bluuebunny/crossref_metadata_2025_split huggingface dataset:
Corneal Irregularity Induced by Transepithelial Photorefractive Keratectomy in a Patient With Partial Limbal Stem Cell Deficiency
Authors: Vakalopoulos Dionysios G. , Chatzea Marina S. , Chronopoulou Konstantina , Katsimpras Marios , Tsopouridou Rodopi D. , Kymionis George D. 
Published: October 2023

Purpose:
The aim of this study was to present a case of transepithelial photorefractive keratectomy (trans-PRK) laser ablation in a patient with partial limbal stem cell deficiency (LSCD) that resulted in corneal irregularity.

Methods:
A 23-year-old man with bilateral partial LSCD underwent trans-PRK for myopia correction 2 months before presentation to our department. Trans-PRK ablation was performed with a phototherapeutic keratectomy ablation profile set at 60 μm in the OD and 57 μm in the OS and 8 mm zone. At the time of presentation, the patient complained of decreased visual acuity. Corrected distant visual acuity was 20/20 (−3.25, −0.75 × 180 degrees) and 20/50 (−3.00, −3.00 × 180 degrees) in the OD and the OS, respectively. No further ocular history was reported other than prolonged soft contact lens use for myopia. Pre–trans-PRK tomography (WaveLight Oculyzer II diagnostic system, WaveLight GmbH, Germany) revealed bilateral superior steepening with corresponding epithelial thinning as obtained by the epithelial map using Optovue optical coherence tomography (Visionix Luneau technology). Slit-lamp examination showed bilateral superficial neovascularization, suggestive of early-stage LSCD.

Results:
A nonuniform laser stromal ablation resulting in corneal irregularity and decreased visual acuity was observed 2 months postoperatively. During the 6-month follow-up, corneal tomography was stable with only minimal improvement. At that time, corrected distant visual acuity remained 20/20 (−2.75, −0.75 × 160 degrees) in the OD and 20/50 (−3.00, −3.00 × 180 degrees) in the OS.

Conclusions:
Trans-PRK seems to be a contraindication in cases with corneal epithelial irregularities and could lead to abnormal and nonuniform stromal ablation.
Malignant Mimicry in a Rare Case of Hepatic Malakoplakia
Authors: Strayve Daniel , Ruby Jarom , Abidalhassan Mustafa , Hutfles Gerald J. , Schaberg Kurt B. , Wei Dongguang , Corwin Michael , Gholami Sepideh 
Published: October 2023

Abstract
We report a rare case of hepatic malakoplakia mimicking malignancy both in its clinical presentation and appearance on 4-phase computed tomography. This case highlights both an interesting variation by which this disease process can manifest and a multidisciplinary approach, which may be used to identify and treat future patients.
Light pollution in complex ecological systems
Authors: Hirt Myriam R. , Evans Darren M. , Miller Colleen R. , Ryser Remo 
Published: October 2023

Light pollution has emerged as a burgeoning area of scientific interest, receiving increasing attention in recent years. The resulting body of literature has revealed a diverse array of species-specific and context-dependent responses to artificial light at night (ALAN). Because predicting and generalizing community-level effects is difficult, our current comprehension of the ecological impacts of light pollution on complex ecological systems remains notably limited. It is critical to better understand ALAN's effects at higher levels of ecological organization in order to comprehend and mitigate the repercussions of ALAN on ecosystem functioning and stability amidst ongoing global change. This theme issue seeks to explore the effects of light pollution on complex ecological systems, by bridging various realms and scaling up from individual processes and functions to communities and networks. Through this integrated approach, this collection aims to shed light on the intricate interplay between light pollution, ecological dynamics and humans in a world increasingly impacted by anthropogenic lighting.
This article is part of the theme issue ‘Light pollution in complex ecological systems’.
Spectral composition of light-emitting diodes impacts aquatic and terrestrial invertebrate communities with potential implications for cross-ecosystem subsidies
Authors: Parkinson Elizabeth , Tiegs Scott D. 
Published: October 2023

Resource exchanges in the form of invertebrate fluxes are a key component of aquatic-terrestrial habitat coupling, but this interface is susceptible to human activities, including the imposition of artificial light at night. To better understand the effects of spectral composition of light-emitting diodes (LEDs)—a technology that is rapidly supplanting other lighting types—on emergent aquatic insects and terrestrial insects, we experimentally added LED fixtures that emit different light spectra to the littoral zone and adjacent riparian habitat of a pond. We installed four replicate LED treatments of different wavelengths (410, 530 and 630 nm), neutral white (4000 k) and a dark control, and sampled invertebrates in both terrestrial and over-water littoral traps. Invertebrate communities differed among light treatments and between habitats, as did total insect biomass and mean individual insect size. Proportional allochthonous biomass was greater in the riparian habitat and among some light treatments, demonstrating an asymmetrical effect of differently coloured LEDs on aquatic-terrestrial resource exchanges. Overall, our findings demonstrate that variation in wavelength from LEDs may impact the flux of resources between systems, as well as the communities of insects that are attracted to particular spectra of LED lighting, with probable implications for consumers.
This article is part of the theme issue ‘Light pollution in complex ecological systems’.
A Biallelic Variant of the RNA Exosome GeneEXOSC4Causes Translational Defects Associated with a Neurodevelopmental Disorder
Authors: Fasken Milo B. , Leung Sara W. , Cureton Lauryn A. , Al-Awadi Maha , Al-Kindy Adila , Khoshnevis Sohail , Ghalei Homa , Al-Maawali Almundher , Corbett Anita H. 
Published: October 2023

ABSTRACTThe RNA exosome is an evolutionarily conserved complex required for both precise RNA processing and decay. Mutations inEXOSCgenes encoding structural subunits of the complex are linked to several autosomal recessive disorders. Here, we describe a missense allele of theEXOSC4gene, which causes a collection of clinical features in two affected siblings. This missense mutation (NM_019037.3: exon3:c.560T>C), changes a leucine residue within a highly conserved region of EXOSC4 to proline (p.Leu187Pro). The two affected individuals presented with prenatal growth restriction, failure to thrive, global developmental delay, intracerebral and basal ganglia calcifications, and kidney failure. Homozygosity for the damaging variant was identified through exome sequencing and Sanger sequencing confirmed segregation. To explore the functional consequences of this amino acid change, we modeled EXOSC4-L187P in the corresponding budding yeast protein, Rrp41 (Rrp41-L187P). Cells that express Rrp41-L187P as the sole copy of the essential Rrp41 protein show significant growth defects. The steady-state level of both the Rrp41-L187P and the EXOSC4-L187P proteins is significantly decreased compared to control Rrp41/EXOSC4. Consistent with this observation, targets of the RNA exosome accumulate inrrp41-L187Pcells, including the 7S precursor of 5.8S rRNA. Polysome profiles show a significant decrease in translation inrrp41-L187Pcells as compared to control cells with apparent incorporation of 7S pre-rRNA into polysomes. Taken together, this work adds the EXOSC4 subunit of the RNA exosome to the structural subunits of this complex that have been linked to human disease and defines foundational molecular defects that could contribute to the adverse growth phenotypes caused by this novel EXOSC4 pathogenic variant.
DREDge: robust motion correction for high-density extracellular recordings across species
Authors: Windolf Charlie , Yu Han , Paulk Angelique C. , Meszéna Domokos , Muñoz William , Boussard Julien , Hardstone Richard , Caprara Irene , Jamali Mohsen , Kfir Yoav , Xu Duo , Chung Jason E. , Sellers Kristin K. , Ye Zhiwen , Shaker Jordan , Lebedeva Anna , Raghavan Manu , Trautmann Eric , Melin Max , Couto João , Garcia Samuel , Coughlin Brian , Horváth Csaba , Fiáth Richárd , Ulbert István , Movshon J. Anthony , Shadlen Michael N. , Churchland Mark M. , Churchland Anne K. , Steinmetz Nicholas A. , Chang Edward F. , Schweitzer Jeffrey S. , Williams Ziv M. , Cash Sydney S. , Paninski Liam , Varol Erdem 
Published: October 2023

AbstractHigh-density microelectrode arrays (MEAs) have opened new possibilities for systems neuroscience in human and non-human animals, but brain tissue motion relative to the array poses a challenge for downstream analyses, particularly in human recordings. We introduce DREDge (Decentralized Registration of Electrophysiology Data), a robust algorithm which is well suited for the registration of noisy, nonstationary extracellular electrophysiology recordings. In addition to estimating motion from spikes in the action potential (AP) frequency band, DREDge enables automated tracking of motion at high temporal resolution in the local field potential (LFP) frequency band. In human intraoperative recordings, which often feature fast (period <1s) motion, DREDge correction in the LFP band enabled reliable recovery of evoked potentials, and significantly reduced single-unit spike shape variability and spike sorting error. Applying DREDge to recordings made during deep probe insertions in nonhuman primates demonstrated the possibility of tracking probe motion of centimeters across several brain regions while simultaneously mapping single unit electrophysiological features. DREDge reliably delivered improved motion correction in acute mouse recordings, especially in those made with an recent ultra-high density probe. We also implemented a procedure for applying DREDge to recordings made across tens of days in chronic implantations in mice, reliably yielding stable motion tracking despite changes in neural activity across experimental sessions. Together, these advances enable automated, scalable registration of electrophysiological data across multiple species, probe types, and drift cases, providing a stable foundation for downstream scientific analyses of these rich datasets.
AI-Powered Smart Glasses for Sensing and Recognition of Human-Robot Walking Environments
Authors: Rossos Daniel , Mihailidis Alex , Laschowski Brokoslaw 
Published: October 2023

AbstractEnvironment sensing and recognition can allow humans and robots to dynamically adapt to different walking terrains. However, fast and accurate visual perception is challenging, especially on embedded devices with limited computational resources. The purpose of this study was to develop a novel pair of AI-powered smart glasses for onboard sensing and recognition of human-robot walking environments with high accuracy and low latency. We used a Raspberry Pi Pico microcontroller and an ArduCam HM0360 low-power camera, both of which interface with the eyeglass frames using 3D-printed mounts that we custom-designed. We trained and optimized a lightweight and efficient convolutional neural network using a MobileNetV1 backbone to classify the walking terrain as either indoor surfaces, outdoor surfaces (grass and dirt), or outdoor surfaces (paved) using over 62,500 egocentric images that we adapted and manually labelled from the Meta Ego4D dataset. We then compiled and deployed our deep learning model using TensorFlow Lite Micro and post-training quantization to create a minimized byte array model of size 0.31MB. Our system was able to accurately predict complex walking environments with 93.6% classification accuracy and had an embedded inference speed of 1.5 seconds during online experiments using the integrated camera and microcontroller. Our AI-powered smart glasses open new opportunities for visual perception of human-robot walking environments where embedded inference and a low form factor is required. Future research will focus on improving the onboard inference speed and miniaturization of the mechatronic components.
Resolving spatiotemporal electrical signaling within the islet via CMOS microelectrode arrays
Authors: Gresch Anne , Hüwel Jan D. , Briggs Jennifer , Berger Tim , Koch Ruben , Deickert Thomas , Beecks Christian , Benninger Richard , Düfer Martina 
Published: October 2023

AbstractGlucose-stimulated beta-cells synchronize calcium waves across the islet to recruit more beta-cells for insulin secretion. Compared to calcium dynamics, the formation and cell-to-cell propagation of electrical signals within the islet are poorly characterized. To determine factors that influence the propagation of electrical activity across the islet underlying calcium oscillations and beta-cell synchronization, we used high-resolution CMOS multielectrode arrays (MEA) to measure voltage changes associated with the membrane potential of individual cells within intact mouse islets. We measured both fast (milliseconds, spikes) and slow (seconds, waves) voltage changes and analyzed the spatiotemporal voltage dynamics. Treatment of islets from C57BL6 mice with increasing glucose concentrations revealed that single spike activity and wave signal velocity were both glucose-dependent. A repeated glucose stimulus involved a highly active subset of cells in terms of spike activity. When islets were pretreated for 72 hours with glucolipotoxic medium, the wave velocity was significantly reduced. Network analysis confirmed that the synchrony of islet cells was affected due to slower propagating electrical waves and not due to altered spike activity. In summary, this approach provided novel insight regarding the propagation of electrical activity and opens a wide field for further studies on signal transduction in the islet cell network.Article HighlightsThis study presents a new method for characterizing islet spatiotemporal electrical dynamics and subpopulations of beta-cells. We asked whether a high-resolution CMOS-MEA is suited to detect electrical signals on a level close to single cells, and whether we can track the propagation of electrical activity through the islet on a cellular scale. A highly active subpopulation of islet cells was identified by action potential-like spike activity, whereas slower waves were a measure for synchronized electrical activity. Further, propagating waves were slowed by glucolipotoxicity. The technique is a useful tool for exploring the pancreatic islet network in health and disease.
DAP12 deficiency alters microglia-oligodendrocyte communication and enhances resilience against tau toxicity
Authors: Chen Hao , Fan Li , Guo Qi , Wong Man Ying , Yu Fangmin , Foxe Nessa , Wang Winston , Nessim Aviram , Carling Gillian , Liu Bangyan , Lopez-Lee Chloe , Huang Yige , Amin Sadaf , Patel Tark , Mok Sue-Ann , Song Won-min , Zhang Bin , Ma Qin , Fu Hongjun , Gan Li , Luo Wenjie 
Published: October 2023

AbstractPathogenic tau accumulation fuels neurodegeneration in Alzheimer’s disease (AD). Enhancing aging brain’s resilience to tau pathology would lead to novel therapeutic strategies. DAP12 (DNAX-activation protein 12) is critically involved in microglial immune responses. Previous studies have showed that mice lacking DAP12 in tauopathy mice exhibit higher tau pathology but are protected from tau-induced cognitive deficits. However, the exact mechanism remains elusive. Our current study uncovers a novel resilience mechanism via microglial interaction with oligodendrocytes. Despite higher tau inclusions, Dap12 deletion curbs tau-induced brain inflammation and ameliorates myelin and synapse loss. Specifically, removal of Dap12 abolished tau-induced disease-associated clusters in microglia (MG) and intermediate oligodendrocytes (iOli), which are spatially correlated with tau pathology in AD brains. Our study highlights the critical role of interactions between microglia and oligodendrocytes in tau toxicity and DAP12 signaling as a promising target for enhancing resilience in AD.
Integration of QTL and transcriptome approaches for the identification of genes involved in tomato response to nitrogen deficiency
Authors: Desaint H. , Héreil A. , Belinchon-Moreno J. , Carretero Y. , Pelpoir E. , Pascal M. , Brault M , Dumont D. , Lecompte F. , Laugier P. , Duboscq R. , Bitton F. , Grumic M. , Giraud C. , Ferrante P. , Giuliano G , Sunseri F. , Causse M. 
Published: October 2023

AbstractOptimising plant nitrogen (N) usage and inhibiting N leaching loss in the soil-crop system is crucial to maintain crop yield and reduce environmental pollution. This study aimed at identifying quantitative trait loci (QTL) and differential expressed genes (DEGs) between two N treatments in order to list candidate genes related to nitrogen-related contrasting traits in tomato varieties. We characterised a genetic diversity core-collection (CC) and a multi-parental advanced generation intercross (MAGIC) tomato population grown in greenhouse under two nitrogen levels and assessed several N-related traits and mapped QTLs. Transcriptome response under the two N conditions was also investigated through RNA sequencing of fruit and leaves in four parents of the MAGIC population.Significant differences in response to N input reduction were observed at the phenotypic level for biomass and N-related traits. Twenty-seven (27) QTLs were detected for three target traits (Leaf N content, leaf Nitrogen Balance Index and petiole NO3-content), ten and six at low and high N condition, respectively; while 19 QTLs were identified for plasticity traits. At the transcriptome level, 4,752 and 2,405 DEGs were detected between the two N conditions in leaves and fruits, respectively, among which 3,628 (50.6%) in leaves and 1,717 (71.4%) in fruit were genotype specific. When considering all the genotypes, 1,677 DEGs were shared between organs or tissues.Finally, we integrated DEGs and QTLs analyses to identify the most promising candidate genes. The results highlighted a complex genetic architecture of N homeostasis in tomato and novel putative genes useful for breeding improved-NUE tomato.HighlightTomato response to nitrogen deficiency is genetically controlled by a few QTLs and impacts the expression of a large number of genes, among which some are good targets for breeding sober varieties.
Systematic transcriptomics analysis of calorie restriction and rapamycin unveils their synergistic interaction in prolonging cellular lifespan
Authors: Zhang Yizhong , Naaz Arshia , Cheng Trishia Yi Ning , Lin Jovian Jing , Alfatah Mohammad 
Published: October 2023

AbstractAging is a multifaceted biological process marked by the decline in both mitotic and postmitotic cellular function, often central to the development of age-related diseases. In the pursuit of slowing or even reversing the aging process, a prominent strategy of significant interest is calorie restriction (CR), also known as dietary restriction, and the potential influence of a drug called rapamycin (RM). Both CR and RM have demonstrated the capacity to extend healthspan and lifespan across a diverse array of species, including yeast, worms, flies, and mice. Nevertheless, their individual and combined effects on mitotic and postmitotic cells, as well as their comparative analysis, remain areas that demand a thorough investigation. In this study, we employ RNA-sequencing methodologies to comprehensively analyze the impact of CR, RM, and their combination (CR+RM) on gene expression in yeast cells. Our analysis uncovers distinctive, overlapping, and even contrasting patterns of gene regulation, illuminating the unique and shared effects of CR and RM. Most notably, our findings reveal a synergistic effect of CR+RM in extending the lifespan of postmitotic cells, a result validated in both yeast and human cells. This research offers valuable insights into the processes of aging and presents potential strategies for enhancing healthspan and delaying the onset of age-related diseases. These findings have the potential to revolutionize our approach to implementing these interventions under specific conditions and within the context of age-related diseases.
Single-nucleus RNA sequencing provides insights into the GL261-GSC syngeneic mouse model of glioblastoma
Authors: García-Vicente Laura , Borja Michael , Tran Vanessa , Álvarez-Vázquez Andrea , Flores-Hernández Raquel , Granados Alejandro , McGeever Aaron , Kim Yang-Joon , Dorman Leah , Detweiler Angela , Mekonen Honey , Paul Sheryl , Pisco Angela O , Neff Norma F , Tabernero Arantxa 
Published: October 2023

AbstractGlioblastoma (GBM) is an aggressive tumor with very bad prognosis. The urgent need to find new effective therapies is challenged by the unique characteristics of GBM, including high intra and intertumoral heterogeneity. Using single-nucleus transcriptomics (snRNA-seq), we characterized the panorama of a preclinical immunocompetent murine model based in the implantation of mouse glioblastoma stem cells (GL261-GSCs) into the brain parenchyma. Additionally, we performed Visium spatial transcriptomics in the in vivo model to confirm the location of annotated cells. To understand the technical bias of this approach, we performed two scRNA-seq methods in GBM cells. We thoroughly characterized the tumor microenvironment (TME) at early and late stages of tumor development and upon treatment with temozolomide (TMZ), the standard of care for patients with GBM, and with Tat-Cx43266-283, a promising experimental treatment. We identified prominent GBM targets that can be addressed using this preclinical model, such asGrik2,Nlgn3,Gap43orKcnn4, which are involved in electrical and synaptic integration of GBM cells into neural circuits, as well as the expression ofNt5e,Cd274orIrf8, which indicates the development of immune evasive properties in these GBM cells. In agreement, snRNA-seq unveiled high expression of several immunosuppressive-associated molecules in immune cells, such asCsf1r, Arg1, Mrc1andTgfb1, suggesting the development of an immunosuppressive microenvironment. We also show the landscape of cytokines, cytokine receptors, checkpoint ligands and receptors in tumor and TME cells, which are crucial data for a rational design of immunotherapy studies. Thus, Mrc1, PD-L1, TIM-3 or B7-H3 are among the immunotherapy targets that can be addressed in this model. Finally, the comparison of the preclinical GL261-GSC GBM model with human GBM subtypes unveiled important similarities with the recently identified TMEmed human GBM, indicating that preclinical data obtained in GL261-GSC GBM model might be applied to TMEmed human GBM, improving patient stratification in clinical trials. In conclusion, this work provides crucial information for future preclinical studies in GBM improving their clinical application.
Thalamocortical Spindles occur during Rapid Eye Movement Sleep in Mouse Somatosensory Pathway
Authors: Boscher Flore , Jumel Katlyn , Dvořáková Tereza , Gentet Luc , Urbain Nadia 
Published: October 2023

SUMMARYRapid eye movement sleep (REM) is often considered as a homogeneous state of sleep. However, the frequent occurrence of transient events indicates that it may be separated into two distinct, phasic and tonic, substates. During tonic REM, we found local appearances of spindle waves in the barrel cortex concomitant with strong delta power on the local field potential. Subthreshold spindle oscillations in neurons of the ventral posterior medial nucleus further confirmed the thalamic origin of these cortical spindles. Spindle oscillations were suppressed in phasic REM, while thalamus spike firing increased associated with rapid whisker movements of mice and cortical activity transitioned to an activated state. During REM, sensory thalamus and barrel cortex therefore alternate between high (wake-like) and low (non-REM sleep-like) activation states, possibly allowing transient sensory integration windows to emerge throughout this paradoxical sleep stage.