bluuebunny/crossref_metadata_2025 huggingface dataset:
Translation factor eIF5a is essential for IFNγ production and cell cycle regulation in primary CD8+ T lymphocytes
Authors: Tan Thomas C. J. , Kelly Van , Zou Xiaoyan , Wright David , Ly Tony , Zamoyska Rose
Published: December 2022

Control of mRNA translation adjusts protein production rapidly and facilitates local cellular responses to environmental conditions. Traditionally initiation of translation is considered to be a major translational control point, however, control of peptide elongation is also important. Here we show that the function of the elongation factor, eIF5a, is regulated dynamically in naïve CD8+T cells upon activation by post-translational modification, whereupon it facilitates translation of specific subsets of proteins. eIF5a is essential for long-term survival of effector CD8+T cells and sequencing of nascent polypeptides indicates that the production of proteins which regulate proliferation and key effector functions, particularly the production of IFNγ and less acutely TNF production and cytotoxicity, is dependent on the presence of functional eIF5a. Control of translation in multiple immune cell lineages is required to co-ordinate immune responses and these data illustrate that translational elongation contributes to post-transcriptional regulons important for the control of inflammation.
Extensive substrate recognition by the streptococcal antibody-degrading enzymes IdeS and EndoS
Authors: Sudol Abigail S. L. , Butler John , Ivory Dylan P. , Tews Ivo , Crispin Max
Published: December 2022

Enzymatic cleavage of IgG antibodies is a common strategy used by pathogenic bacteria to ablate immune effector function. The Streptococcus pyogenes bacterium secretes the protease IdeS and the glycosidase EndoS, which specifically catalyse cleavage and deglycosylation of human IgG, respectively. IdeS has received clinical approval for kidney transplantation in hypersensitised individuals, while EndoS has found application in engineering antibody glycosylation. We present crystal structures of both enzymes in complex with their IgG1 Fc substrate, which was achieved using Fc engineering to disfavour preferential Fc crystallisation. The IdeS protease displays extensive Fc recognition and encases the antibody hinge. Conversely, the glycan hydrolase domain in EndoS traps the Fc glycan in a “flipped-out” conformation, while additional recognition of the Fc peptide is driven by the so-called carbohydrate binding module. In this work, we reveal the molecular basis of antibody recognition by bacterial enzymes, providing a template for the development of next-generation enzymes.
Seismic multi-hazard and impact estimation via causal inference from satellite imagery
Authors: Xu Susu , Dimasaka Joshua , Wald David J. , Noh Hae Young
Published: December 2022

Rapid post-earthquake reconnaissance is important for emergency responses and rehabilitation by providing accurate and timely information about secondary hazards and impacts, including landslide, liquefaction, and building damage. Despite the extensive collection of geospatial data and satellite images, existing physics-based and data-driven methods suffer from low estimation performance due to the complex and event-specific causal dependencies underlying the cascading processes of earthquake-triggered hazards and impacts. Herein, we present a rapid seismic multi-hazard and impact estimation system that leverages advanced statistical causal inference and remote sensing techniques. The unique feature of this system is that it provides accurate and high-resolution estimations on a regional scale by jointly inferring multiple hazards and building damage from satellite images through modeling their causal dependencies. We evaluate our system on multiple seismic events from diverse countries around the globe. Our results corroborate that incorporating causal dependencies significantly improves large-scale estimation accuracy for multiple hazards and impacts compared to existing systems. The results also reveal quantitative causal mechanisms among earthquake-triggered multi-hazard and impact for multiple seismic events. Our system establishes a new way to extract and utilize the complex interactions of multiple hazards and impacts for effective disaster responses and advancing understanding of seismic geological processes.
Seismic evidence for uniform crustal accretion along slow-spreading ridges in the equatorial Atlantic Ocean
Authors: Wang Zhikai , Singh Satish C.
Published: December 2022

The crustal accretion along mid-ocean ridges is known to be spreading-rate dependent. Along fast-spreading ridges, two-dimensional sheet-like mantle upwelling creates relatively uniform crust. In contrast, the crust formed along slow-spreading ridges shows large along-axis thickness variations with thicker crust at segment centres, which is hypothesised to be due a three-dimensional plume-like mantle upwelling or due to focused melt migration to segment centres. Using wide-angle seismic data acquired from the equatorial Atlantic Ocean, here we show that the crustal thickness is nearly uniform (~5.5 km) across five crustal segments for crust formed at the slow-spreading Mid-Atlantic Ridge with age varying from 8 to 70 Ma. The crustal velocities indicate that this crust is predominantly of magmatic origin. We suggest that this uniform magmatic crustal accretion is due to a two-dimensional sheet-like mantle upwelling facilitated by the long-offset transform faults in the equatorial Atlantic region and the presence of a high concentration of volatiles in the primitive melt in the mantle.
Ultrahigh dynamic range and low noise figure programmable integrated microwave photonic filter
Authors: Daulay Okky , Liu Gaojian , Ye Kaixuan , Botter Roel , Klaver Yvan , Tan Qinggui , Yu Hongxi , Hoekman Marcel , Klein Edwin , Roeloffzen Chris , Liu Yang , Marpaung David
Published: December 2022

Microwave photonics has adopted a number of important concepts and technologies over the recent pasts, including photonic integration, versatile programmability, and techniques for enhancing key radio frequency performance metrics such as the noise figure and the dynamic range. However, to date, these aspects have not been achieved simultaneously in a single circuit. Here, we report a multi-functional photonic integrated circuit that enables programmable filtering functions with record-high performance. We demonstrate reconfigurable filter functions with record-low noise figure and a RF notch filter with ultra-high dynamic range. We achieve this unique feature using versatile complex spectrum tailoring enabled by an all integrated modulation transformer and a double injection ring resonator as a multi-function optical filtering component. Our work breaks the conventional and fragmented approach of integration, functionality and performance that currently prevents the adoption of integrated MWP systems in real applications.
Lossless enrichment of trace analytes in levitating droplets for multiphase and multiplex detection
Authors: Chen Xueyan , Ding Qianqian , Bi Chao , Ruan Jian , Yang Shikuan
Published: December 2022

Concentrating a trace amount of molecules from liquids, solid objects, or the gas phase and delivering them to a localized area are crucial for almost any trace analyte detection device. Analytes within a liquid droplet resting on micro/nanostructured surfaces with liquid-repellent coatings can be concentrated during solvent evaporation. However, these coatings suffer from complex manufacturing procedures, poor versatility, and limited analyte enrichment efficiency. Here, we report on the use of an acoustic levitation platform to losslessly concentrate the analyte molecules dissolved in any volatile liquid, attached to solid objects, or spread in air. Gold nanoparticles can be simultaneously concentrated with the analytes in different phases, realizing sensitive, surface-enhanced Raman scattering detection even at attomolar (10−18 mol/L) concentration levels. The acoustic levitation platform-enabled, lossless analyte enrichment can significantly increase the analytical performance of many conventional microsensing techniques.
Biodiversity stabilizes plant communities through statistical-averaging effects rather than compensatory dynamics
Authors: Zhao Lei , Wang Shaopeng , Shen Ruohong , Gong Ying , Wang Chong , Hong Pubin , Reuman Daniel C.
Published: December 2022

Understanding the relationship between biodiversity and ecosystem stability is a central goal of ecologists. Recent studies have concluded that biodiversity increases community temporal stability by increasing the asynchrony between the dynamics of different species. Theoretically, this enhancement can occur through either increased between-species compensatory dynamics, a fundamentally biological mechanism; or through an averaging effect, primarily a statistical mechanism. Yet it remains unclear which mechanism is dominant in explaining the diversity-stability relationship. We address this issue by mathematically decomposing asynchrony into components separately quantifying the compensatory and statistical-averaging effects. We applied the new decomposition approach to plant survey and experimental data from North American grasslands. We show that statistical averaging, rather than compensatory dynamics, was the principal mediator of biodiversity effects on community stability. Our simple decomposition approach helps integrate concepts of stability, asynchrony, statistical averaging, and compensatory dynamics, and suggests that statistical averaging, rather than compensatory dynamics, is the primary means by which biodiversity confers ecological stability.
Closed-loop direct control of seizure focus in a rodent model of temporal lobe epilepsy via localized electric fields applied sequentially
Authors: Kang Wonok , Ju Chanyang , Joo Jaesoon , Lee Jiho , Shon Young-Min , Park Sung-Min
Published: December 2022

Direct electrical stimulation of the seizure focus can achieve the early termination of epileptic oscillations. However, direct intervention of the hippocampus, the most prevalent seizure focus in temporal lobe epilepsy is thought to be not practicable due to its large size and elongated shape. Here, in a rat model, we report a sequential narrow-field stimulation method for terminating seizures, while focusing stimulus energy at the spatially extensive hippocampal structure. The effects and regional specificity of this method were demonstrated via electrophysiological and biological responses. Our proposed modality demonstrates spatiotemporal preciseness and selectiveness for modulating the pathological target region which may have potential for further investigation as a therapeutic approach.
Muscle 4EBP1 activation modifies the structure and function of the neuromuscular junction in mice
Authors: Ang Seok-Ting J. , Crombie Elisa M. , Dong Han , Tan Kuan-Ting , Hernando Adriel , Yu Dejie , Adamson Stuart , Kim Seonyoung , Withers Dominic J. , Huang Hua , Tsai Shih-Yin
Published: December 2022

Dysregulation of mTOR complex 1 (mTORC1) activity drives neuromuscular junction (NMJ) structural instability during aging; however, downstream targets mediating this effect have not been elucidated. Here, we investigate the roles of two mTORC1 phosphorylation targets for mRNA translation, ribosome protein S6 kinase 1 (S6K1) and eukaryotic translation initiation factor 4E-binding protein 1 (4EBP1), in regulating NMJ structural instability induced by aging and sustained mTORC1 activation. While myofiber-specific deletion of S6k1 has no effect on NMJ structural integrity, 4EBP1 activation in murine muscle induces drastic morphological remodeling of the NMJ with enhancement of synaptic transmission. Mechanistically, structural modification of the NMJ is attributed to increased satellite cell activation and enhanced post-synaptic acetylcholine receptor (AChR) turnover upon 4EBP1 activation. Considering that loss of post-synaptic myonuclei and reduced NMJ turnover are features of aging, targeting 4EBP1 activation could induce NMJ renewal by expanding the pool of post-synaptic myonuclei as an alternative intervention to mitigate sarcopenia.
Steps dominate gas evasion from a mountain headwater stream
Authors: Botter Gianluca , Carozzani Anna , Peruzzo Paolo , Durighetto Nicola
Published: December 2022

Steps are dominant morphologic traits of high-energy streams, where climatically- and biogeochemically-relevant gases are processed, transported to downstream ecosystems or released into the atmosphere. Yet, capturing the imprint of the small-scale morphological complexity of channel forms on large-scale river outgassing represents a fundamental unresolved challenge. Here, we combine theoretical and experimental approaches to assess the contribution of localized steps to the gas evasion from river networks. The framework was applied to a representative, 1 km-long mountain reach in Italy, where carbon dioxide concentration drops across several steps and a reference segment without steps were measured under different hydrologic conditions. Our results indicate that local steps lead the reach-scale outgassing, especially for high and low discharges. These findings suggest that steps are key missing components of existing scaling laws used for the assessment of gas fluxes across water-air interfaces. Therefore, global evasion from rivers may differ substantially from previously reported estimates.
USP5-Beclin 1 axis overrides p53-dependent senescence and drives Kras-induced tumorigenicity
Authors: Li Juan , Wang Yang , Luo Yue , Liu Yang , Yi Yong , Li Jinsong , Pan Yang , Li Weiyuxin , You Wanbang , Hu Qingyong , Zhao Zhiqiang , Zhang Yujun , Cao Yang , Zhang Lingqiang , Yuan Junying , Xiao Zhi-Xiong Jim
Published: December 2022

Non-small cell lung cancers (NSCLC) frequently contain KRAS mutation but retain wild-type TP53. Abundant senescent cells are observed in premalignant but not in malignant tumors derived from the Kras-driven mouse model, suggesting that KRAS oncogenic signaling would have to overcome the intrinsic senescence burden for cancer progression. Here, we show that the nuclear Beclin 1-mediated inhibition of p53-dependent senescence drives Kras-mediated tumorigenesis. KRAS activates USP5 to stabilize nuclear Beclin 1, leading to MDM2-mediated p53 protein instability. KrasG12D mice lacking Beclin 1 display retarded lung tumor growth. Knockdown of USP5 or knockout of Becn1 leads to increased senescence and reduced autophagy. Mechanistically, KRAS elevates ROS to induce USP5 homodimer formation by forming the C195 disulfide bond, resulting in stabilization and activation of USP5. Together, these results demonstrate that activation of the USP5-Beclin 1 axis is pivotal in overriding intrinsic p53-dependent senescence in Kras-driven lung cancer development.
Chemical reaction-mediated covalent localization of bacteria
Authors: Luo Huilong , Chen Yanmei , Kuang Xiao , Wang Xinyue , Yang Fengmin , Cao Zhenping , Wang Lu , Lin Sisi , Wu Feng , Liu Jinyao
Published: December 2022

Methods capable of manipulating bacterial colonization are of great significance for modulating host-microbiota relationships. Here, we describe a strategy of in-situ chemical reaction-mediated covalent localization of bacteria. Through a simple one-step imidoester reaction, primary amino groups on bacterial surface can be converted to free thiols under cytocompatible conditions. Surface thiolation is applicable to modify diverse strains and the number of introduced thiols per bacterium can be easily tuned by varying feed ratios. These chemically reactive bacteria are able to spontaneously bond with mucous layer by catalyst-free thiol-disulfide exchange between mucin-associated disulfides and newly converted thiols on bacterial surface and show thiolation level-dependent attachment. Bacteria optimized with 9.3 × 107 thiols per cell achieve 170-fold higher attachment in mucin-enriched jejunum, a challenging location for gut microbiota to colonize. As a proof-of-concept application for microbiota transplantation, covalent bonding-assisted localization of an oral probiotic in the jejunum generates an improved remission of jejunal mucositis. Our findings demonstrate that transforming bacteria with a reactive surface provides an approach to chemically control bacterial localization, which is highly desirable for developing next-generation bacterial living bioagents.
Tubular epithelial cells-derived small extracellular vesicle-VEGF-A promotes peritubular capillary repair in ischemic kidney injury
Authors: Zhong Xin , Tang Tao-Tao , Shen An-Ran , Cao Jing-Yuan , Jing Jing , Wang Cui , Zhu Xiao-Xiao , Wen Yi , Li Zuo-Lin , Wang Bin , Qin Suo-Fu , Liu Bi-Cheng , Lv Lin-Li
Published: December 2022

Peritubular capillaries (PTCs) are closely related to renal tubules in structure and function, and both are pivotal regulators in the development and progression of acute kidney injury (AKI). However, the mechanisms that underlie the interaction between PTCs and tubules during AKI remain unclear. Here we explored a new mode of tubulovascular crosstalk mediated by small extracellular vesicles (sEV) after AKI. In response to renal ischemia/reperfusion (I/R) injury, endothelial proliferation of PTCs and tubular expression of vascular endothelial growth factor-A (VEGF-A) were increased, accompanied by a remarkable redistribution of cytoplasmic VEGF-A to the basolateral side of tubular cells. Meanwhile, the secretion mode of VEGF-A was converted in the injured tubular cells, which showed a much greater tendency to secrete VEGF-A via sEV other than the free form. Interestingly, tubular cell-derived VEGF-A-enriched sEV (sEV-VEGF-A) turned out to promote endothelial proliferation which was regulated by VEGF receptors 1 and 2. Furthermore, inhibition of renal sEV secretion by Rab27a knockdown resulted in a significant decrease in the proliferation of peritubular endothelial cells in vivo. Importantly, taking advantage of the newly recognized endogenous repair response of PTCs, exogenous supplementation of VEGF-A + sEV efficiently recused PTC rarefaction, improved renal perfusion, and halted the AKI to CKD transition. Taken together, our study uncovered a novel intrinsic repair response after AKI through renal tubule-PTC crosstalk via sEV-VEGF-A, which could be exploited as a promising therapeutic angiogenesis strategy in diseases with ischemia.
Evidence supporting the use of a brief cognitive assessment in routine clinical assessment for psychosis
Authors: Cowman M. , Lonergan E. , Burke T. , Bowie C. R. , Corvin A. , Morris D. W. , O’Connor K. , Donohoe G.
Published: December 2022

Cognitive impairment is a core feature of psychosis. Full cognitive assessments are not often conducted in routine clinical practice as administration is time-consuming. Here, we investigated whether brief tests of cognition could be used to predict broader neurocognitive performance in a manner practical for screening use in mental health services. We carried out a principal component analysis (PCA) to obtain an estimate of general cognitive function (N = 415). We investigated whether brief tests of memory accounted for a significant percentage of variation in the PCA scores. We used discriminant function analysis to determine if measures could predict classification as lower, intermediate or higher level of cognitive function and to what extent these groups overlapped with groups based on normative data. Memory tests correctly classified 65% of cases in the highest scoring group, 35% of cases in the intermediate group, and 77% of cases in the lowest scoring group. These PCA-derived groups and groups based on normative scores for the two tests were significantly associated (χ2 = 164.00, p < 0.001). These measures accurately identified three quarters of the low performing group, the group of greatest interest from the perspective of identifying those likely to need greater supports as part of clinical care. In so doing they suggest a potentially useful approach to screening for cognitive impairment in clinical services, upon which further assessment can be built if required.
Comparative transcriptome profiles of four sexually size dimorphic fish
Authors: Luo Li-Fei , Xu Zi-Sheng , Li Dan-Yang , Hu Zhen , Gao Ze-Xia
Published: December 2022

Sexual size dimorphism is widespread in fish species. Although sex growth differences in multiple species have been studied successively, the commonalities of regulatory mechanisms across sexually dimorphic species are unknown. In this study, we performed RNA-seq analysis of four representative fish (loach, half-smooth tongue sole, yellow catfish, and Nile tilapia) with significant growth differences between females and males. Clean reads were identified from four fish species, ranging from 45,718,052 to 57,733,120. Following comparison transcriptome analysis, there were 1,132 and 1,108, 1,290 and 1,102, 4,732 and 4,266, 748 and 192 differentially expressed genes (DEGs) in the brain and muscle of loach, half-smooth tongue sole, yellow catfish, and Nile tilapia, respectively. Furthermore, the expression levels were validated by quantitative real-time PCR (qRT-PCR). Comparative transcriptome profiles of four fish described here will provide fundamental information for further studies on the commonalities of sexually size dimorphic fish in regulating growth differences between females and males.
Magnetic signatures of a creosote oil contaminated site: case study in São Paulo, Brazil
Authors: de Moraes Carolina Silveira , Ustra Andrea Teixeira , Barbosa Alexandre Muselli , Imbernon Rosely Aparecida Liguori , Tengan Cinthia Midory Uehara
Published: December 2022

Soils and groundwater contamination modifies the physical–chemical conditions of the environment, altering natural biogeochemical processes of the ground. As a result, several mineral transformations occur, in which iron plays a decisive role. The presence of iron enables the study of magnetic properties, improving the understanding of the geophysical signatures of highly dynamic environments (e.g., biogeochemical hotspots and contamination plumes). In this work, we seek to identify creosote biodegradation related to the precipitation of magnetic minerals on sediments at a contaminated site in São Paulo, Brazil. Several rock magnetism analyses were carried out to provide the magnetic mineralogy of the samples in terms of their composition, size, and abundance. We conducted high-temperature thermomagnetic curves, frequency-dependent magnetic susceptibility, anesthetic remanent magnetization (ARM) and isothermal remanent magnetization (IRM) data, superparamagnetic concentration and dipole moment (SPCDM), and scanning electron microscopy (SEM) analyses. The magnetic signatures of the contaminated samples suggest an increase of superparamagnetic grains in the water table fluctuation zone if compared to the magnetic signatures of the uncontaminated samples. Thermomagnetic curves of contaminated samples showed a lower heterogeneity of the magnetic mineral phases than the uncontaminated ones. This work contributes to the advancement of the understanding of how natural biogeochemical processes are impacted by human actions, such as soil contamination, and even by climate change, which should affect soil redox conditions in periods of drought and flooding.
Pre-contrast MAGiC in treated gliomas: a pilot study of quantitative MRI
Authors: Nunez-Gonzalez Laura , van Garderen Karin A. , Smits Marion , Jaspers Jaap , Romero Alejandra Méndez , Poot Dirk H. J. , Hernandez-Tamames Juan A.
Published: December 2022

Quantitative MR imaging is becoming more feasible to be used in clinical work since new approaches have been proposed in order to substantially accelerate the acquisition and due to the possibility of synthetically deriving weighted images from the parametric maps. However, their applicability has to be thoroughly validated in order to be included in clinical practice. In this pilot study, we acquired Magnetic Resonance Image Compilation scans to obtain T1, T2 and PD maps in 14 glioma patients. Abnormal tissue was segmented based on conventional images and using a deep learning segmentation technique to define regions of interest (ROIs). The quantitative T1, T2 and PD values inside ROIs were analyzed using the mean, the standard deviation, the skewness and the kurtosis and compared to the quantitative T1, T2 and PD values found in normal white matter. We found significant differences in pre-contrast T1 and T2 values between abnormal tissue and healthy tissue, as well as between T1w-enhancing and non-enhancing regions. ROC analysis was used to evaluate the potential of quantitative T1 and T2 values for voxel-wise classification of abnormal/normal tissue (AUC = 0.95) and of T1w enhancement/non-enhancement (AUC = 0.85). A cross-validated ROC analysis found high sensitivity (73%) and specificity (73%) with AUCs up to 0.68 on the a priori distinction between abnormal tissue with and without T1w-enhancement. These results suggest that normal tissue, abnormal tissue, and tissue with T1w-enhancement are distinguishable by their pre-contrast quantitative values but further investigation is needed.
A conserved MTMR lipid phosphatase increasingly suppresses autophagy in brain neurons during aging
Authors: Kovács Tibor , Szinyákovics Janka , Billes Viktor , Murányi Gábor , Varga Virginia B. , Bjelik Annamária , Légrádi Ádám , Szabó Melinda , Sándor Sára , Kubinyi Enikő , Szekeres-Paracky Cecília , Szocsics Péter , Lőke János , Mulder Jun , Gulyás Balázs , Renner Éva , Palkovits Miklós , Gulya Károly , Maglóczky Zsófia , Vellai Tibor
Published: December 2022

Ageing is driven by the progressive, lifelong accumulation of cellular damage. Autophagy (cellular self-eating) functions as a major cell clearance mechanism to degrade such damages, and its capacity declines with age. Despite its physiological and medical significance, it remains largely unknown why autophagy becomes incapable of effectively eliminating harmful cellular materials in many cells at advanced ages. Here we show that age-associated defects in autophagic degradation occur at both the early and late stages of the process. Furthermore, in the fruit fly Drosophila melanogaster, the myotubularin-related (MTMR) lipid phosphatase egg-derived tyrosine phosphatase (EDTP) known as an autophagy repressor gradually accumulates in brain neurons during the adult lifespan. The age-related increase in EDTP activity is associated with a growing DNA N6-adenine methylation at EDTP locus. MTMR14, the human counterpart of EDTP, also tends to accumulate with age in brain neurons. Thus, EDTP, and presumably MTMR14, promotes brain ageing by increasingly suppressing autophagy throughout adulthood. We propose that EDTP and MTMR14 phosphatases operate as endogenous pro-ageing factors setting the rate at which neurons age largely independently of environmental factors, and that autophagy is influenced by DNA N6-methyladenine levels in insects.
Human-built environment interactions: the relationship between subjective well-being and perceived neighborhood environment characteristics
Authors: Sadeghi Ali Reza , Ebadi Maryam , Shams Fatemeh , Jangjoo Sina
Published: December 2022

The neighborhood is one of the most fundamental urban elements and acts as the intermediary link between the city and citizens to enhance the quality of life. The present study examined the significance of the relationship between the subjective well-being of citizens and perceived neighborhood environment characteristics in urban historical fabrics for creating healthy neighborhoods. To this end, a survey research method was employed, and the data were collected via questionnaires. The population consisted of all the citizens of the historical neighborhood of Sange Siah in Shiraz, Iran, who lived or worked in the neighborhood and used the neighborhood spaces daily. A Nonparametric Spearman correlation coefficient was run to assess the correlation between the variables. The results showed that the component of social inclusion from among the six components of subjective well-being had a significant positive correlation with perceived neighborhood environment characteristics (r = 0.712). In the following, the components of satisfaction with life (0.614), mental well-being (0.569), positive and negative effect (0.526), and feeling of happiness (0.468) had a moderate positive correlation; and the component of physical and mental health also had a weak positive correlation with perceived neighborhood environment characteristics (0.230). In addition, the concept of subjective well-being with a correlation coefficient of 0.579 had a moderate positive correlation with perceived neighborhood environment characteristics, which indicates that the structural characteristics of the neighborhood have a significant relationship with the subjective well-being of the people living in the neighborhood.
The effect of tumor shape irregularity on Gamma Knife treatment plan quality and treatment outcome: an analysis of 234 vestibular schwannomas
Authors: Sümer Esra , Tek Ece , Türe O. Artunç , Şengöz Meriç , Dinçer Alp , Özcan Alpay , Pamir M. Necmettin , Özduman Koray , Ozturk-Isik Esin
Published: December 2022

The primary aim of Gamma Knife (GK) radiosurgery is to deliver high-dose radiation precisely to a target while conforming to the target shape. In this study, the effects of tumor shape irregularity (TSI) on GK dose-plan quality and treatment outcomes were analyzed in 234 vestibular schwannomas. TSI was quantified using seven different metrics including volumetric index of sphericity (VioS). GK treatment plans were created on a single GK-Perfexion/ICON platform. The plan quality was measured using selectivity index (SI), gradient index (GI), Paddick’s conformity index (PCI), and efficiency index (EI). Correlation and linear regression analyses were conducted between shape irregularity features and dose plan indices. Machine learning was employed to identify the shape feature that predicted dose plan quality most effectively. The treatment outcome analysis including tumor growth control and serviceable hearing preservation at 2 years, were conducted using Cox regression analyses. All TSI features correlated significantly with the dose plan indices (P < 0.0012). With increasing tumor volume, vestibular schwannomas became more spherical (P < 0.05) and the dose plan indices varied significantly between tumor volume subgroups (P < 0.001 and P < 0.01). VioS was the most effective predictor of GK indices (P < 0.001) and we obtained 89.36% accuracy (79.17% sensitivity and 100% specificity) for predicting PCI. Our results indicated that TSI had significant effects on the plan quality however did not adversely affect treatment outcomes.
Analyzing and predicting success of professional musicians
Authors: Kang Inwon , Mandulak Michael , Szymanski Boleslaw K.
Published: December 2022

The emergence of streaming services, e.g., Spotify, has changed the way people listen to music and the way professional musicians achieve fame and success. Classical music has been the backbone of Western media for a long time, but Spotify has introduced the public to a much wider variety of music, also opening a new venue for professional musicians to gain exposure. In this paper, we use open-source data from Spotify and Musicbrainz databases to construct collaboration-based and genre-based networks. We call genres defined in these databases primary genres. Our goal is to find the correlation between various features of each professional musician, the current stage of their career, and the level of their success in the music field. We build regression models using XGBoost to first analyze correlation between features provided by Spotify. We then analyze the correlation between the digital music world of Spotify and the more traditional world of Billboard charts. We find that within certain bounds, machine learning techniques such as decision tree classifiers and Q-based models perform quite well on predicting success of professional musicians from the data on their early careers. We also find features that are highly predictive of their success. The most prominent among them are the musicians’ collaboration counts and the span of their career. Our findings also show that classical musicians are still very centrally placed in the general, genre-agnostic network of musicians. Using these models and success metrics, aspiring professional musicians can check if their chances for career success could be improved by increasing their specific success measures in both Spotify and Billboard charts.
Development of an implantable three-dimensional model of a functional pathogenic multispecies biofilm to study infected wounds
Authors: Cárdenas-Calderón Camila , Veloso-Giménez Valentina , González Tamara , Wozniak Aniela , García Patricia , Martín Sebastián San , Varas Juan F. , Carrasco-Wong Ivo , Vera Mario , Egaña José Tomás
Published: December 2022

Chronic wounds cannot heal due to impairment of regeneration, mainly caused by the persistent infection of multispecies biofilms. Still, the effects of biofilm wound infection and its interaction with the host are not fully described. We aimed to study functional biofilms in physiological conditions in vitro, and their potential effects in health and regeneration in vivo. Therefore, Pseudomonas aeruginosa, Staphylococcus aureus and Enterococcus faecalis were seeded in collagen-based scaffolds for dermal regeneration. After 24 h, scaffolds had bacterial loads depending on the initial inoculum, containing viable biofilms with antibiotic tolerance. Afterwards, scaffolds were implanted onto full skin wounds in mice, together with daily supervision and antibiotic treatment. Although all mice survived their health was affected, displaying fever and weight loss. After ten days, histomorphology of scaffolds showed high heterogeneity in samples and within groups. Wounds were strongly, mildly, or not infected according to colony forming units, and P. aeruginosa had higher identification frequency. Biofilm infection induced leucocyte infiltration and elevated interferon-γ and interleukin-10 in scaffolds, increase of size and weight of spleen and high systemic pro-calcitonin concentrations. This functional and implantable 3D biofilm model allows to study host response during infection, providing a useful tool for infected wounds therapy development.
The reverse mode of the Na+/Ca2+ exchanger contributes to the pacemaker mechanism in rabbit sinus node cells
Authors: Tóth Noémi , Loewe Axel , Szlovák Jozefina , Kohajda Zsófia , Bitay Gergő , Levijoki Jouko , Papp Julius Gy. , Varró András , Nagy Norbert
Published: December 2022

Sinus node (SN) pacemaking is based on a coupling between surface membrane ion-channels and intracellular Ca2+-handling. The fundamental role of the inward Na+/Ca2+ exchanger (NCX) is firmly established. However, little is known about the reverse mode exchange. A simulation study attributed important role to reverse NCX activity, however experimental evidence is still missing. Whole-cell and perforated patch-clamp experiments were performed on rabbit SN cells supplemented with fluorescent Ca2+-tracking. We established 2 and 8 mM pipette NaCl groups to suppress and enable reverse NCX. NCX was assessed by specific block with 1 μM ORM-10962. Mechanistic simulations were performed by Maltsev–Lakatta minimal computational SN model. Active reverse NCX resulted in larger Ca2+-transient amplitude with larger SR Ca2+-content. Spontaneous action potential (AP) frequency increased with 8 mM NaCl. When reverse NCX was facilitated by 1 μM strophantin the Ca2+i and spontaneous rate increased. ORM-10962 applied prior to strophantin prevented Ca2+i and AP cycle change. Computational simulations indicated gradually increasing reverse NCX current, Ca2+i and heart rate with increasing Na+i. Our results provide further evidence for the role of reverse NCX in SN pacemaking. The reverse NCX activity may provide additional Ca2+-influx that could increase SR Ca2+-content, which consequently leads to enhanced pacemaking activity.
A versatile approach to evaluate the occurrence of microfibers in mussels Mytilus galloprovincialis
Authors: Volgare Michela , Santonicola Serena , Cocca Mariacristina , Avolio Roberto , Castaldo Rachele , Errico Maria Emanuela , Gentile Gennaro , Raimo Gennaro , Gasperi Maurizio , Colavita Giampaolo
Published: December 2022

Microplastics of fibrous shape are esteemed to be the most abundant micro-debris form present in the environment. Despite the occurrence of microfibers in fish may pose a risk to human health, the literature is scarce regarding studies on the contamination in commercial marine fish mostly due to methodological issues. In this study, a versatile approach, able to discriminate among natural and synthetic microfibers according to the evaluation of specific morphological features, is proposed in farmed mussels (Mytilus galloprovincialis). The approach was useful to determine that microfibers were present in 74% of mussel samples, with a mean number of 14.57 microfibers/individual, corresponding to 3.13 microfibers/g w.w. A negative correlation between the size of analysed mussels and the amount of microfibers/g w.w. was detected, showing that smaller specimens contained more microfibers than the larger ones. This work paves the way to further studies aimed to adequately assess the risk that microfibers may pose to marine biota, also considering the commercial value as seafood items of many species of the Mytilus genus and the potential implication for human exposure.
Associative memory of structured knowledge
Authors: Steinberg Julia , Sompolinsky Haim
Published: December 2022

A long standing challenge in biological and artificial intelligence is to understand how new knowledge can be constructed from known building blocks in a way that is amenable for computation by neuronal circuits. Here we focus on the task of storage and recall of structured knowledge in long-term memory. Specifically, we ask how recurrent neuronal networks can store and retrieve multiple knowledge structures. We model each structure as a set of binary relations between events and attributes (attributes may represent e.g., temporal order, spatial location, role in semantic structure), and map each structure to a distributed neuronal activity pattern using a vector symbolic architecture scheme.We then use associative memory plasticity rules to store the binarized patterns as fixed points in a recurrent network. By a combination of signal-to-noise analysis and numerical simulations, we demonstrate that our model allows for efficient storage of these knowledge structures, such that the memorized structures as well as their individual building blocks (e.g., events and attributes) can be subsequently retrieved from partial retrieving cues. We show that long-term memory of structured knowledge relies on a new principle of computation beyond the memory basins. Finally, we show that our model can be extended to store sequences of memories as single attractors.
Deep-learning-based AI for evaluating estimated nonperfusion areas requiring further examination in ultra-widefield fundus images
Authors: Inoda Satoru , Takahashi Hidenori , Yamagata Hitoshi , Hisadome Yoichiro , Kondo Yusuke , Tampo Hironobu , Sakamoto Shinichi , Katada Yusaku , Kurihara Toshihide , Kawashima Hidetoshi , Yanagi Yasuo
Published: December 2022

We herein propose a PraNet-based deep-learning model for estimating the size of non-perfusion area (NPA) in pseudo-color fundus photos from an ultra-wide-field (UWF) image. We trained the model with focal loss and weighted binary cross-entropy loss to deal with the class-imbalanced dataset, and optimized hyperparameters in order to minimize validation loss. As expected, the resultant PraNet-based deep-learning model outperformed previously published methods. For verification, we used UWF fundus images with NPA and used Bland–Altman plots to compare estimated NPA with the ground truth in FA, which demonstrated that bias between the eNPA and ground truth was smaller than 10% of the confidence limits zone and that the number of outliers was less than 10% of observed paired images. The accuracy of the model was also tested on an external dataset from another institution, which confirmed the generalization of the model. For validation, we employed a contingency table for ROC analysis to judge the sensitivity and specificity of the estimated-NPA (eNPA). The results demonstrated that the sensitivity and specificity ranged from 83.3–87.0% and 79.3–85.7%, respectively. In conclusion, we developed an AI model capable of estimating NPA size from only an UWF image without angiography using PraNet-based deep learning. This is a potentially useful tool in monitoring eyes with ischemic retinal diseases.
Topological network features determine convergence rate of distributed average algorithms
Authors: Sirocchi Christel , Bogliolo Alessandro
Published: December 2022

Gossip algorithms are message-passing schemes designed to compute averages and other global functions over networks through asynchronous and randomised pairwise interactions. Gossip-based protocols have drawn much attention for achieving robust and fault-tolerant communication while maintaining simplicity and scalability. However, the frequent propagation of redundant information makes them inefficient and resource-intensive. Most previous works have been devoted to deriving performance bounds and developing faster algorithms tailored to specific structures. In contrast, this study focuses on characterising the effect of topological network features on performance so that faster convergence can be engineered by acting on the underlying network rather than the gossip algorithm. The numerical experiments identify the topological limiting factors, the most predictive graph metrics, and the most efficient algorithms for each graph family and for all graphs, providing guidelines for designing and maintaining resource-efficient networks. Regression analyses confirm the explanatory power of structural features and demonstrate the validity of the topological approach in performance estimation. Finally, the high predictive capabilities of local metrics and the possibility of computing them in a distributed manner and at a low computational cost inform the design and implementation of a novel distributed approach for predicting performance from the network topology.
Compensability of an enhanced incidence of spermatozoa with cytoplasmic droplets in boar semen for use in artificial insemination: a single cell approach
Authors: Henning Heiko , Luther Anne-Marie , Höfner-Schmiing Lisa , Waberski Dagmar
Published: December 2022

This single cell study aimed to clarify whether an elevated incidence of sperm with a retained cytoplasmic droplet (CD) can be compensated by a higher sperm number in boar semen doses to maintain fertility. Cluster analysis of motile spermatozoa (ten boars) revealed that spermatozoa with a CD are underrepresented in the fast, linearly moving sperm cohort compared to morphologically normal sperm. Nonetheless, the response to the motility stimulator procaine was barely affected in spermatozoa with distal CD (Cramer’s V = 0.14), but moderately affected in sperm with proximal CD (V = 0.28). Viability was lower in sperm with distal CD (p < 0.05) but not with proximal CD compared to normal sperm during 168 h storage of extended semen samples (n = 11) and subsequent thermic stress. Morphologically normal sperm from normospermic samples (n = 10) or samples with a high incidence (≥ 15%) of sperm with CD (n = 9) had similar motility patterns and responses to procaine. The origin of morphologically normal sperm had no effect on sperm viability (p > 0.05; n = 26). In conclusion, a moderately enhanced prevalence of sperm with CD seems to be compensable by an increase in sperm numbers in boar semen doses.
Optical monitoring of the plant growth status using polarimetry
Authors: Kim Jongyoon , Shin Yu Kyeong , Nam Yunsu , Lee Jun Gu , Lee Ji-Hoon
Published: December 2022

Polarimetry is a powerful characterization technique that uses a wealth of information from electromagnetic waves, including polarization. Using the rich information provided by polarimetry, it is being actively studied in biomedical fields such as cancer and tumor diagnosis. Despite its importance and potential in agriculture, polarimetry for living plants has not been well studied. A Stokes polarimetric imaging system was built to determine the correlation between the polarization states of the light passing through the leaf and the growth states of lettuce. The Stokes parameter s3 associated with circular polarization increased over time and was strongly correlated with the growth of lettuce seedlings. In the statistical analysis, the distribution of s3 followed the generalized extreme value (GEV) probability density function. Salt stress retarded plant growth, and the concentration of treated sodium chloride (NaCl) showed a negative correlation with the location parameter μ of GEV. The clear correlation reported here will open the possibility of polarization measurements on living plants, enabling real-time monitoring of plant health.
Residual ST-segment elevation to predict long-term clinical and CMR-derived outcomes in STEMI
Authors: Merenciano-González Héctor , Marcos-Garcés Víctor , Gavara Jose , Pedro-Tudela Ana , Lopez-Lereu Maria P. , Monmeneu Jose V. , Perez Nerea , Rios-Navarro Cesar , de Dios Elena , Gabaldón-Pérez Ana , Albiach Cristina , Racugno Paolo , Bonanad Clara , Canoves Joaquim , Chorro Francisco J. , Bodi Vicente
Published: December 2022

Residual ST-segment elevation after ST-segment elevation myocardial infarction (STEMI) has traditionally been considered a predictor of left ventricular (LV) dysfunction and ventricular aneurism. However, the implications in terms of long-term prognosis and cardiac magnetic resonance (CMR)-derived structural consequences are unclear. A total of 488 reperfused STEMI patients were prospectively included. The number of Q wave leads with residual ST-segment elevation > 1 mm (Q-STE) at pre-discharge ECG was assessed. LV ejection fraction (LVEF, %) and infarct size (IS, % of LV mass) were quantified in 319 patients at 6-month CMR. Major adverse cardiac events (MACE) were defined as all-cause death and/or re-admission for acute heart failure (HF), whichever occurred first. During a mean follow-up of 6.1 years, 92 MACE (18.9%), 39 deaths and 53 HF were recorded. After adjustment for baseline characteristics, Q-STE (per lead with > 1 mm) was independently associated with a higher risk of long-term MACE (HR 1.24 [1.07–1.44] per lead, p = 0.004), reduced (< 40%) LVEF (HR 1.36 [1.02–1.82] per lead, p = 0.04) and large (> 30% of LV mass) IS (HR 1.43 [1.11–1.85] per lead, p = 0.006) at 6-month CMR. Patients with Q-STE ≥ 2 leads (n = 172, 35.2%) displayed lower MACE-free survival, more depressed LVEF, and larger IS at 6-month CMR (p < 0.001 for all comparisons). Residual ST-segment elevation after STEMI represents a universally available tool that predicts worse long-term clinical and CMR-derived structural outcomes.