bluuebunny/crossref_metadata_2025_split huggingface dataset:
Ripa-56 protects retinal ganglion cells in glutamate-induced retinal excitotoxic model of glaucoma
Authors: Feng Lemeng , Dai Shirui , Zhang Cheng , Zhang Wulong , Zhu Weiming , Wang Chao , He Ye , Song Weitao 
Published: February 2024

AbstractGlaucoma is a prevalent cause of blindness globally, characterized by the progressive degeneration of retinal ganglion cells (RGCs). Among various factors, glutamate excitotoxicity stands out as a significant contributor of RGCs loss in glaucoma. Our study focused on Ripa-56 and its protective effect against NMDA-induced retinal damage in mice, aiming to delve into the potential underlying mechanism. The R28 cells were categorized into four groups: glutamate (Glu), Glu + Ripa-56, Ripa-56 and Control group. After 24 h of treatment, cell death was assessed by PI / Hoechst staining. Mitochondrial membrane potential changes, apoptosis and reactive oxygen species (ROS) production were analyzed using flow cytometry. The alterations in the expression of RIP-1, p-MLKL, Bcl-2, BAX, Caspase-3, Gpx4 and SLC7A11 were examined using western blot analysis. C57BL/6j mice were randomly divided into NMDA, NMDA + Ripa-56, Ripa-56 and control groups. Histological changes in the retina were evaluated using hematoxylin and eosin (H&E) staining. RGCs survival and the protein expression changes of RIP-1, Caspase-3, Bcl-2, Gpx4 and SLC7A11 were observed using immunofluorescence. Ripa-56 exhibited a significant reduction in the levels of RIP-1, p-MLKL, Caspase-3, and BAX induced by glutamate, while promoting the expression of Bcl-2, Gpx-4, and SLC7A1 in the Ripa-56-treated group. In our study, using an NMDA-induced normal tension glaucoma mice model, we employed immunofluorescence and H&E staining to observe that Ripa-56 treatment effectively ameliorated retinal ganglion cell loss, mitigating the decrease in retinal ganglion cell layer and bipolar cell layer thickness caused by NMDA. In this study, we have observed that Ripa-56 possesses remarkable anti- necroptotic, anti-apoptotic and anti-ferroptosis properties. It demonstrates the ability to combat not only glutamate-induced excitotoxicity in R28 cells, but also NMDA-induced retinal excitotoxicity in mice. Therefore, Ripa-56 could be used as a potential retinal protective agent.
Iron-based compounds coordinated with phospho-polymers as biocompatible probes for dual 31P/1H magnetic resonance imaging and spectroscopy
Authors: Kracíková Lucie , Androvič Ladislav , Červený David , Jirát-Ziółkowska Natalia , Babič Michal , Švábová Monika , Jirák Daniel , Laga Richard 
Published: February 2024

AbstractIn this work, we present the synthesis and evaluation of magnetic resonance (MR) properties of novel phosphorus/iron-containing probes for dual 31P and 1H MR imaging and spectroscopy (MRI and MRS). The presented probes are composed of biocompatible semitelechelic and multivalent phospho-polymers based on poly(2-methacryloyloxyethyl phosphorylcholine) (pMPC) coordinated with small paramagnetic Fe3+ ions or superparamagnetic maghemite (γ-Fe2O3) nanoparticles via deferoxamine group linked to the end or along the polymer chains. All probes provided very short 1H T1 and T2 relaxation times even at low iron concentrations. The presence of iron had a significant impact on the shortening of 31P relaxation, with the effect being more pronounced for probes based on γ-Fe2O3 and multivalent polymer. While the water-soluble probe having one Fe3+ ion per polymer chain was satisfactorily visualized by both 31P-MRS and 31P-MRI, the probe with multiple Fe3+ ions could only be detected by 31P-MRS, and the probes consisting of γ-Fe2O3 nanoparticles could not be imaged by either technique due to their ultra-short 31P relaxations. In this proof-of-principle study performed on phantoms at a clinically relevant magnetic fields, we demonstrated how the different forms and concentrations of iron affect both the 1H MR signal of the surrounding water molecules and the 31P MR signal of the phospho-polymer probe. Thus, this double contrast can be exploited to simultaneously visualize body anatomy and monitor probe biodistribution.
Evolutionary origin and distribution of amino acid mutations associated with resistance to sodium channel modulators in onion thrips, Thrips tabaci
Authors: Jouraku Akiya , Tomizawa Yui , Watanabe Kazuki , Yamada Kiyoshi , Kuwazaki Seigo , Aizawa Misato , Toda Satoshi , Sonoda Shoji 
Published: February 2024

AbstractIn onion thrips Thrips tabaci, reduced sensitivity of the sodium channel caused by several sodium channel mutations have been correlated with pyrethroid resistance. For this study, using mitochondrial cytochrome c oxidase subunit I gene sequences, we examined the phylogenetic relation among a total of 52 thelytokous and arrhenotokous strains with different genotypes of the sodium channel mutations. Then, we used flow cytometry to estimate their ploidy. Results showed that the strains are divisible into three groups: diploid thelytoky, triploid thelytoky, and diploid arrhenotoky. Using 23 whole genome resequencing data obtained from 20 strains out of 52, we examined their genetic relation further using principal component analysis, admixture analysis, and a fixation index. Results showed that diploid and triploid thelytokous groups are further classifiable into two based on the sodium channel mutations harbored by the respective group members (strains). The greatest genetic divergence was observed between thelytokous and arrhenotokous groups with a pair of T929I and K1774N. Nevertheless, they shared a genomic region with virtually no polymorphism around the sodium channel gene loci, suggesting a hard selective sweep. Based on these findings, we discuss the evolutionary origin and distribution of the sodium channel mutations in T. tabaci.
Enhanced visualization in endoleak detection through iterative and AI-noise optimized spectral reconstructions
Authors: Kazimierczak Wojciech , Kazimierczak Natalia , Wilamowska Justyna , Wojtowicz Olaf , Nowak Ewa , Serafin Zbigniew 
Published: February 2024

AbstractTo assess the image quality parameters of dual-energy computed tomography angiography (DECTA) 40-, and 60 keV virtual monoenergetic images (VMIs) combined with deep learning-based image reconstruction model (DLM) and iterative reconstructions (IR). CT scans of 28 post EVAR patients were enrolled. The 60 s delayed phase of DECTA was evaluated. Objective [noise, contrast-to-noise ratio (CNR), signal-to-noise ratio (SNR)] and subjective (overall image quality and endoleak conspicuity – 3 blinded readers assessment) image quality analyses were performed. The following reconstructions were evaluated: VMI 40, 60 keV VMI; IR VMI 40, 60 keV; DLM VMI 40, 60 keV. The noise level of the DLM VMI images was approximately 50% lower than that of VMI reconstruction. The highest CNR and SNR values were measured in VMI DLM images. The mean CNR in endoleak in 40 keV was accounted for as 1.83 ± 1.2; 2.07 ± 2.02; 3.6 ± 3.26 in VMI, VMI IR, and VMI DLM, respectively. The DLM algorithm significantly reduced noise and increased lesion conspicuity, resulting in higher objective and subjective image quality compared to other reconstruction techniques. The application of DLM algorithms to low-energy VMIs significantly enhances the diagnostic value of DECTA in evaluating endoleaks. DLM reconstructions surpass traditional VMIs and IR in terms of image quality.
In-vivo and in-vitro wound healing and tissue repair effect of Trametes versicolor polysaccharide extract
Authors: Teymoorian Seyedeh Kiana , Nouri Hoda , Moghimi Hamid 
Published: February 2024

AbstractRegarding different medical benefits of fungi, using the medical mushroom extracts as wound-healing agents is gaining popularity. This study, evaluated the wound healing characteristics of Trametes versicolor. Anti-oxidant activity addressed by employing the DPPH (2,2-diphenyl-1-picrylhydrazyl) assay resulting 53.7% inhibitory effect. Besides, for anti-microbial ability determination, the MIC (Minimum Inhibitory Concentration) of extract measured which Escherichia coli growth was inhibited at 1.1 mg/ml, and Staphylococcus aureus did not grow at 4.38 mg/ml of extract. The MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) method indicated dose dependence of the extract with 63 ± 3% and 28 ± 3% viability at 1250 μg/ml and 156.25 μg/ml of extract, which higher concentration caused higher cell viability. The outcome of gene expression analysis determined that overall expression of FGF2 (Fibroblast Growth Factor 2), IL-1β (Interleukin-1β), and TGF-β1 (Transforming Growth Factor-β1) was 4 times higher at 48 h than at 24 h in treated cells, suggesting a stimulating effect on cell growth. An in-vivo animal model suggested enhanced wound healing process after treatment with 0.01 g of extract. Furthermore, the number of fibroblasts, epidermal thickness, and collagen fiber was respectively 2, 3, and threefold higher in treated mice when compared to untreated mice. The treated wounds of mice showed 100% and 60% of untreated mice of healing within 14 days. The results of this research show promise for the fungus-based wound healing treatments, which may help with tissue regeneration and the healing of cutaneous wounds.
The Drosophila ZNRF1/2 homologue, detour, interacts with HOPS complex and regulates autophagy
Authors: Nicolson Shannon , Manning Jantina A. , Lim Yoon , Jiang Xin , Kolze Erica , Dayan Sonia , Umargamwala Ruchi , Xu Tianqi , Sandow Jarrod J. , Webb Andrew I. , Kumar Sharad , Denton Donna 
Published: February 2024

AbstractAutophagy, the process of elimination of cellular components by lysosomal degradation, is essential for animal development and homeostasis. Using the autophagy-dependent Drosophila larval midgut degradation model we identified an autophagy regulator, the RING domain ubiquitin ligase CG14435 (detour). Depletion of detour resulted in increased early-stage autophagic vesicles, premature tissue contraction, and overexpression of detour or mammalian homologues, ZNRF1 and ZNRF2, increased autophagic vesicle size. The ablation of ZNRF1 or ZNRF2 in mammalian cells increased basal autophagy. We identified detour interacting proteins including HOPS subunits, deep orange (dor/VPS18), Vacuolar protein sorting 16A (VPS16A), and light (lt/VPS41) and found that detour promotes their ubiquitination. The detour mutant accumulated autophagy-related proteins in young adults, displayed premature ageing, impaired motor function, and activation of innate immunity. Collectively, our findings suggest a role for detour in autophagy, likely through regulation of HOPS complex, with implications for healthy aging.
Reusability report: Unpaired deep-learning approaches for holographic image reconstruction
Authors: Zhang Yuhe , Ritschel Tobias , Villanueva-Perez Pablo 
Published: February 2024

AbstractDeep-learning methods using unpaired datasets hold great potential for image reconstruction, especially in biomedical imaging where obtaining paired datasets is often difficult due to practical concerns. A recent study by Lee et al. (Nature Machine Intelligence 2023) has introduced a parameterized physical model (referred to as FMGAN) using the unpaired approach for adaptive holographic imaging, which replaces the forward generator network with a physical model parameterized on the propagation distance of the probing light. FMGAN has demonstrated its capability to reconstruct the complex phase and amplitude of objects, as well as the propagation distance, even in scenarios where the object-to-sensor distance exceeds the range of the training data. We performed additional experiments to comprehensively assess FMGAN’s capabilities and limitations. As in the original paper, we compared FMGAN to two state-of-the-art unpaired methods, CycleGAN and PhaseGAN, and evaluated their robustness and adaptability under diverse conditions. Our findings highlight FMGAN’s reproducibility and generalizability when dealing with both in-distribution and out-of-distribution data, corroborating the results reported by the original authors. We also extended FMGAN with explicit forward models describing the response of specific optical systems, which improved performance when dealing with non-perfect systems. However, we observed that FMGAN encounters difficulties when explicit forward models are unavailable. In such scenarios, PhaseGAN outperformed FMGAN.
Pathophysiological profile of non-ventilated lung injury in healthy female pigs undergoing mechanical ventilation
Authors: Spinelli Elena , Damia Anna , Damarco Francesco , Gregori Beatrice , Occhipinti Federica , Busani Zara , Leali Marco , Battistin Michele , Lonati Caterina , Zhao Zhanqi , Storaci Alessandra Maria , Lopez Gianluca , Vaira Valentina , Ferrero Stefano , Rosso Lorenzo , Gatti Stefano , Mauri Tommaso 
Published: February 2024

Abstract
Background
Lung regions excluded from mechanical insufflation are traditionally assumed to be spared from ventilation-associated lung injury. However, preliminary data showed activation of potential mechanisms of injury within these non-ventilated regions (e.g., hypoperfusion, inflammation).

Methods
In the present study, we hypothesized that non-ventilated lung injury (NVLI) may develop within 24 h of unilateral mechanical ventilation in previously healthy pigs, and we performed extended pathophysiological measures to profile NVLI. We included two experimental groups undergoing exclusion of the left lung from the ventilation with two different tidal volumes (15 vs 7.5 ml/kg) and a control group on bilateral ventilation. Pathophysiological alteration including lung collapse, changes in lung perfusion, lung stress and inflammation were measured. Lung injury was quantified by histological score.

Results
Histological injury score of the non-ventilated lung is significantly higher than normally expanded lung from control animals. The histological score showed lower intermediate values (but still higher than controls) when the tidal volume distending the ventilated lung was reduced by 50%. Main pathophysiological alterations associated with NVLI were: extensive lung collapse; very low pulmonary perfusion; high inspiratory airways pressure; and higher concentrations of acute-phase inflammatory cytokines IL-6, IL-1β and TNF-α and of Angiopoietin-2 (a marker of endothelial activation) in the broncho-alveolar lavage. Only the last two alterations were mitigated by reducing tidal volume, potentially explaining partial protection.

Conclusions
Non-ventilated lung injury develops within 24 h of controlled mechanical ventilation due to multiple pathophysiological alterations, which are only partially prevented by low tidal volume.
Asymmetric cognitive learning mechanisms underlying the persistence of intergroup bias
Authors: Nafcha Orit , Hertz Uri 
Published: February 2024

AbstractIntergroup bias, the tendency to favor ingroups and be hostile towards outgroups, underlies many societal problems and persists even when intergroup members interact and share experiences. Here we study the way cognitive learning processes contribute to the persistence of intergroup bias. Participants played a game with ingroup and outgroup bot-players that entailed collecting stars and could sacrifice a move to zap another player. We found that intergroup bias persisted as participants were more likely to zap outgroup players, regardless of their zapping behavior. Using a computational model, we found that this bias was caused by asymmetries in three learning mechanisms. Participants had a greater prior bias to zap out-group players, they learned more readily about the negative behavior of out-groups and were less likely to attribute the positive behavior of one out-group player to other out-group players. Our results uncover the way cognitive social learning mechanisms shape and confound intergroup dynamics.
RAD51 restricts DNA over-replication from re-activated origins
Authors: Muñoz Sergio , Blanco-Romero Elena , González-Acosta Daniel , Rodriguez-Acebes Sara , Megías Diego , Lopes Massimo , Méndez Juan 
Published: February 2024

AbstractEukaryotic cells rely on several mechanisms to ensure that the genome is duplicated precisely once in each cell division cycle, preventing DNA over-replication and genomic instability. Most of these mechanisms limit the activity of origin licensing proteins to prevent the reactivation of origins that have already been used. Here, we have investigated whether additional controls restrict the extension of re-replicated DNA in the event of origin re-activation. In a genetic screening in cells forced to re-activate origins, we found that re-replication is limited by RAD51 and enhanced by FBH1, a RAD51 antagonist. In the presence of chromatin-bound RAD51, forks stemming from re-fired origins are slowed down, leading to frequent events of fork reversal. Eventual re-initiation of DNA synthesis mediated by PRIMPOL creates ssDNA gaps that facilitate the partial elimination of re-duplicated DNA by MRE11 exonuclease. In the absence of RAD51, these controls are abrogated and re-replication forks progress much longer than in normal conditions. Our study uncovers a safeguard mechanism to protect genome stability in the event of origin reactivation.
Shared and distinct mechanisms of UBA1 inactivation across different diseases
Authors: Collins Jason C , Magaziner Samuel J , English Maya , Hassan Bakar , Chen Xiang , Balanda Nicholas , Anderson Meghan , Lam Athena , Fernandez-Pol Sebastian , Kwong Bernice , Greenberg Peter L , Terrier Benjamin , Likhite Mary E , Kosmider Olivier , Wang Yan , Samara Nadine L , Walters Kylie J , Beck David B , Werner Achim 
Published: February 2024

AbstractMost cellular ubiquitin signaling is initiated by UBA1, which activates and transfers ubiquitin to tens of E2 enzymes. Clonally acquired UBA1 missense mutations cause an inflammatory-hematologic overlap disease called VEXAS (vacuoles, E1, X-linked, autoinflammatory, somatic) syndrome. Despite extensive clinical investigation into this lethal disease, little is known about the underlying molecular mechanisms. Here, by dissecting VEXAS-causing UBA1 mutations, we discovered that p.Met41 mutations alter cytoplasmic isoform expression, whereas other mutations reduce catalytic activity of nuclear and cytoplasmic isoforms by diverse mechanisms, including aberrant oxyester formation. Strikingly, non-p.Met41 mutations most prominently affect transthioesterification, revealing ubiquitin transfer to cytoplasmic E2 enzymes as a shared property of pathogenesis amongst different VEXAS syndrome genotypes. A similar E2 charging bottleneck exists in some lung cancer-associated UBA1 mutations, but not in spinal muscular atrophy-causing UBA1 mutations, which instead, render UBA1 thermolabile. Collectively, our results highlight the precision of conformational changes required for faithful ubiquitin transfer, define distinct and shared mechanisms of UBA1 inactivation in diverse diseases, and suggest that specific E1-E2 modules control different aspects of tissue differentiation and maintenance.
ND3$\text{D}^{3}$ QNet: Noisy dueling‐double‐deep q‐network for reconfigurable intelligent surfaces
Authors: Kim Jihyung , Kim Junghyun 
Published: February 2024

AbstractLow‐cost passive reconfigurable intelligent surfaces that provide coverage expansion in wireless communication networks are facing challenges in phase shift optimization due to limitations in acquiring channel information for sub‐channels. To overcome this, a new approach that improves both the convergence speed and overall performance relative to the existing state‐of‐the‐art scheme is proposed. Experimental results in an environment with a Rician factor of 20 showed a 9.3% increase in the average sum data rate, and the probability of the sum data rate exceeding the threshold of 10 increased by 30%.
Inflammation, Sepsis, and the Coagulation System
Authors: Kappelmayer János , Debreceni Ildikó Beke , Fejes Zsolt , Nagy Béla 
Published: February 2024

AbstractSepsis has been a major health problem for centuries and it is still the leading cause of hospital deaths. Several studies in the past decades have identified numerous biochemical abnormalities in severe cases, and many of these studies provide evidence of the perturbation of the hemostatic system. This can result in complications, such as disseminated intravascular coagulation that can lead to multiorgan failure. Nevertheless, large clinical studies have demonstrated that the simple approach of inhibiting the coagulation processes by any means fails to provide significant improvement in the survival of septic patients. A cause of this failure could be the fact that in sepsis the major clinical problems result not primarily from the presence of the infective agent or enhanced coagulation but from the complex dysregulated systemic host response to pathogens. If this overt reaction is not fully deciphered, appropriate interference is highly unlikely and any improvement by conventional therapeutic interventions would be limited. Cellular activation in sepsis can be targeted by novel approaches like inhibition of the heterotypic cellular interactions of blood cells by targeting surface receptors or posttranscriptional control of the hemostatic system by noncoding ribonucleic acid (RNA) molecules. Stable RNA molecules can affect the expression of several proteins. Thus, it can be anticipated that modulation of microRNA production would result in a multitude of effects that may be beneficial in septic cases. Here, we highlight some of the recent diagnostic possibilities and potential novel routes of the dysregulated host response.
Pull-out vs. suture in zone Ia-Ib flexor tendon injuries: clinical
results from a multicentre cohort study
Authors: Keller Nicola , Guidi Marco , Tobler- Ammann Bernadette , Beckmann-Fries Vera , Schrepfer Lorena , Kaempfen Alexandre , Vögelin Esther , Calcagni Maurizio 
Published: February 2024

Abstract
Background Several surgical techniques have been reported for flexor
tendon zone 1a-b lacerations without a clear consensus on the gold standard
treatment. The purpose of this multicentre study was to measure the outcomes of
zone 1a-b flexor tendon injuries treated with a pull-out suture (POS) versus
direct suture (DS) technique.
Patients and Methods Fifteen patients were treated with the pull-out
technique and 22 patients with a direct suture technique between 2014 and 2020.
The controlled active motion (CAM) regimen protocol and a standardised follow-up
schedule were used in both groups. Data on the demographics, surgery, and
treatment characteristics were collected at baseline as well as at week 6 and 13
post-operatively. The primary outcome measurement was the complication rate.
Secondary outcome measurements were reoperation rate, finger range of motion
(ROM), strength as well as patient satisfaction.
Results The patient age ranged from 18 to 75 years in both groups with all
patients having a complete FDP lesion after a clean-cut injury. The complication
rate was 41% in the POS group and 16% in the DS group. The
reoperation rate was 29% in the POS group and 8% in the DS
group. Significant between-group differences in favour of the DS group were
found in the passive DIP and passive PIP+DIP ROM at week 6 and week 13.
Mean hand strength was 28.7 (11.6) kg in the POS group at week 13 and 21.3 (7.9)
kg in the DS group. This difference was statistically significant
(p=0.012) with a medium effect size (r=-0.41). Average patient
satisfaction at week 13 was 7.5 (2.2) points in the POS and 7.7 (1.3) points in
the DS group. The difference between groups was not significant
(p=0.839).
Conclusion This register-based study demonstrates lower complication and
reoperation rates with the direct suture approach compared with a pull-out
button technique. Although clinical results were similar between the two surgery
techniques at week 13 post-surgery, a direct suture approach should always be
attempted whenever possible. If necessary, other local structures should be
included to increase suture strength and allow for early active motion
rehabilitation regimens.