% CI = 0.11 to 0.69, p = <0.01) and after (SMDH = 0.52; 95% CI = 0.33 to 0.71, p = <0.01) antibiotic administration. Log-transformed time was positively associated with effect size during (Slope = 0.63; 95% CI = 0.1 to 1.16, p = 0.02), and negatively associated after (Slope = -0.65; 95% CI = -1.24 to -0.06, p = 0.03) DiscussionAvailable evidence indicates time-dependent selection for antibiotic resistance in beef cattle, warranting further regulation to limit human health risks. Simultaneously, uncertainty about precise effect sizes warrants further research. FundingBBSRC Registrationhttps://doi.org/10.17605/OSF.IO/RXQHT

microbiology↗

bioRxiv2025

Eucalyptus cover as the primary driver of native forest bird reductions: evidence from a stand-scale analysis in NW Iberia

The rapid expansion of exotic eucalyptus plantations across the Iberian Peninsula, particularly in northwest Spain, where they now cover 30% of the regions forested area, has profoundly transformed rural landscapes, raising serious concerns about its impact on native biodiversity. This study investigates the influence of structural and floristic attributes of eucalyptus plantations and native forests on forest bird communities, focusing on species abundance and occurrence at the stand level. We conducted point count surveys and vegetation assessments across 240 plots, applying Generalized Linear Models (GLMs) and multimodel inference (MMI) to identify key drivers of avian diversity. Vegetation structure and composition differed substantially between native forests and eucalyptus plantations. Bird species richness and abundance were significantly lower in eucalyptus plantations. The proportion of eucalyptus emerged as the strongest predictor of these reductions, likely due to the limited availability of key resources such as natural cavities and arthropods. Mature native trees were pivotal in supporting forest bird species, particularly those associated with mature forest ecosystems. In contrast, mature eucalyptus trees failed to serve as adequate surrogates for mature native trees, benefiting only a small subset of forest specialists. Similarly, the well-developed shrub layer in eucalyptus plantations provided limited support for generalist bird species. To mitigate biodiversity loss, we recommend integrating unmanaged retention strips within eucalyptus plantations to enhance habitat heterogeneity and structural diversity, ensuring critical resources for birds and other forest wildlife while balancing forestry productivity with conservation goals.

ecology↗

bioRxiv2024

Enhanced Treatment Efficiency of Holmium:YAG Laser Lithotripsy by Using PEDOT:PSS Nanofluid

Urinary stone disease, characterized by the formation of hard mineral deposits in the urinary tract, has seen a rising prevalence in the U.S. in recent years. This condition often leads to severe pain and typically requires medical intervention. Laser lithotripsy, a minimally invasive treatment, uses laser energy to fragment urinary stones into smaller pieces, facilitating easier removal or natural passage. Among available laser technologies, the holmium:yttrium-aluminum-garnet (Ho:YAG) laser has established itself as the gold standard over the past three decades. Efforts to improve Ho:YAG laser ablation efficiency have largely focused on adjusting laser parameters such as pulse energy and frequency. In this study, we proposed a nanoplasmonic engineering strategy by incorporating nanoparticles (NPs) with strong near-infrared (NIR) absorption into the fluid surrounding the stone, enhancing the light-matter interaction. Using a 0.03 wt.% PEDOT:PSS nanofluid, stone ablation efficiency improved by 38-727% in spot treatment and 26-75% in scanning treatment with a clinical laser lithotripter. The highly absorbing nanofluid accelerates vapor tunnel formation, boosts laser energy transmission to the stone, and permeates stone pores to enhance damage, without increasing thermal tissue injury risk. Cytotoxicity tests also confirmed minimal toxicity at appropriate concentrations. This nanofluid-based approach offers a promising advancement for more efficient and safer laser lithotripsy.

bioengineering↗

bioRxiv2024

Multiscale characterization of the mechanics of curved fibered structures with application to biological materials

Curved fibered structures are ubiquitous in nature and this organization is found in the majority of biological tissues. Indeed, the mechanical behavior of these materials is of pivotal importance in biomechanics and mechanobiology fields. In this paper, we develop a multiscale formulation to characterize the macroscopic mechanical nonlinear behavior from the microstructure of fibered matrices. From the analysis of the mechanics of a randomly curved single fiber, a fibered matrix model is built to determine the macroscopic behavior following a homogenization approach. The model is tested for tensile, compression and shear loads in a number of applications reminiscent to collagen extracellular matrices. However, any other fibered microstructures can be studied following the proposed formulation. The presented approach naturally recovers instabilities at compression as well as the strain stiffening regime, which are observed experimentally in the mechanical behavior of collagen matrices. Indeed, it was found that the bending energy associated to fiber unrolling, is the most important source of energy developed by fibers for the analyzed cases in tensile and shear in all deformation regions (except the strain stiffening region), whereas bending energy dominates at compression too during buckling. The proposed computational framework can also be used to perform multiscale simulations in the referred applications. As a result, the developed methodology may be an interesting and complementary tool to characterize the nonlinear behavior and evolution of curved fibered structures present in biology and engineered materials.

bioengineering↗

bioRxiv2022

Wide-field Calcium Imaging Reveals Widespread Changes in Cortical Connectivity Following Repetitive, Mild Traumatic Brain Injury in the Mouse

The physiologic basis underlying the long-term consequences of repetitive, mild traumatic brain injury (mTBI) remains poorly understood. Mild traumatic brain injury often results in brief loss of consciousness, impaired attention and concentration, memory problems, impulsivity, and headache, without objective findings on clinical imaging or examination. The effects of mTBI can persist and become cumulative with repetitive injury, suggesting global alterations in cortical networks. Using transparent polymer skulls, we performed mesoscopic Ca2+ imaging in mice to evaluate how repetitive mTBI alters patterns of neuronal interactions across the dorsal cerebral cortex. Spatial Independent Component Analysis (sICA) and Localized semi-Nonnegative Matrix Factorization (LocaNMF) were used to quantify changes in cerebral functional connectivity (FC). Repetitive, mild, controlled cortical impacts induce temporary neuroinflammatory responses, characterized by increased density of microglia exhibiting de-ramified morphology. These temporary neuro-inflammatory changes were not associated with compromised cognitive performance in the Barnes maze or motor function as assessed by rotarod. However, long-term alterations in functional connectivity were observed. Widespread, bilateral changes in FC occurred immediately following impact and persisted for up to 7 weeks, the duration of the experiment. Network alterations include decreases in global efficiency, clustering coefficient, and nodal strength, thereby disrupting functional interactions and information flow throughout the dorsal cerebral cortex. A subnetwork analysis shows the largest disruptions in FC were concentrated near the impact site. Therefore, repetitive mTBI induces a transient neuroinflammation, without alterations in cognitive or motor behavior, and a reorganized cortical network evidenced by the widespread, chronic alterations in cortical FC. Significance StatementMore than 2.5 million individuals in the United States suffer minor traumatic brain injuries annually. Because these injuries are typically not associated with visible anatomic injuries or objective clinical findings, they were thought benign and fully recoverable. However, there is increasing awareness of the long-term deleterious consequences, particularly in patients who suffer repeated mTBI. Using long-term, mesoscopic neuronal Ca2+ imaging to characterize the dorsal cerebral cortical connectome following repetitive mTBI, we show extensive, persistent changes in functional connectivity, not only at the site of injury but throughout the cortex. These findings provide new insights into the pathophysiology of mTBI.

neuroscience↗

bioRxiv2020

Miniaturized head-mounted device for whole cortex mesoscale imaging in freely behaving mice

The advent of genetically encoded calcium indicators, along with surgical preparations such as thinned skulls or refractive index matched skulls, have enabled mesoscale cortical activity imaging in head-fixed mice. Such imaging studies have revealed complex patterns of coordinated activity across the cortex during spontaneous behaviors, goal-directed behavior, locomotion, motor learning, and perceptual decision making. However, neural activity during unrestrained behavior significantly differs from neural activity in head-fixed animals. Whole-cortex imaging in freely behaving mice will enable the study of neural activity in a larger, more complex repertoire of behaviors not possible in head-fixed animals. Here we present the "Mesoscope," a wide-field miniaturized, head-mounted fluorescence microscope compatible with transparent polymer skulls recently developed by our group. With a field of view of 8 mm x 10 mm and weighing less than 4 g, the Mesoscope can image most of the mouse dorsal cortex with resolution ranging from 39 to 56 {micro}m. Stroboscopic illumination with blue and green LEDs allows for the measurement of both fluorescence changes due to calcium activity and reflectance signals to capture hemodynamic changes. We have used the Mesoscope to successfully record mesoscale calcium activity across the dorsal cortex during sensory-evoked stimuli, open field behaviors, and social interactions. Finally, combining the mesoscale imaging with electrophysiology enabled us to measure dynamics in extracellular glutamate release in the cortex during the transition from wakefulness to natural sleep.

neuroscience↗

bioRxiv2020

Electrophysiological Frequency Band Ratio Measures Conflate Periodic and Aperiodic Neural Activity

A common analysis measure for neuro-electrophysiological recordings is to compute the power ratio between two frequency bands. Applications of band ratio measures include investigations of cognitive processes as well as biomarkers for conditions such as attention-deficit hyperactivity disorder. Band ratio measures are typically interpreted as reflecting quantitative measures of periodic, or oscillatory, activity, which implicitly assumes that a ratio is measuring the relative powers of two distinct periodic components that are well captured by predefined frequency ranges. However, electrophysiological signals contain periodic components and a 1/f-like aperiodic component, which contributes power across all frequencies. In this work, we investigate whether band ratio measures reflect power differences between two oscillations, as intended. We examine to what extent ratios may instead reflect other periodic changes--such as in center frequency or bandwidth--and/or aperiodic activity. We test this first in simulation, exploring how band ratio measures relate to changes in multiple spectral features. In simulation, we show how multiple periodic and aperiodic features affect band ratio measures. We then validate these findings in a large electroencephalography (EEG) dataset, comparing band ratio measures to parameterizations of power spectral features. In EEG, we find that multiple disparate features influence ratio measures. For example, the commonly applied theta / beta ratio is most reflective of differences in aperiodic activity, and not oscillatory theta or beta power. Collectively, we show how periodic and aperiodic features can drive the same observed changes in band ratio measures. Our results demonstrate how ratio measures reflect different features in different contexts, inconsistent with their typical interpretations. We conclude that band ratio measures are non-specific, conflating multiple possible underlying spectral changes. Explicit parameterization of neural power spectra is better able to provide measurement specificity, elucidating which components of the data change in what ways, allowing for more appropriate physiological interpretations. Materials Descriptions & Availability StatementsO_ST_ABSProject RepositoryC_ST_ABSThis project is also made openly available through an online project repository in which the code and data are made available, with step-by-step guides through the analyses. Project Repository: http://github.com/voytekresearch/BandRatios DatasetsThis project uses simulated data, literature text mining data, and electroencephalography data. Simulated DataThe simulations used in this project are created with openly available software packages. Settings and code to re-generate simulated data is available with the open-access code for the project. Copies of the simulated data that were used in this investigation are available in the project repository. Literature DataLiterature data for this project was collected from the PubMed database. Exact search terms used to collect the data are available in the project repository. The exact data collected from the literature and meta-data about the collection are saved and available in the project repository. EEG DataThe EEG data used in this project is from the openly available dataset, the Multimodal Resource for Studying Information processing in the Developing Brain (MIPDB) database. This dataset is created and released by the Childmind Institute. This dataset was released and is re-used here under the terms of the Creative Commons-Attribution-Non-Commercial-Share-Alike License (CC-BY-NC-SA), and is described in (Langer et al., 2017). Child Mind Institute: https://childmind.org Data Portal: http://fcon_1000.projects.nitrc.org/indi/cmi_eeg/ SoftwareCode used and written for this project was written in the Python programming language. All the code used within this project is deposited in the project repository and is made openly available and licensed for re-use. As well as standard library Python, this project uses 3rd party software packages numpy and pandas for data management, scipy for data processing, matplotlib and seaborn for data visualization and MNE for managing and pre-processing data. This project also uses open-source Python packages developed and released by the authors: Simulations and spectral parameterization were done using the FOOOF toolbox. Code Repository: https://github.com/fooof-tools/fooof Literature collection and analyses were done using the LISC toolbox. Code Repository: https://github.com/lisc-tools/lisc

neuroscience↗

bioRxiv2019

Local adaptation fuels cryptic speciation in terrestrial annelids

Uncovering the genetic and evolutionary basis of cryptic speciation is a major focus of evolutionary biology. Next Generation Sequencing (NGS) allows the identification of genome-wide local adaptation signatures, but has rarely been applied to cryptic complexes - particularly in the soil milieu - as is the case with integrative taxonomy. The earthworm genus Carpetania, comprising six previously suggested putative cryptic lineages, is a promising model to study the evolutionary phenomena shaping cryptic speciation in soil-dwelling lineages. Genotyping-By-Sequencing (GBS) was used to provide genome-wide information about genetic variability between seventeen populations, and geometric morphometrics analyses of genital chaetae were performed to investigate unexplored cryptic morphological evolution. Genomic analyses revealed the existence of three cryptic species, with half of the previously-identified potential cryptic lineages clustering within them. Local adaptation was detected in more than 800 genes putatively involved in a plethora of biological functions (most notably reproduction, metabolism, immunological response and morphogenesis). Several genes with selection signatures showed shared mutations for each of the cryptic species, and genes under selection were enriched in functions related to regulation of transcription, including SNPs located in UTR regions. Finally, geometric morphometrics approaches partially confirmed the phylogenetic signal of relevant morphological characters such as genital chaetae. Our study therefore unveils that local adaptation and regulatory divergence are key evolutionary forces orchestrating genome evolution in soil fauna.

evolutionary biology↗

bioRxiv2019

Genome-informed integrative taxonomic description of three cryptic species in the earthworm genus Carpetania (Oligochaeta, Hormogastridae)

Research on cryptic species complexes has reached a consensus on the necessity of integrating multiple sources of evidence. Low-coverage genomic scan techniques like Genotyping-by-Sequencing (GBS) have proven useful to study these groups. Both integrative taxonomy and genome-wide single nucleotide polymorphism (SNP) data remain to be widely applied to earthworms, an animal group with widespread presence of cryptic diversity. The genus Carpetania (formerly the Hormogaster elisae species complex) was found to contain six deeply divergent genetic lineages and some inconspicuous morphological differentiation based in a handful of Sanger-sequenced markers. Marchan et al. (submitted) delimited three well supported species-level clades on the basis of a genomewide SNP dataset and geometric morphometric analyses, highlighting the necessity of a formal taxonomic description of these taxa. In this work, further analyses are applied to the SNP data and a thorough morphological study is performed in order to provide an integrative description of two new species and to redescribe Carpetania elisae. Species-specific SNPs are identified and used as diagnostic characters, and genome-wide and cytochrome oxidase C subunit 1 (COI) genetic distances are compared finding a strong correlation between them. The taxonomic description of these three cryptic species provides a useful tool to include them effectively in ecological studies and biodiversity conservation actions.

zoology↗

bioRxiv2018

Antimicrobial activity of Mycobacteriophage D29 Lysin B during Mycobacterium ulcerans infection

Buruli Ulcer (BU) is a cutaneous disease caused by Mycobacterium ulcerans. The pathogenesis of this disease is closely related to the secretion of the toxin mycolactone that induces extensive destruction of the skin and soft tissues. Although the World Health Organization recommends a combination of rifampicin and streptomycin for the treatment of BU, clinical management of advanced stages often requires extensive surgical resection of the infected tissue. Therefore, it is important to develop alternative strategies for the treatment of BU.\n\nEndolysins (lysins) are phage encoded enzymes that degrade peptidoglycan of bacterial cell walls. Over the past years, lysins have been emerging as alternative antimicrobial agents against Gram-positive bacteria. Amongst Gram-positive bacteria, mycobacteria have an unusual outer membrane that is covalently attached to the mycolylarabinogalactan-peptidoglycan complex. To overcome this additional barrier to phage-mediated lysis, some mycobacteriophages encode a lipolytic enzyme, Lysin B (Lys B).\n\nIn this study, we demonstrated for the first time that recombinant Lys B displays lytic activity against M. ulcerans isolates. Moreover, using a mouse model of M. ulcerans footpad infection, we show that subcutaneous treatment with Lys B leads to a reduction in bacterial burdens, associated with IFN-{gamma} and TNF production in the draining lymph node. These findings highlight the potential use of lysins as a novel therapeutic approach against this neglected tropical disease.\n\nAUTHOR SUMMARYBuruli Ulcer (BU) is a necrotizing skin disease caused by Mycobacterium ulcerans. Standard treatment for BU lesions consists of a combination of rifampicin and streptomycin for 8 weeks. However, clinical management of advanced stages of the disease often requires extensive surgical resection of the infected tissue. Therefore, it is important to develop alternative strategies for the treatment of BU. In that sense, we tested the efficacy of Lysin B (Lys B), a phage encoded lipolytic enzyme that degrades the mycolylarabinogalactan-peptidoglycan complex present in the mycobacterial cell wall. In this study, we show that Lys B not only displays lytic activity against M. ulcerans isolates in vitro, but also leads to a reduction in bacterial burdens in M. ulcerans-infected mouse footpads. These findings highlight the potential use of lysins as a novel therapeutic approach against this neglected tropical disease.

microbiology↗

bioRxiv2018

Cortex-wide neural interfacing via transparent polymer skulls

Neural computations occurring simultaneously in multiple cerebral cortical regions are critical for mediating cognition, perception and sensorimotor behaviors. Enormous progress has been made in understanding how neural activity in specific cortical regions contributes to behavior. However, there is a lack of tools that allow simultaneous monitoring and perturbing neural activity from multiple cortical regions. To fill this need, we have engineered \"See-Shells\" - digitally designed, morphologically realistic, transparent polymer skulls that allow long-term (>200 days) optical access to 45 mm2 of the dorsal cerebral cortex in the mouse. We demonstrate the ability to perform mesoscopic imaging, as well as cellular and subcellular resolution two-photon imaging of neural structures up to 600 {micro}m through the See-Shells. See-Shells implanted on transgenic mice expressing genetically encoded calcium (Ca2+) indicators allow tracking of neural activities from multiple, non-contiguous regions spread across millimeters of the cortex. Further, neural probes can access the brain through perforated See-Shells, either for perturbing or recording neural activity from localized brain regions simultaneously with whole cortex imaging. As See-Shells can be constructed using readily available desktop fabrication tools and modified to fit a range of skull geometries, they provide a powerful tool for investigating brain structure and function.

neuroscience↗