bluuebunny/crossref_metadata_2025 huggingface dataset:
Computer vision-aided DEM study on the compaction characteristics of graded subgrade filler considering realistic coarse particle shapes
Authors: Li Taifeng , Xie Kang , Chen Xiaobin , Deng Zhixing , Su Qian
Published: December 2023

The compaction quality of subgrade filler strongly affects subgrade settlement. The main objective of this research is to analyze the macro- and micro-mechanical compaction characteristics of subgrade filler based on the real shape of coarse particles. First, an improved Viola–Jones algorithm is employed to establish a digitalized 2D particle database for coarse particle shape evaluation and discrete modeling purposes of subgrade filler. Shape indexes of 2D subgrade filler are then computed and statistically analyzed. Finally, numerical simulations are performed to quantitatively investigate the effects of the aspect ratio (AR) and interparticle friction coefficient (μ) on the macro- and micro-mechanical compaction characteristics of subgrade filler based on the discrete element method (DEM). The results show that with the increasing AR, the coarse particles are narrower, leading to the increasing movement of fine particles during compaction, which indicates that it is difficult for slender coarse particles to inhibit the migration of fine particles. Moreover, the average displacement of particles is strongly influenced by the AR, indicating that their occlusion under power relies on particle shapes. The displacement and velocity of fine particles are much greater than those of the coarse particles, which shows that compaction is primarily a migration of fine particles. Under the cyclic load, the interparticle friction coefficient μ has little effect on the internal structure of the sample; under the quasi-static loads, however, the increase in μ will lead to a significant increase in the porosity of the sample. This study could not only provide a novel approach to investigate the compaction mechanism but also establish a new theoretical basis for the evaluation of intelligent subgrade compaction.
Road Blocks or Building Blocks? A Qualitative Study on Challenges and Resilience in Romantic Relationships of Youth Exposed to Family Violence
Authors: Lünnemann M. K. M. , Van der Horst F. C. P. , Van de Bongardt D. , Steketee M.
Published: December 2023

Romantic relationships are an important part of many people’s lives and at least partly shaped by experiences during childhood. Youth exposed to family violence during childhood are more likely to experience difficulties in their later romantic relationships. However, a more holistic perspective on the romantic relationships of youth with a history of family violence is lacking. Using both theoretical and inductive thematic analysis, this qualitative study explored challenges as well as positive experiences within romantic relationships of youth exposed to family violence during childhood. In-depth individual interviews were conducted with 18 youth aged between 16 and 20 years, who were reported to child protection services. The narratives reflected that youth experienced challenges related to support, connection, trust, boundary setting, emotion regulation and conflict resolution. Furthermore, family violence during childhood seemed to be important in the emergence of these challenges, consistent with theoretical mechanisms described in observational learning theory and attachment theory. However, youth also described positive experiences in their romantic relationships and demonstrated an ability to learn from others (e.g., their current romantic partner) how to communicate effectively or solve problems. Therefore, with the right social or professional support, at-risk youth may be able to overcome these challenges.
The Impact of Childhood Trauma on Sensory Processing and Connected Motor Planning and Skills: A Scoping Review
Authors: Matson Rebecca , Barnes-Brown Vikki , Stonall Rachel
Published: December 2023

Background

Traumatic experiences during childhood have been suggested to alter the course of sensory and motor development due to the impact on neural connections within the brain at integral periods. This connection has been alluded to in literature and is discussed anecdotally by practitioners suggesting the impact is commonly seen in practice. Previous scoping reviews in this area have focused solely on the process of sensory modulation without exploring the connection to motor planning.

Objective

This scoping review considers what is known from the existing literature about the impact of childhood trauma on sensory processing and motor skills.

Method

This scoping review followed the JBI methodology for scoping reviews (Peters et al., 2020), searching CINAHL plus, Proquest, Scopus, PsycINFO, EThOS, as well as a search of the reference lists of the articles and citation chaining, to locate both published and unpublished sources. Articles were reviewed by two reviewers independently, with a third reviewer verifying those that met inclusion criteria where there was disagreement.

Results

Six articles were identified that met the inclusion criteria for the study. While all included studies suggested the concurrence of sensory processing and motor difficulties in individuals who have experienced childhood trauma they did not conclusively make the link between the two suggesting an overall low level of evidence. Commonalities were identified in relation to the areas of the brain impacted and the nature of difficulties experienced with some suggestion of this varying according to stage of development and the specific nature of the trauma.

Conclusions

This study suggests emerging evidence in relation to the connection between trauma, sensory processing and motor development but that further empirical research is needed to verify this and inform practice.
Chemical Scissors Tailored Nano-Tellurium with High-Entropy Morphology for Efficient Foam-Hydrogel-Based Solar Photothermal Evaporators
Authors: Xing Chenyang , Li Zihao , Wang Ziao , Zhang Shaohui , Xie Zhongjian , Zhu Xi , Peng Zhengchun
Published: December 2023

The development of tellurium (Te)-based semiconductor nanomaterials for efficient light-to-heat conversion may offer an effective means of harvesting sunlight to address global energy concerns. However, the nanosized Te (nano-Te) materials reported to date suffer from a series of drawbacks, including limited light absorption and a lack of surface structures. Herein, we report the preparation of nano-Te by electrochemical exfoliation using an electrolyzable room-temperature ionic liquid. Anions, cations, and their corresponding electrolytic products acting as chemical scissors can precisely intercalate and functionalize bulk Te. The resulting nano-Te has high morphological entropy, rich surface functional groups, and broad light absorption. We also constructed foam hydrogels based on poly (vinyl alcohol)/nano-Te, which achieved an evaporation rate and energy efficiency of 4.11 kg m−2 h−1 and 128%, respectively, under 1 sun irradiation. Furthermore, the evaporation rate was maintained in the range 2.5–3.0 kg m−2 h−1 outdoors under 0.5–1.0 sun, providing highly efficient evaporation under low light conditions.
Relationship Between ADHD-Like Traits and Emotion Dysregulation in the Adult General Population
Authors: Albesisi Siham , Overton Paul G.
Published: December 2023

Objectives

Attention Deficit Hyperactivity Disorder (ADHD) is a neurodevelopmental disorder classically characterised by inattention and/or hyperactivity/impulsivity. However, emotion-related problems are also common in people with ADHD, although there is disagreement about their relationship with the classical symptoms of ADHD. Here, we investigated the relationship between emotion dysregulation and ADHD-like traits in a non-clinical group of adults.

Method

In a group of 1074 individuals, average age 30.27 years, 656 females, 402 males and 16 who identified as ‘other’, with 76.8% describing themselves as ‘white’, were administered the Adult ADHD Self-Report Scale (ASRS) and the Difficulties in Emotion Regulation Scale (DERS) to measure ADHD-like traits and emotion dysregulation, respectively.

Results

The Inattention subscale of the ASRS was significantly correlated with all subscales of the DERS. Similarly, the Hyperactivity/impulsivity subscale was correlated with all subscales of the DERS except for the Lack of emotional awareness. The Lack of emotional clarity and Difficulties engaging in goal-directed behaviour subscales of the DERS were significant independent positive predictors of ASRS inattention scores. Non-acceptance of emotional responses, Difficulties engaging in goal-directed behaviour, Impulse control difficulties and Lack of emotional clarity subscales of the DERS were significant independent positive predictors of ASRS hyperactivity/impulsivity scores. In other words, as inattention and hyperactive/impulsive symptoms increased in severity, there was a concomitant increase in the severity of most aspects of emotion dysregulation.

Conclusions

The close association between emotion dysregulation and the classical symptoms of ADHD suggests that they may arise from a common dysfunctional substrate and hence treating emotion dysregulation may provide a novel pathway by which to treat the classical symptoms.
Roles and mechanisms of carbonaceous materials in advanced oxidation coupling processes for degradation organic pollutants in wastewater: a review
Authors: Zou Qianqian , Wang Bing , Gao Bin , Jiang Tao , Feng Qianwei , Chen Miao , Zhang Jian , Zhang Xueyang
Published: December 2023

The widespread organic pollutants in wastewater are one of the global environmental problems. Advanced oxidation processes (AOPs) are widely used because of their characteristics of high efficiency and strong oxidation. However, AOPs may have some defects, such as incomplete mineralization of organic pollutants and the generation of toxic by-products during the degradation process, thus it is essential to seek efficient and green wastewater treatment technologies. Coupling different AOPs or other processes is beneficial for the mineralization of pollutants and reduces ecological risks to the environment. It is worth noting that carbonaceous materials (CMs) have received widespread attention and application in the degradation of organic pollutants in water by advanced oxidation coupling processes (C-AOPs) due to their excellent physicochemical properties in recent years. However, the behaviors and mechanisms of C-AOPs based on CMs on the degradation of organic pollutants are still unknown. Therefore, it is essential to comprehensively summarize the recent research progress. In this review, the applications of different CMs in C-AOPs were reviewed first. Secondly, the synergistic mechanisms of the C-AOPs based on different CMs were discussed. Then, toxic intermediates were explored and important toxicity assessment methods were proposed. Finally, the application potential of the C-AOPs in the future and the challenges were proposed. This review provides an important reference for the application and optimization of the C-AOPs in organic wastewater treatment in the future.

Graphical Abstract
Parametrized Optimization Based on an Investigation of Musical Similarities Using SPARK and Hadoop
Authors: Chaudhary Savita , Karthik V. , Shankar R. , Taranum Ayesha , Naresh E.
Published: December 2023

The big data processing framework Spark is used to power a parameterizable recommender system that can make recommendations for music based on a user’s individual tastes and take into account a variety of musical tonal qualities. The system as it is presently built is completely scalable, which means that additional songs can be contributed to the data, the cluster size could be increased, and new types of audio information, in addition to more cutting-edge similarity evaluations, may be included. Another issue discussed in this research paper is the parallel collection of required audio characteristics on a computer cluster. Song recommendations for a dataset including more than 114,000 songs may be created on a Spark cluster with 16 nodes in under 12 s by integrating eight distinct audio feature types and similarity assessments. After the features have been retrieved, they are sent to the Spark-based recommender system to be processed. The calculated distance was displayed, examined, and graphically depicted. By computing the distance depending on the melody, rhythmic, and timbral components of the music, the final software controls song suggestion.
The Proportion of Normalized Hips with Growth in Japanese Adolescents Aged > 10 years with Acetabular Dysplasia who Presented with Suspected Scoliosis
Authors: Nishimura Takahiro , Watanabe Hideaki , Taki Naoya , Kikkawa Ichiro
Published: December 2023

Background

If asymptomatic acetabular dysplasia (AD) is incidentally identified in adolescence, it is difficult to determine the appropriate follow-up or treatment strategy because the acetabulum is still developing. We investigated the rate of AD normalization at the end of acetabular growth.

Methods

This cross-sectional study involved 653 patients (1306 hips) aged 10–14 years with scoliosis or suspected scoliosis. All patients underwent plain standing whole-spine radiography (with the pelvis included) at the first visit. We measured the lateral center–edge angle, Sharp angle, Tönnis angle, and acetabular head index on radiographs. The criterion for AD was a lateral center–edge angle of < 20°. We extracted the data of patients aged < 12 (10–11) years and ≥ 12 (12–14) years with AD. Furthermore, we analyzed the radiographic follow-up data at 15 years of age to identify the AD normalization rate.

Results

AD was diagnosed in 19 hips from patients aged < 12 years and in 36 hips from patients aged ≥ 12 years. The AD normalization rate at 15 years of age was 31.6% in those diagnosed at < 12 years of age and 5.6% in those diagnosed at ≥ 12 years of age.

Conclusion

AD in adolescence was predictive of AD at the end of growth in 95% of cases diagnosed at ≥ 12 years of age compared with approximately 70% of cases diagnosed at < 12 years of age. Surgical treatment before completion of acetabular growth is beneficial for acetabular remodeling, but the decision to operate should be carefully evaluated in patients aged < 12 years.

Graphical Abstract
A Noninvasive Approach to Evaluate Tumor Immune Microenvironment and Predict Outcomes in Hepatocellular Carcinoma
Authors: Wu Jianmin , Liu Wanmin , Qiu Xinyao , Li Jing , Song Kairong , Shen Siyun , Huo Lei , Chen Lu , Xu Mingshuang , Wang Hongyang , Jia Ningyang , Chen Lei
Published: December 2023

It is widely recognized that tumor immune microenvironment (TIME) plays a crucial role in tumor progression, metastasis, and therapeutic response. Despite several noninvasive strategies have emerged for cancer diagnosis and prognosis, there are still lack of effective radiomic-based model to evaluate TIME status, let alone predict clinical outcome and immune checkpoint inhibitor (ICIs) response for hepatocellular carcinoma (HCC). In this study, we developed a radiomic model to evaluate TIME status within the tumor and predict prognosis and immunotherapy response. A total of 301 patients who underwent magnetic resonance imaging (MRI) examinations were enrolled in our study. The intra-tumoral expression of 17 immune-related molecules were evaluated using co-detection by indexing (CODEX) technology, and we construct Immunoscore (IS) with the least absolute shrinkage and selection operator (LASSO) algorithm and Cox regression method to evaluate TIME. Of 6115 features extracted from MRI, five core features were filtered out, and the Radiomic Immunoscore (RIS) showed high accuracy in predicting TIME status in testing cohort (area under the curve = 0.753). More importantly, RIS model showed the capability of predicting therapeutic response to anti-programmed cell death 1 (PD-1) immunotherapy in an independent cohort with advanced HCC patients (area under the curve = 0.731). In comparison with previously radiomic-based models, our integrated RIS model exhibits not only higher accuracy in predicting prognosis but also the potential guiding significance to HCC immunotherapy.
Multiscale transforms for signals on simplicial complexes
Authors: Saito Naoki , Schonsheck Stefan C. , Shvarts Eugene
Published: December 2023

Our previous multiscale graph basis dictionaries/graph signal transforms—Generalized Haar-Walsh Transform (GHWT); Hierarchical Graph Laplacian Eigen Transform (HGLET); Natural Graph Wavelet Packets (NGWPs); and their relatives—were developed for analyzing data recorded on vertices of a given graph. In this article, we propose their generalization for analyzing data recorded on edges, faces (i.e., triangles), or more generally $$\kappa $$
κ
-dimensional simplices of a simplicial complex (e.g., a triangle mesh of a manifold). The key idea is to use the Hodge Laplacians and their variants for hierarchical partitioning of a set of $$\kappa $$
κ
-dimensional simplices in a given simplicial complex, and then build localized basis functions on these partitioned subsets. We demonstrate their usefulness for data representation on both illustrative synthetic examples and real-world simplicial complexes generated from a co-authorship/citation dataset and an ocean current/flow dataset.
8 Greek art: recent developments and current trends
Authors: Smith Tyler Jo
Published: December 2023

This review essay focuses on recent developments and trends in the study of ancient Greek art. The publications covered date primarily to the period beginning in 2017–2018, though selected earlier works have been included where considered to be of particular merit or importance. Examples have been chosen to span and represent the long Archaic to Hellenistic phases (eighth–first century BC), and a full range of artistic categories and media have been featured in the discussions. In order to structure the large quantity of bibliography available, the presentation is divided into several broad categories according to themes (e.g. sites, reports, guides; exhibitions, conferences, Festschriften) or materials (e.g. sculpture and terracottas; metals, coins, gems, and jewellery). Where possible, digital resources applicable to the discipline have also been mentioned and cited. By way of conclusion, some general observations are made about the subjects of Greek art that seem not only to be the most prevalent in recent scholarship, but also transcend artistic medium, style, and scale – among them the body and adornment, senses and emotion, aesthetics and beauty, religion and performance, and archaeological contexts and intercultural connections.
3 Newsround
Authors: Evans Matthew P. , Mouratidis Georgios
Published: December 2023

‘Newsround’ offers a platform for new discoveries that do not appear within the specialist contributions of this year’s Archaeological Reports, but which nevertheless warrant emphasis, either as a result of their particular characteristics or for the contribution they make to broader archaeological narratives. This section is not intended to be exhaustive, but rather an overview of archaeological research in Greece. It comprises largely preliminary reports (results of excavations that took place up to and including August 2023, where possible) that complement the digital content made available through Archaeology in Greece Online (https://chronique.efa.gr). Due to the diachronic nature of a number of the sites, and for ease of reference, the material is organized geographically in the first instance and then chronologically (earliest to latest) within each section as far as possible.
Elasticity of Anhydrous Phase B Under Mantle Conditions: Implications for the Deep X‐Discontinuity in the Subduction Zones
Authors: Song Jian , Wang Wenzhong , Wu Zhongqing
Published: December 2023

Anhydrous phase B (anh‐B) is a dense magnesium silicate with the composition Mg14Si5O24 and space group Pmcb. In magnesium‐rich environments, forsterite reacts with periclase to form anh‐B, and the formation of anh‐B was proposed as a plausible mechanism for the origin of the X‐discontinuity. However, the elastic properties of anh‐B, which are critical for evaluating the seismic features associated with its formation, have not been determined. In this study, we investigated the elasticity of anh‐B at high pressure and temperature via first‐principles calculations. Combining with the elasticity of other minerals, we determined the contrasts caused by the formation of anh‐B: ∼3%, ∼7%, and ∼10% jumps for density, VP, and VS, respectively. The 2%–8% impedance contrasts of the X‐discontinuity can be explained by the formation of 15–60 vol% anh‐B, which requires 3–12 vol% MgO as a reactant.
Ozone Fluxes Over a Boreal Lake Exhibit Enhanced Deposition at Nights
Authors: Fung P. L. , Rannik Ü. , Mammarella I. , Vesala T.
Published: December 2023

A few studies on ozone deposition over lake water are available and so far only one using the eddy covariance technique (Wesely et al., 1981, https://doi.org/10.1007/BF00122295). A 23‐day field campaign was held in August‐September 2012 at the Lake Kuivajärvi in Hyytiälä, Finland. The results showed a mean flux of −30 ± 1 ng m−2 s−1 and deposition velocity of 0.86 ± 0.05 mm s−1. Deposition velocity showed a weak diurnal cycle over the lake with elevated values during the nighttime. The daytime and nighttime portions of the data set differed statistically. Analysis showed that waterside convective mixing enhanced deposition and such conditions pre‐dominantly occurred during nighttime. We compared the measured deposition velocities with the dry deposition model of air‐sea exchange, adjusted for the chemical sinks relevant for the lake. We suggest that the buoyant mixing and unaccounted chemistry can be responsible for the difference between the model results and observations.
A Potential Reason for a More CP El Nino‐Like SSTA Performance in CMIP6 Simulations
Authors: Wang Li‐Chiao , Lin Yu‐Shen
Published: December 2023

A systematic bias of the extremely westward zonal current (EWZC) was revealed over the equatorial Pacific in Coupled Model Intercomparison Project 6 (CMIP6) models. It tends to weaken the modeled interannual variability of equatorial zonal current anomaly (ZCA) with its maximum variability concentrated in the western Pacific. A mixed‐layer heat budget analysis demonstrates that the simulation of mean circulation effect is slightly affected by the zonal current bias. However, the zonal advective feedback is closely linked to the biased equatorial ZCA variability and is overestimated (underestimated) in the Niño‐4 (Niño‐3) region. The magnitude of zonal advective feedback is even greater than that of thermocline feedback and becomes the most dominant process contributing to the growth of mixed‐layer temperature anomaly tendency in the Niño‐4 region. Such a bias is essential for a more central‐Pacific El Niño‐like performance in CMIP6 models.
The Effects of African Easterly Wave Suppression by Wave Track on Atlantic Tropical Cyclones
Authors: Bercos‐Hickey Emily , Patricola Christina M.
Published: December 2023

It is well established that African easterly waves (AEWs) can serve as seedling disturbances for Atlantic tropical cyclones (TCs). However, research has shown that AEWs are not necessary to maintain specifically basin‐wide TC frequency. Here, we for the first time investigate the effects of AEW suppression by wave track on Atlantic TC activity. Regional model simulations were performed, where AEWs were either prescribed or suppressed from the eastern lateral boundary condition. We found that without AEWs, there was an increase in TC frequency and strength, with the most pronounced increases occurring when the waves were suppressed in the south track. These changes coincided with more favorable environmental conditions and disturbances associated with increased convective activity over the Atlantic. Our results indicate that AEWs are not a limiting factor for TCs, and that AEW suppression, specifically in the south track, can affect the large‐scale environment to enhance favorability for TC genesis.
Combined Effect of Anthropogenic and “Natural” Carbon on Acidification of the Subsurface Ocean Water at the Tip of the Antarctic Peninsula
Authors: Zhan Liyang , Zhang Jiexia , Wu Man , Liu Jian , Ye Wangwang , Sun Heng , Guo Xianghui , Zhao Jun , Gao Zhongyong
Published: December 2023

Dissolved inorganic carbon, total alkalinity, and dissolved N2O samples of upper 500 m were collected at the tip of the Antarctic Peninsula during the 32nd Chinese Antarctic National Research Expedition. The pH and anthropogenic carbon were calculated and the results show that the patterns of anthropogenic carbon uptake and acidification progresses are different in two adjacent regions of this study area. In the region of Weddell‐Scotia confluence, hydrographic processes such as convection prompt the transport of anthropogenic carbon into the subsurface layer, whereas in the region east of Powell Basin, where stratification existed, the downward transport of anthropogenic carbon to this depth is inhibited. However, the pH values indicate that the acidification status of the subsurface waters that are influenced by the above two hydrographic features are similar or even identical at a certain depth range. The progress of ocean acidification in the well‐ventilated region are dominated by anthropogenic carbon uptake, while in the adjacent well‐stratified region, anthropogenic carbon uptake and in situ remineralization of organic matter or horizontal advection of carbon rich water masses or both. In the later region, anthropogenic carbon uptake and in situ remineralization (or horizontal advection) contribute 40% and 60% to pH decline, respectively, suggesting that pH value in water mass of this region may significantly influenced by natural processes.
Occurrence of Large Geomagnetically Induced Currents Within the EPRI SUNBURST Monitoring Network
Authors: Ngwira Chigomezyo M. , Arritt Robert , Perry Charles , Weygand James M. , Sharma Rishi
Published: December 2023

Space weather, a natural hazard, can adversely impact human technological assets. High‐voltage electric power transmission grids constitute one of the most critical technological systems vulnerable to space weather driven geomagnetically induced currents (GICs). One of the major challenges pertaining to the study of GICs over the continental United States has been the availability of GIC measurements, which are critical for validation of geoelectric field and power flow models, for example. In this study, we analyze GIC measurements collected at 17 Electrical Power Research Institute (EPRI) SUNBURST transformer locations across the United States for which a GIC value of 10 A or greater was recorded. This data set includes 52 individual geomagnetic storms with Kp index 6 and above during the period from 2010 to 2021. The analysis confirms that there is a good correlation between the number of geomagnetic storms per year and the number of recorded GIC events. Our results also show that about 76% of the top 17 GIC events are associated with the storm main phase, while only 24% are attributed to storm sudden commencements. In addition, it is shown, for the first time, that mid‐latitude positive bays can cause large GICs over the continental United States. Finally, this study shows that the largest measured GIC event in the data set was associated with a localized intense dB/dt structure, which could be attributed to substorm activity.
Secreted miR-210-3p, miR-183-5p and miR-96-5p reduce sensitivity to docetaxel in prostate cancer cells
Authors: Canovai Maristella , Evangelista Monica , Mercatanti Alberto , D’Aurizio Romina , Pitto Letizia , Marrocolo Francesca , Casieri Valentina , Pellegrini Marco , Lionetti Vincenzo , Bracarda Sergio , Rizzo Milena
Published: December 2023

Docetaxel (DCT) resistance is one of the main factors responsible for treatment failure in metastatic prostate cancer (PCa). Although several mechanisms of DCT resistance have been elucidated, the issue is still far from comprehensive. In this work we show that miR-96-5p, miR-183-5p and miR-210-3p (referred to as sDCTR-miRNAs) are specifically released by DCT resistant (DCTR) PCa clones and decrease the efficacy of DCT in PCa cells when overexpressed. Through bioinformatic analysis, we identified several potential targets of sDCTR-miRNAs’ activity including FOXO1, IGFBP3, and PDCD4 known to exert a role in DCT resistance. Additionally, we found that PPP2CB and INSIG1 mediated the ability of sDCTR-miRNAs to reduce the efficacy of DCT. We explored whether secreted sDCTR-miRNAs could affect the phenotype of PCa cells. We found that exposure to exosomes derived from DCTR PCa clones (in which the content of sDCTR-miRNAs was higher than in exosomes from parental cells), as well as exposure to exosome loaded with sDCTR-miRNAs, reduced the cytotoxicity of DCT in PCa cells sensitive to the drug. Finally, we validated circulating miR-183-5p and miR-21-5p as potential predictive biomarkers of DCT resistance in PCa patients. Our study suggests a horizontal transfer mechanism mediated by exosomal miRNAs that contributes to reduce docetaxel sensitivity and highlights the relevance of cell-to-cell communication in drug resistance.
Quantitative proteomics defines mechanisms of antiviral defence and cell death during modified vaccinia Ankara infection
Authors: Albarnaz Jonas D. , Kite Joanne , Oliveira Marisa , Li Hanqi , Di Ying , Christensen Maria H. , Paulo Joao A. , Antrobus Robin , Gygi Steven P. , Schmidt Florian I. , Huttlin Edward L. , Smith Geoffrey L. , Weekes Michael P.
Published: December 2023

Modified vaccinia Ankara (MVA) virus does not replicate in human cells and is the vaccine deployed to curb the current outbreak of mpox. Here, we conduct a multiplexed proteomic analysis to quantify >9000 cellular and ~80% of viral proteins throughout MVA infection of human fibroblasts and macrophages. >690 human proteins are down-regulated >2-fold by MVA, revealing a substantial remodelling of the host proteome. >25% of these MVA targets are not shared with replication-competent vaccinia. Viral intermediate/late gene expression is necessary for MVA antagonism of innate immunity, and suppression of interferon effectors such as ISG20 potentiates virus gene expression. Proteomic changes specific to infection of macrophages indicate modulation of the inflammatory response, including inflammasome activation. Our approach thus provides a global view of the impact of MVA on the human proteome and identifies mechanisms that may underpin its abortive infection. These discoveries will prove vital to design future generations of vaccines.
STalign: Alignment of spatial transcriptomics data using diffeomorphic metric mapping
Authors: Clifton Kalen , Anant Manjari , Aihara Gohta , Atta Lyla , Aimiuwu Osagie K. , Kebschull Justus M. , Miller Michael I. , Tward Daniel , Fan Jean
Published: December 2023

Spatial transcriptomics (ST) technologies enable high throughput gene expression characterization within thin tissue sections. However, comparing spatial observations across sections, samples, and technologies remains challenging. To address this challenge, we develop STalign to align ST datasets in a manner that accounts for partially matched tissue sections and other local non-linear distortions using diffeomorphic metric mapping. We apply STalign to align ST datasets within and across technologies as well as to align ST datasets to a 3D common coordinate framework. We show that STalign achieves high gene expression and cell-type correspondence across matched spatial locations that is significantly improved over landmark-based affine alignments. Applying STalign to align ST datasets of the mouse brain to the 3D common coordinate framework from the Allen Brain Atlas, we highlight how STalign can be used to lift over brain region annotations and enable the interrogation of compositional heterogeneity across anatomical structures. STalign is available as an open-source Python toolkit at https://github.com/JEFworks-Lab/STalign and as Supplementary Software with additional documentation and tutorials available at https://jef.works/STalign.
IgG and IgM cooperate in coating of intestinal bacteria in IgA deficiency
Authors: Eriksen Carsten , Moll Janne Marie , Myers Pernille Neve , Pinto Ana Rosa Almeida , Danneskiold-Samsøe Niels Banhos , Dehli Rasmus Ibsen , Rosholm Lisbeth Buus , Dalgaard Marlene Danner , Penders John , Jonkers Daisy MAE , Pan-Hammarström Qiang , Hammarström Lennart , Kristiansen Karsten , Brix Susanne
Published: December 2023

Immunoglobulin A (IgA) is acknowledged to play a role in the defence of the mucosal barrier by coating microorganisms. Surprisingly, IgA-deficient humans exhibit few infection-related complications, raising the question if the more specific IgG may help IgM in compensating for the lack of IgA. Here we employ a cohort of IgA-deficient humans, each paired with IgA-sufficient household members, to investigate multi-Ig bacterial coating. In IgA-deficient humans, IgM alone, and together with IgG, recapitulate coating of most bacterial families, despite an overall 3.6-fold lower Ig-coating. Bacterial IgG coating is dominated by IgG1 and IgG4. Single-IgG2 bacterial coating is sparse and linked to enhanced Escherichia coli load and TNF-α. Although single-IgG2 coating is 1.6-fold more prevalent in IgA deficiency than in healthy controls, it is 2-fold less prevalent than in inflammatory bowel disease. Altogether we demonstrate that IgG assists IgM in coating of most bacterial families in the absence of IgA and identify single-IgG2 bacterial coating as an inflammatory marker.
A toolkit for capturing a representative and equitable sample in health research
Authors: Retzer Ameeta , Ciytak Bircan , Khatsuria Foram , El-awaisi Juma , Harris Isobel M. , Chapman Laura , Kelly Tony , Richards Jenny , Lam Emily , Newsome Philip N. , Calvert Melanie ,   NIHR Birmingham Biomedical Research Centre REP-EQUITY Group, El-awaisi Juma , Filer Andrew , Shetty Shishir , Parish Jo , Watson Steve , Sapey Elizabeth , Gillet Caroline , Palmer Jo , Yonel Zehra , Miah Zohur , Alderman Joseph , Laws Elinor , Liu Xiaoxuan
Published: December 2023

Research participants often do not represent the general population. Systematic exclusion of particular groups from research limits the generalizability of research findings and perpetuates health inequalities. Groups considered underserved by research include those whose inclusion is lower than expected based on population estimates, those with a high healthcare burden but limited research participation opportunities and those whose healthcare engagement is less than others. The REP-EQUITY toolkit guides representative and equitable inclusion in research. The toolkit was developed through a methodological systematic review and synthesis and finalized in a consensus workshop with 24 participants. The REP-EQUITY toolkit describes seven steps for investigators to consider in facilitating representative and equitable sample selection. This includes clearly defining (1) the relevant underserved groups, (2) the aims relating to equity and representativeness, (3) the sample proportion of individuals with characteristics associated with being underserved by research, (4) the recruitment goals, (5) the strategies by which external factors will be managed, (6) the methods by which representation in the final sample will be evaluated and (7) the legacy of having used the toolkit. Using the REP-EQUITY toolkit could promote trust between communities and research institutions, increase diverse participation in research and improve the generalizability of health research. National Institute for Health and Care Research PROSPERO identifier: CRD42022355391.
FilGAP regulates tumor growth in Glioma through the regulation of mTORC1 and mTORC2
Authors: Tsutsumi Koji , Nohara Ayumi , Tanaka Taiki , Murano Moe , Miyagaki Yurina , Ohta Yasutaka
Published: December 2023

The mechanistic target of rapamycin (mTOR) is a serine/threonine protein kinase that forms the two different protein complexes, known as mTORC1 and mTORC2. mTOR signaling is activated in a variety of tumors, including glioma that is one of the malignant brain tumors. FilGAP (ARHGAP24) is a negative regulator of Rac, a member of Rho family small GTPases. In this study, we found that FilGAP interacts with mTORC1/2 and is involved in tumor formation in glioma. FilGAP interacted with mTORC1 via Raptor and with mTORC2 via Rictor and Sin1. Depletion of FilGAP in KINGS-1 glioma cells decreased phosphorylation of S6K and AKT. Furthermore, overexpression of FilGAP increased phosphorylation of S6K and AKT, suggesting that FilGAP activates mTORC1/2. U-87MG, glioblastoma cells, showed higher mTOR activity than KINGS-1, and phosphorylation of S6K and AKT was not affected by suppression of FilGAP expression. However, in the presence of PI3K inhibitors, phosphorylation of S6K and AKT was also decreased in U-87MG by depletion of FilGAP, suggesting that FilGAP may also regulate mTORC2 in U-87MG. Finally, we showed that depletion of FilGAP in KINGS-1 and U-87MG cells significantly reduced spheroid growth. These results suggest that FilGAP may contribute to tumor growth in glioma by regulating mTORC1/2 activities.
Hippocampal CaMKII inhibition induces reactivation-dependent amnesia for extinction memory and causes fear relapse
Authors: Radiske Andressa , de Castro Carla Miranda , Rossato Janine I. , Gonzalez Maria Carolina , Cammarota Martín
Published: December 2023

Hippocampal GluN2B subunit-containing NMDAR (GluN2B-NMDAR) activation during recall destabilizes fear extinction memory, which must undergo brain-derived neurotrophic factor (BDNF)-dependent reconsolidation to persist. Ca2+/calmodulin-dependent protein kinase II (CaMKII) is a Ser/Thr protein kinase essential for hippocampus-dependent memory processing that acts downstream GluN2B-NMDAR and controls BDNF expression, but its participation in fear extinction memory reconsolidation has not yet been studied. Using a combination of pharmacological and behavioral tools, we found that in adult male Wistar rats, intra dorsal-CA1 administration of the CaMKII inhibitors autocamtide-2-related inhibitory peptide (AIP) and KN-93, but not of their inactive analogs scrambled AIP and KN-92, after fear extinction memory recall impaired extinction and caused GluN2B-NMDAR-dependent recovery of fear. Our results indicate that hippocampal CaMKII is necessary for fear extinction reconsolidation, and suggest that modulation of its activity around the time of recall controls the inhibition that extinction exerts on learned fear.
Designing secure PUF-based authentication protocols for constrained environments
Authors: Lee Sang-Woong , Safkhani Masoumeh , Le Quynh , Ahmed Omed Hassan , Hosseinzadeh Mehdi , Rahmani Amir Masoud , Bagheri Nasour
Published: December 2023

Physical Unclonable Functions (PUFs) are widely used in cryptographic authentication and key-agreement protocols due to their unique physical properties. This article presents a comprehensive cryptanalysis of two recently developed authentication protocols, namely PLAKE and EV-PUF, both relying on PUFs. Our analysis reveals significant vulnerabilities in these protocols, including susceptibility to impersonation and key leakage attacks, which pose serious threats to the security of the underlying systems. In the case of PLAKE, we propose an attack that can extract the shared secret key with negligible complexity by eavesdropping on consecutive protocol sessions. Similarly, we demonstrate an efficient attack against EV-PUF that enables the determination of the shared key between specific entities. Furthermore, we highlight the potential for a single compromised client in the EV-PUF protocol to compromise the security of the entire network, leaving it vulnerable to pandemic attacks. These findings underscore the critical importance of careful design and rigorous evaluation when developing PUF-based authentication protocols. To address the identified vulnerabilities, we present an improved PUF-based authentication protocol that ensures robust security against all the attacks described in the context of PLAKE and EV-PUF. Through this research, we contribute to the field by exposing vulnerabilities in existing PUF-based authentication protocols and offering an improved protocol that enhances security and safeguards against various attack vectors. This work serves as a valuable reference for researchers and practitioners involved in the design and implementation of secure authentication schemes for IoT systems and dynamic charging systems for electric vehicles.
Effects of mobile phone electromagnetic fields on brain waves in healthy volunteers
Authors: van der Meer Johan N. , Eisma Yke B. , Meester Ronald , Jacobs Marc , Nederveen Aart J.
Published: December 2023

The interaction between biological tissue and electromagnetic fields (EMF) is a topic of increasing interest due to the rising prevalence of background EMF in the past decades. Previous studies have attempted to measure the effects of EMF on brainwaves using EEG recordings, but are typically hampered by experimental and environmental factors. In this study, we present a framework for measuring the impact of EMF on EEG while controlling for these factors. A Bayesian statistical approach is employed to provide robust statistical evidence of the observed EMF effects. This study included 32 healthy participants in a double-blinded crossover counterbalanced design. EEG recordings were taken from 63 electrodes across 6 brain regions. Participants underwent a measurement protocol comprising two 18-min sessions with alternating blocks of eyes open (EO) and eyes closed (EC) conditions. Group 1 (n = 16) had EMF during the first session and sham during the second session; group 2 (n = 16) had the opposite. Power spectral density plots were generated for all sessions and brain regions. The Bayesian analysis provided statistical evidence for the presence of an EMF effect in the alpha band power density in the EO condition. This measurement protocol holds potential for future research on the impact of novel transmission protocols.
Dictionary-based matching graph network for biomedical named entity recognition
Authors: Lou Yinxia , Zhu Xun , Tan Kai
Published: December 2023

Biomedical named entity recognition (BioNER) is an essential task in biomedical information analysis. Recently, deep neural approaches have become widely utilized for BioNER. Biomedical dictionaries, implemented through a masked manner, are frequently employed in these methods to enhance entity recognition. However, their performance remains limited. In this work, we propose a dictionary-based matching graph network for BioNER. This approach utilizes the matching graph method to project all possible dictionary-based entity combinations in the text onto a directional graph. The network is implemented coherently with a bi-directional graph convolutional network (BiGCN) that incorporates the matching graph information. Our proposed approach fully leverages the dictionary-based matching graph instead of a simple masked manner. We have conducted numerous experiments on five typical Bio-NER datasets. The proposed model shows significant improvements in F1 score compared to the state-of-the-art (SOTA) models: 2.8% on BC2GM, 1.3% on BC4CHEMD, 1.1% on BC5CDR, 1.6% on NCBI-disease, and 0.5% on JNLPBA. The results show that our model, which is superior to other models, can effectively recognize natural biomedical named entities.
Socioeconomic status and healthcare utilization disparities among children with epilepsy in the United States: Results from a nationally representative sample
Authors: Muthiah Nallammai , Rothenberger Scott , Abel Taylor J.
Published: December 2023

Epilepsy affects 1% of the US population. Healthcare disparities are well-studied among adults with epilepsy but less so among children. We examined whether children with epilepsy (1) have lower income than or (2) utilize the emergency department (ED) differently from children without epilepsy, and (3) if income moderates ED utilization. Data from the 2016–2019 National Survey of Children’s Health were used to identify children with active “epilepsy or seizure disorder”. Children with versus without epilepsy were compared. Income and ED visits were modeled with logistic and Poisson regressions. This analysis included 131,326 children; 835 were diagnosed with epilepsy. Estimated population prevalence of epilepsy was 0.6%. Children from higher-income-households were less likely to have epilepsy (aOR: 0.7). Children with epilepsy were more likely to visit EDs (aOR = 10.2), see healthcare professionals (aOR: 2.7), and receive care from specialists (aOR: 10.3). Income moderated the relationship between having epilepsy and ED visits. 7.7% of children with epilepsy did not receive needed healthcare. Some barriers were acquiring appointments (aOR: 3.9) and transportation (aOR: 4.7). In conclusion, children with epilepsy were more likely than children without epilepsy to live in lower-income-households, visit EDs, see healthcare professionals, and not receive needed healthcare. Barrier-specific policy interventions may improve medical access for children with epilepsy.
Stability analysis of dual solutions for mixed convection and thermal radiation with hybrid nanofluid flow past shrinking/stretching curved surface
Authors: Ibrahim Wubshet , Gizewu Tezera
Published: December 2023

This study portrays the stability analysis and dual solutions of mixed convection and thermal radiation of hybrid nano-fluid flow past stretching/shrinking a curved surface in the presence of injection/suction conditions. A hybrid nano-fluid, in which water is used as the base fluid, copper and alumina are used as nano-particles, and the magnetic field is taken into account. The present study’s findings will provide fruitful implications for future research in the field of fluid dynamics. The bvp4c method using Matlab software is implemented to get the numerical solution of the nonlinear partial differential equation transformed into the ordinary differential equation. The behavior of the first and second solutions under the governing parameters on the curved surface of dimensionless velocity $$g'(\xi )$$

g
′

(
ξ
)

, shear stress profile $$g''(\xi )$$

g

′
′

(
ξ
)

, temperature profile $$\theta (\xi )$$

θ
(
ξ
)

, skin friction coefficient Cfs, and local Nusselt’s number Nus were visualized in figurative and tabular form. From this the following are investigated: as the values of $$\phi j$$

ϕ
j

increase, the velocity profile for the second solution decreases, and the opposite trend is observed for the first solution. For the values of K and $$\lambda 1$$

λ
1

, the shear stress profile increased for the first solution, and the opposite trend was observed for the second solution, though after some interval points, the inverse of this statement was observed.For the values of $$S,Pr,Rd,M, \;\text{and}\; \lambda$$

S
,
P
r
,
R
d
,
M
,

and

λ

, the upwind thermal boundary layer of the first solution is larger than the second solution.For the value of M uphill, the estimation of the absolute value of $$\lambda ci$$

λ
c
i

increases for both the skin friction coefficient and the local Nusselt number. In the second solution, increasing the values of $$\beta$$
β
, Pr, S, Ec, and M has a similar effect on $$g''(0)$$

g

′
′

(
0
)

, Cfs, -$$\theta '(0)$$

θ
′

(
0
)

, and Nus. In the first solution, increasing the values of Ec, S, and Pr on $$g''(0)$$

g

′
′

(
0
)

and Cfs results in a decrease. The first solution has a positive eigenvalue, whereas the second solution has a negative eigenvalue. Agreement between the present analysis and literature is acceptable.