bluuebunny/crossref_metadata_2025_split huggingface dataset:
Patients With Post–COVID-19 Respiratory Condition: Chest Computed Tomography Findings and Pulmonary Function Tests and Comparison With Asymptomatic Participants
Authors: Ufuk Furkan , Yitik Ahmet Yasin , Sarilar Burak , Altinisik Goksel 
Published: January 2024

Objective
The aims of this study were to assess the chest computed tomography (CT) findings in post–COVID-19 respiratory condition (rPCC) patients and compare the findings with asymptomatic participants (APs). It also aimed to evaluate the relationship between CT findings and pulmonary function tests (PFTs) in rPCC patients. Finally, it aimed to compare the quantitative chest CT findings and PFT results of patients with rPCC and APs.

Methods
We retrospectively enrolled consecutive patients with rPCC who underwent unenhanced chest CT and PFTs between June 2020 and September 2022. In addition, a control group (APs) was prospectively formed and underwent nonenhanced chest CT and PFTs. The presence and extent of abnormalities in unenhanced chest CT images were evaluated qualitatively and semiquantitatively in a blinded manner. We used fully automatic software for automatic lung and airway segmentation and quantitative analyses.

Results
Sixty-three patients with rPCC and 23 APs were investigated. Reticulation/interstitial thickening and extent of parenchymal abnormalities on CT were significantly greater in the rPCC group than in the control group (P = 0.001 and P = 0.004, respectively). Computed tomography extent score was significantly related to length of hospital stay, age, and intensive care unit stay (all Ps ≤ 0.006). The rPCC group also had a lower 85th percentile attenuation lung volume (P = 0.037). The extent of parenchymal abnormalities was significantly correlated with carbon monoxide diffusing capacity (r = −0.406, P = 0.001), forced vital capacity (FVC) (r = −0.342, P = 0.002), and forced expiratory volume in 1 second/FVC (r = 0.427, P < 0.001) values. Pulmonary function tests revealed significantly lower carbon monoxide diffusing capacity (P < 0.001), FVC (P = 0.036), and total lung capacity (P < 0.001) values in the rPCC group.

Conclusions
The rPCC is characterized by impaired PFTs, a greater extent of lung abnormalities on CT, and decreased 85th percentile attenuation lung volume. Advanced age, intensive care unit admission history, and extended hospital stay are risk factors for chest CT abnormalities.
Prototype Description and Ex Vivo Evaluation of a System for Combined Endorectal Magnetic Resonance Imaging and In-Bore Biopsy of the Prostate
Authors: Coakley Fergus V. , Foster Bryan R. , Schroeder David W. , Rooney William D. , Jones Randall W. , Amling Christopher L. 
Published: January 2024

Abstract
We describe early ex vivo proof-of-concept testing of a novel system composed of a disposable endorectal coil and converging multichannel needle guide with a reusable clamp stand, embedded electronics, and baseplate to allow for endorectal magnetic resonance (MR) imaging and in-bore MRI-targeted biopsy of the prostate as a single integrated procedure. Using prostate phantoms imaged with standard T2-weighted sequences in a Siemens 3T Prisma MR scanner, we measured the signal-to-noise ratio in successive 1-cm distances from the novel coil and from a commercially available inflatable balloon coil and measured the lateral and longitudinal deviation of the tip of a deployed MR compatible needle from the intended target point. Signal-to-noise ratio obtained with the novel system was significantly better than the inflatable balloon coil at each of five 1-cm intervals, with a mean improvement of 78% (P < 0.05). In a representative sampling of 15 guidance channels, the mean lateral deviation for MR imaging–guided needle positioning was 1.7 mm and the mean longitudinal deviation was 2.0 mm. Our ex vivo results suggest that our novel system provides significantly improved signal-to-noise ratio when compared with an inflatable balloon coil and is capable of accurate MRI-guided needle deployment.
Visualization of Renal Glomeruli in Human Native Kidneys With Sensing Ultrasound Localization Microscopy
Authors: Bodard Sylvain , Denis Louise , Chabouh Georges , Battaglia Jacques , Anglicheau Dany , Hélénon Olivier , Correas Jean-Michel , Couture Olivier 
Published: January 2024

Objectives
Kidney diseases significantly impact individuals' quality of life and strongly reduce life expectancy. Glomeruli play a crucial role in kidney function. Current imaging techniques cannot visualize them due to their small size. Sensing ultrasound localization microscopy (sULM) has shown promising results for visualizing in vivo the glomeruli of human kidney grafts. This study aimed to evaluate the ability of sULM to visualize glomeruli in vivo in native human kidneys despite their depth and a shorter duration of ultrasound acquisition limited by the period of the patient's apnea. Sensing ultrasound localization microscopy parameters in native kidneys and kidney grafts and their consequence regarding glomeruli detection were also compared.

Materials and Methods
Exploration by sULM was conducted in 15 patients with native kidneys and 5 with kidney allografts. Glomeruli were counted using a normalized distance metric projected onto sULM density maps. The difference in the acquisition time, the kidney depth, and the frame rate between native kidneys and kidney grafts and their consequence regarding glomeruli detection were assessed.

Results
Glomerular visualization was achieved in 12 of 15 patients with native kidneys. It failed due to impossible breath-holding for 2 patients and a too-deep kidney for 1 patient. Sensing ultrasound localization microscopy found 16 glomeruli per square centimeter in the native kidneys (6–31) and 33 glomeruli per square centimeter in kidney transplant patients (18–55).

Conclusions
This study demonstrated that sULM can visualize glomeruli in native human kidneys in vivo. The proposed method may have many hypothetical applications, including biomarker development, assisting biopsy, or potentially avoiding it. It establishes a framework for improving the detection of local microstructural pathology, influencing the evaluation of allografts, and facilitating disease monitoring in the native kidney.
Characterizing CSNK2A1 Mutant-Induced Morphological Phenotypes in Zebrafish (Danio rerio): Insights into Okur-Chung Neurodevelopmental Syndrome (OCNDS)
Authors: Hassett Katie , Potu Sai Srihaas , Sankaramoorthy Aravind , Kaneshamoorthy Sukanniya , Leka Kamawela , Huentelman Matthew J. , Narayanan Vinodh , Rangasamy Sampath 
Published: January 2024

AbstractOkur-Chung Neurodevelopmental Syndrome (OCNDS) is a rare, autosomal dominant disorder caused by heterozygous pathogenic variants in the CSNK2A1 gene. CSNK2A1 encodes the α subunit of protein kinase CK2, involved in diverse biological processes. In 2016, Okur et al. reported the discovery of germlinede novomissense and canonical splice site mutations in CSNK2A1 in five female patients with OCNDS. The syndrome is characterized by developmental delays, intellectual disability, hypotonia, feeding difficulties, dysmorphic facial features, and disrupted circadian rhythms, leading to sleep disturbances. The complex phenotypic spectrum of OCNDS underscores the need for robust model systems to investigate genotype-phenotype correlations, disease mechanisms, and potential therapies. In this study, we employed an overexpression strategy in a zebrafish model to investigate the functional consequences of select CSNK2A1 variants implicated in OCNDS. Our findings revealed distinct morphological phenotypes resulting from the overexpression of different CSNK2A1 mutants, indicating a direct correlation between genetic alterations and phenotypic manifestations. Notably, the CSNK2A1 p.Arg191Ter (R191X) mutation had a significant impact on the phenotype. Co-injection of wild-type CSNK2A1 mRNA with mutant CSNK2A1 mRNA rescued morphological abnormalities in zebrafish embryos. Overall our study highlights the utility of zebrafish as an adaptable model system for examining the functional impact of CSNK2A1 mutations and exploring novel therapeutic avenues.
Developing and evaluating a brief, socially primed video intervention to enable bystander cardiopulmonary resuscitation: A randomised control trial
Authors: Skelton Jean , Templeton Anne , Guay Jennifer Dang , MacInnes Lisa , Clegg Gareth 
Published: January 2024

AbstractBackgroundOver 30,000 people experience out-of-hospital cardiac arrest in the United Kingdom annually, with only 7-8% of patients surviving. One of the most effective methods of improving survival outcomes is prompt bystander intervention in the form of calling the emergency services and initiating chest compressions, also known as CPR. Additionally, the public must feel empowered to take action and use this knowledge in an emergency. This study aimed to evaluate an ultra-brief CPR familiarisation video that uses empowering social priming language to frame CPR as a norm in Scotland.MethodsIn a randomised control trial, participants (n= 86) were assigned to view either an ultra-brief CPR video intervention or a traditional long form CPR video intervention. Following completion of a pre-intervention questionnaire examining demographic variables and prior CPR knowledge, participants completed an emergency services-led resuscitation simulation in a portable simulation suite using a CPR manikin that measures resuscitation quality. Participants then completed questionnaires examining social identity and attitudes towards performing CPR.ResultsAside from the CPR quality metrics of time carrying out CPR chest compressions (where the ultra-brief video condition scored higher scores) and average compressions per minute (where the long form video condition scored higher scores), there were no significant differences in CPR quality between the two conditions. Regarding the social identity measures, participants in the ultra-brief video condition scored higher on measures of “shared social identity with the video instructor” and “expected emergency support from other Scottish people”. There were no significant group differences in attitudes towards performing CPR.ConclusionsUltra-brief CPR video interventions hold promise as a method of equipping the public with basic resuscitation skills and empowering the viewer to intervene in an emergency. These interventions may be an effective avenue for equipping at-risk groups with resuscitation skills and for supplementing traditional resuscitation training courses.
Extracting interpretable signatures of whole-brain dynamics through systematic comparison
Authors: Bryant Annie G. , Aquino Kevin , Parkes Linden , Fornito Alex , Fulcher Ben D. 
Published: January 2024

AbstractThe brain’s complex distributed dynamics are typically quantified using a limited set of manually selected statistical properties, leaving the possibility that alternative dynamical properties may outperform those reported for a given application. Here, we address this limitation by systematically comparing diverse, interpretable features of both intra-regional activity and inter-regional functional coupling from resting-state functional magnetic resonance imaging (rs-fMRI) data, demonstrating our method using case–control comparisons of four neuropsychiatric disorders. Our findings generally support the use of linear time-series analysis techniques for rs-fMRI case–control analyses, while also identifying new ways to quantify informative dynamical fMRI structures. While simple statistical representations of fMRI dynamics performed surprisingly well (e.g., properties within a single brain region), combining intra-regional properties with inter-regional coupling generally improved performance, underscoring the distributed, multifaceted changes to fMRI dynamics in neuropsychiatric disorders. The comprehensive, data-driven method introduced here enables systematic identification and interpretation of quantitative dynamical signatures of multivariate time-series data, with applicability beyond neuroimaging to diverse scientific problems involving complex time-varying systems.
Human neural rosettes secrete bioactive extracellular vesicles enriched in neuronal and glial cellular components
Authors: Lopez Malena Herrera , Arolfo Matías Bertone , Remedi Mónica , Gastaldi Laura , Wilson Carlos , Guendulain Gonzalo G. , Ceschin Danilo , Gizzi Andrés Cardozo , Cáceres Alfredo , Moyano Ana Lis 
Published: January 2024

AbstractExtracellular vesicles (EVs) play a critical role in the development of neural cells in the central nervous system (CNS). Human neural rosettes (hNRs) are radial cell structures that assemble from induced pluripotent stem cells (hiPSCs) and recapitulate some stages of neural tube morphogenesis. Here we show that hiPSCs and hNRs secrete EVs (hiPSC-EVs and hNR-EVs) with distinct protein cargoes. Remarkably, hNR-EVs carry neuronal and glial cellular components involved in CNS development. Byin silicoanalysis, we found hNR-EVs protein signature is expressedin vivoandin vitroduring human brain development. Importantly, hNR-EVs stimulate hiPSCs to change their cellular morphology with a significant reduction in the pluripotency regulator SOX2. Interestingly, these effects were inhibited by antibodies against an unexpected neuroglial cargo of hNR-EVs: the major proteolipid protein (PLP1). These findings show that hNRs secrete bioactive EVs containing neural components and might contribute as trophic factors during human CNS development.
Neural Ensembles in the Lateral Prefrontal Cortex Temporally Multiplex Task Features During Virtual Navigation
Authors: Abbass Mohamad , Corrigan Benjamin , Johnston Renée , Gulli Roberto , Sachs Adam , Lau Jonathan C. , Martinez-Trujillo Julio 
Published: January 2024

AbstractNeuronal populations can expand their information encoding capacity using mixed selective neurons. This is particularly prominent in association areas such as the Lateral Prefrontal Cortex (LPFC) that integrate information from multiple sensory systems. During naturalistic conditions where subjects have agency, it is unclear how LPFC neuronal ensembles process space and time varying information. Here we show that during a virtual navigation task that requires associative memory and decision making, individual neurons and neuronal ensembles in the LPFC time-multiplex their selectivity for different task features to fluidly encode the temporal contingencies of the task and the animal’s choice. Neurons in ventral regions showed more selectivity for non-spatial features, while dorsal regions showed selectivity for space and eye movements. These results demonstrate that during naturalistic tasks with fluid scenery and spatiotemporal dynamics, LPFC neurons and neuronal ensembles time-multiplex the components of their selectivity, expanding the spatiotemporal capacity of their neural codes.
USP50 suppresses alternative RecQ helicase use and deleterious DNA2 activity during replication
Authors: Mackay Hannah L. , Stone Helen R. , Ellis Katherine , Ronson George E. , Walker Alexandra K. , Starowicz Katarzyna , Garvin Alexander J. , van Eijk Patrick , Vaitsiankova Alina , Vijayendran Sobana , Beesley James F. , Petermann Eva , Brown Eric J. , Densham Ruth M. , Reed Simon H. , Dobbs Felix , Saponaro Marco , Morris Joanna R. 
Published: January 2024

AbstractMammalian DNA replication employs several RecQ DNA helicases to orchestrate the faithful duplication of genetic information. Helicase function is often coupled to the activity of specific nucleases, but how helicase and nuclease activities are co-directed is unclear. Here we identify the inactive ubiquitin-specific protease, USP50, as a ubiquitin-binding and chromatin-associated protein required for ongoing replication, fork restart, telomere maintenance and cellular survival during replicative stress. USP50 supports WRN:FEN1 at stalled replication forks, suppresses MUS81-dependent fork collapse and restricts double-strand DNA breaks at GC-rich sequences. Surprisingly we find that cells depleted for USP50 and recovering from a replication block exhibit increased DNA2 and RECQL4 foci and that the defects in ongoing replication, poor fork restart and increased fork collapse seen in these cells are mediated by DNA2, RECQL4 and RECQL5. These data define a novel ubiquitin-dependent pathway that promotes the balance of helicase: nuclease use at ongoing and stalled replication forks.
Chemogenetic attenuation of PFC pyramidal neurons restores deficits in recognition memory following adolescent NMDA receptor blockade
Authors: Bauminger Hagar , Chandran Sailendrakumar Kolatt , Akirav Irit , Gaisler-Salomon Inna 
Published: January 2024

AbstractDuring adolescence, the prefrontal cortex (PFC) undergoes dramatic developmental changes, including fine-tuning the balance between excitatory glutamate and inhibitory GABA transmission (i.e., the E/I balance). This process is critical for intact cognitive function and social behavior in adulthood, and its disruption is associated with several psychiatric disorders including schizophrenia (SZ). While acute NMDA receptor (NMDAr) blockade leads to excess glutamate transmission in the PFC, the long-term consequences of MK-801 administration during early adolescence on the E/I balance in adulthood have not been extensively studied. In the current study, we show that chronic MK-801 administration during early adolescence leads to abnormalities in recognition memory and social behavior as well as reduced frequency of miniature inhibitory post-synaptic currents (mIPSCs) in mPFC of adult male rats, with no change in excitatory currents or basal activity. We further show that chemogenetic attenuation of prelimbic mPFC pyramidal neurons reversed deficits in recognition memory, but not social behavior. These findings emphasize the critical role played by NMDAr during adolescence on the E/I balance as well as cognition and social function in adulthood. Moreover, these findings implicate the therapeutic outcomes of reduced mPFC pyramidal neuron activity in recognition memory deficits in early-adolescence MK-801-treated rats. Since recognition memory deficits are key components of the cognitive deficits in SZ, these findings suggest that the future development of treatments aimed at alleviating the cognitive deficits in SZ should focus on regulating the prefrontal E/I balance.
Developmental toxicity of pre-production plastic pellets affects a large swathe of invertebrate taxa
Authors: Jimenez-Guri Eva , Paganos Periklis , Vecchia Claudia La , Annona Giovanni , Caccavale Filomena , Molina Maria Dolores , Ferrández-Roldán Alfonso , Donnellan Rory Daniel , Salatiello Federica , Johnstone Adam , Eliso Maria Concetta , Spagnuolo Antonietta , Cañestro Cristian , Albalat Ricard , Martín-Durán José María , Williams Elizabeth A. , D’Aniello Enrico , Arnone Maria Ina 
Published: January 2024

AbstractMicroplastics pose risks to marine organisms through ingestion, entanglement, and as carriers of toxic additives and environmental pollutants. Plastic pre-production pellet leachates have been shown to affect the development of sea urchins and, to some extent, mussels. The extent of those developmental effects on other animal phyla remains unknown. Here, we test the toxicity of environmental mixed nurdle samples and new PVC pellets for the embryonic development or asexual reproduction by regeneration of animals from all the major animal superphyla (Lophotrochozoa, Ecdysozoa, Deuterostomia and Cnidaria). Our results show diverse, concentration-dependent impacts in all the species sampled for new pellets, and for molluscs and deuterostomes for environmental samples. Embryo axial formation, cell specification and, specially, morphogenesis seem to be the main processes affected by plastic leachate exposure. Our study serves as a proof of principle for the potentially catastrophic effects that increasing plastic concentrations in the oceans and other ecosystems can have across animal populations from all major animal superphyla.
A quantitative description of light-limited cyanobacterial growth using flux balance analysis
Authors: Höper R. , Komkova D. , Zavřel T. , Steuer R. 
Published: January 2024

AbstractThe metabolism of phototrophic cyanobacterial is an integral part of global biogeochemical cycles, and the capability of cyanobacteria to assimilate atmospheric CO2into organic carbon has manifold potential applications for a sustainable biotechnology. To elucidate the properties of cyanobacterial metabolism and growth, computational reconstructions of the genome-scale metabolic networks play an increasingly important role. Here, we present an updated reconstruction of the metabolic network of the cyanobacteriumSynechocystissp. PCC 6803 and its analysis using flux balance analysis (FBA). To overcome limitations of conventional FBA, and to allow for the integration of quantitative experimental analyses, we develop a novel approach to describe light absorption and light utilization. Our approach incorporates photoinhibition and a variable quantum yield into the constraint-based description of light-limited phototrophic growth. We show that the resulting model is capable to predict quantitative properties of cyanobacterial growth, including photosynthetic oxygen evolution and the ATP/NADPH ratio required for growth and cellular maintenance. Our approach retains the computational and conceptual simplicity of FBA and is readily applicable to other phototropic microorganisms.
DNA methylation patterns in the frontal lobe white matter of multiple system atrophy, Parkinson’s disease, and progressive supranuclear palsy: A cross-comparative investigation
Authors: Murthy Megha , Fodder Katherine , Miki Yasuo , Rambarack Naiomi , De Pablo Fernandez Eduardo , Mill Jonathan , Warner Thomas T , Lashley Tammaryn , Bettencourt Conceição 
Published: January 2024

AbstractMultiple system atrophy (MSA) is a rare neurodegenerative disease characterized by neuronal loss and gliosis, with oligodendroglial cytoplasmic inclusions (GCI’s) containing α-synuclein being the primary pathological hallmark. Clinical presentations of MSA overlap with other parkinsonian disorders such as Parkinson’s disease (PD), dementia with Lewy bodies (DLB), and progressive supranuclear palsy (PSP), posing challenges in early diagnosis. Numerous studies have reported perturbations in DNA methylation in neurodegenerative diseases, with candidate loci being identified in various parkinsonian disorders including MSA, PD, and PSP. Although MSA and PSP present with substantial white matter pathology, alterations in white matter have also been reported in PD. However, studies comparing the DNA methylation architectures of white matter in these diseases are lacking. We therefore aimed to investigate three parkinsonian diseases, MSA, PD, and PSP, to identify shared and disease-specific DNA methylation alterations in white matter. Genome-wide DNA methylation profiling of frontal lobe white matter of individuals with MSA (n=17), PD (n=17), and PSP (n=16) and controls (n=15), using the Illumina EPIC array, revealed substantial commonalities in DNA methylation perturbations in MSA, PD, and PSP. We further used weighted gene correlation network analysis to identify disease-associated co-methylation signatures and identified dysregulation in processes relating to Wnt signalling, signal transduction, endoplasmic reticulum stress, mitochondrial processes, RNA interference, and endosomal transport. Our results highlight several shared DNA methylation perturbations and pathways indicative of converging molecular mechanisms contributing towards neurodegeneration in the white matter of all three parkinsonian diseases.