bluuebunny/crossref_metadata_2025 huggingface dataset:
Broad protection against clade 1 sarbecoviruses after a single immunization with cocktail spike-protein-nanoparticle vaccine
Authors: Halfmann Peter J. , Loeffler Kathryn , Duffy Augustine , Kuroda Makoto , Yang Jie E. , Wright Elizabeth R. , Kawaoka Yoshihiro , Kane Ravi S.
Published: February 2024

The 2002 SARS outbreak, the 2019 emergence of COVID-19, and the continuing evolution of immune-evading SARS-CoV-2 variants together highlight the need for a broadly protective vaccine against ACE2-utilizing sarbecoviruses. While updated variant-matched formulations are a step in the right direction, protection needs to extend beyond SARS-CoV-2 and its variants to include SARS-like viruses. Here, we introduce bivalent and trivalent vaccine formulations using our spike protein nanoparticle platform that completely protect female hamsters against BA.5 and XBB.1 challenges with no detectable virus in the lungs. The trivalent cocktails elicit highly neutralizing responses against all tested Omicron variants and the bat sarbecoviruses SHC014 and WIV1. Finally, our 614D/SHC014/XBB trivalent spike formulation completely protects human ACE2-transgenic female hamsters against challenges with WIV1 and SHC014 with no detectable virus in the lungs. Collectively, these results illustrate that our trivalent protein-nanoparticle cocktail can provide broad protection against SARS-CoV-2-like and SARS-CoV-1-like sarbecoviruses.
Functional nanoporous graphene superlattice
Authors: Lv Hualiang , Yao Yuxing , Yuan Mingyue , Chen Guanyu , Wang Yuchao , Rao Longjun , Li Shucong , Kara Ufuoma I. , Dupont Robert L. , Zhang Cheng , Chen Boyuan , Liu Bo , Zhou Xiaodi , Wu Renbing , Adera Solomon , Che Renchao , Zhang Xingcai , Wang Xiaoguang
Published: February 2024

Two-dimensional (2D) superlattices, formed by stacking sublattices of 2D materials, have emerged as a powerful platform for tailoring and enhancing material properties beyond their intrinsic characteristics. However, conventional synthesis methods are limited to pristine 2D material sublattices, posing a significant practical challenge when it comes to stacking chemically modified sublattices. Here we report a chemical synthesis method that overcomes this challenge by creating a unique 2D graphene superlattice, stacking graphene sublattices with monodisperse, nanometer-sized, square-shaped pores and strategically doped elements at the pore edges. The resulting graphene superlattice exhibits remarkable correlations between quantum phases at both the electron and phonon levels, leading to diverse functionalities, such as electromagnetic shielding, energy harvesting, optoelectronics, and thermoelectrics. Overall, our findings not only provide chemical design principles for synthesizing and understanding functional 2D superlattices but also expand their enhanced functionality and extensive application potential compared to their pristine counterparts.
In situ structure of actin remodeling during glucose-stimulated insulin secretion using cryo-electron tomography
Authors: Li Weimin , Li Angdi , Yu Bing , Zhang Xiaoxiao , Liu Xiaoyan , White Kate L. , Stevens Raymond C. , Baumeister Wolfgang , Sali Andrej , Jasnin Marion , Sun Liping
Published: February 2024

Actin mediates insulin secretion in pancreatic β-cells through remodeling. Hampered by limited resolution, previous studies have offered an ambiguous depiction as depolymerization and repolymerization. We report the in situ structure of actin remodeling in INS-1E β-cells during glucose-stimulated insulin secretion at nanoscale resolution. After remodeling, the actin filament network at the cell periphery exhibits three marked differences: 12% of actin filaments reorient quasi-orthogonally to the ventral membrane; the filament network mainly remains as cell-stabilizing bundles but partially reconfigures into a less compact arrangement; actin filaments anchored to the ventral membrane reorganize from a “netlike” to a “blooming” architecture. Furthermore, the density of actin filaments and microtubules around insulin secretory granules decreases, while actin filaments and microtubules become more densely packed. The actin filament network after remodeling potentially precedes the transport and release of insulin secretory granules. These findings advance our understanding of actin remodeling and its role in glucose-stimulated insulin secretion.
Predation and spatial connectivity interact to shape ecosystem resilience to an ongoing regime shift
Authors: Olin Agnes B. , Bergström Ulf , Bodin Örjan , Sundblad Göran , Eriksson Britas Klemens , Erlandsson Mårten , Fredriksson Ronny , Eklöf Johan S.
Published: February 2024

Ecosystem regime shifts can have severe ecological and economic consequences, making it a top priority to understand how to make systems more resilient. Theory predicts that spatial connectivity and the local environment interact to shape resilience, but empirical studies are scarce. Here, we use >7000 fish samplings from the Baltic Sea coast to test this prediction in an ongoing, spatially propagating shift in dominance from predatory fish to an opportunistic mesopredator, with cascading effects throughout the food web. After controlling for the influence of other drivers (including increasing mesopredator densities), we find that predatory fish habitat connectivity increases resilience to the shift, but only when densities of fish-eating top predators (seals, cormorants) are low. Resilience also increases with temperature, likely through boosted predatory fish growth and recruitment. These findings confirm theoretical predictions that spatial connectivity and the local environment can together shape resilience to regime shifts.
O-GlcNAc forces an α-synuclein amyloid strain with notably diminished seeding and pathology
Authors: Balana Aaron T. , Mahul-Mellier Anne-Laure , Nguyen Binh A. , Horvath Mian , Javed Afraah , Hard Eldon R. , Jasiqi Yllza , Singh Preeti , Afrin Shumaila , Pedretti Rose , Singh Virender , Lee Virginia M.-Y. , Luk Kelvin C. , Saelices Lorena , Lashuel Hilal A. , Pratt Matthew R.
Published: February 2024

Amyloid-forming proteins such α-synuclein and tau, which are implicated in Alzheimer’s and Parkinson’s disease, can form different fibril structures or strains with distinct toxic properties, seeding activities and pathology. Understanding the determinants contributing to the formation of different amyloid features could open new avenues for developing disease-specific diagnostics and therapies. Here we report that O-GlcNAc modification of α-synuclein monomers results in the formation of amyloid fibril with distinct core structure, as revealed by cryogenic electron microscopy, and diminished seeding activity in seeding-based neuronal and rodent models of Parkinson’s disease. Although the mechanisms underpinning the seeding neutralization activity of the O-GlcNAc-modified fibrils remain unclear, our in vitro mechanistic studies indicate that heat shock proteins interactions with O-GlcNAc fibril inhibit their seeding activity, suggesting that the O-GlcNAc modification may alter the interactome of the α-synuclein fibrils in ways that lead to reduce seeding activity in vivo. Our results show that posttranslational modifications, such as O-GlcNAc modification, of α-synuclein are key determinants of α-synuclein amyloid strains and pathogenicity.
A paintbrush for delivery of nanoparticles and molecules to live cells with precise spatiotemporal control
Authors: Holler Cornelia , Taylor Richard William , Schambony Alexandra , Möckl Leonhard , Sandoghdar Vahid
Published: February 2024

Delivery of very small amounts of reagents to the near-field of cells with micrometer spatial precision and millisecond time resolution is currently out of reach. Here we present μkiss as a micropipette-based scheme for brushing a layer of small molecules and nanoparticles onto the live cell membrane from a subfemtoliter confined volume of a perfusion flow. We characterize our system through both experiments and modeling, and find excellent agreement. We demonstrate several applications that benefit from a controlled brush delivery, such as a direct means to quantify local and long-range membrane mobility and organization as well as dynamical probing of intercellular force signaling.
Morpho-molecular and nutritional profiling for yield improvement and value addition of indigenous aromatic Joha rice of Assam
Authors: Bordoloi Dibosh , Sarma Debojit , Sarma Barua Nagendra , Das Ranjan , Das Bikram Kishore
Published: February 2024

Short-grain aromatic Joha rice of Assam is a unique class of specialty rice having tremendous potential in domestic and international markets. The poor yielding ability of Assam's Joha rice demands its systematic characterization for an effective breeding program. This study investigates the morphological, molecular and biochemical profiles of twenty popular Joha (aromatic) rice cultivars indigenous to Assam. Distinctiveness, Uniformity and Stability (DUS) characterization of the cultivars revealed polymorphism in thirty-seven traits, establishing distinctiveness for their utilization in breeding programs. Unweighted Neighbor Joining (UNJ) clustering based on usual Euclidean distances for the polymorphic morphological markers grouped the cultivars into three clusters with eight, eleven, and one genotypes. The Joha rice cultivars showed significant differences for all the quantitative traits except for panicle length. The genotypic and phenotypic coefficients of variability (GCV & PCV) were high for grain yield ha−1 (24.62 & 24.85%) and filled grains panicle−1 (23.69 & 25.02%). Mahalanobis D2 analysis revealed three multi-genotypic and four mono-genotypic clusters of the cultivars. The first five principal components explain 85.87% of the variation among the cultivars for the traits under study; filled grain panicle−1 (0.91) and stem thickness (0.55) positively contributed to the first PC. The cultivars' average polyunsaturated fatty acids were 37.9% oleic acid, 39.22% linoleic acid, and 0.5% linolenic acid. Kon Joha 4 and Ronga Joha contained the highest iron (82.88 mg kg−1) and zinc (47.39 mg kg−1), respectively. Kalijeera, Kunkuni Joha, Kon Joha-5, Manimuni Joha and Kon Joha-2 accorded a strong aroma. PCR amplified 174 alleles with a mean value 2.64 across the 66 polymorphic SSR markers. PIC values ranged from 0.091 to 0.698, with an average of 0.326. The highly informative (PIC > 0.50) markers were RM316, RM283, RM585, RM1388, RM3562, RM171, R1M30, RM118, RM11and RM29 for identification of the twenty aromatic rice cultivars. PCR amplification of 27 SSR markers identified 28 unique alleles (97–362 bp) in 13 Joha rice cultivars, which can help their identification/DNA fingerprinting. The UNJ clustering based on Jaccard's coefficients classified the cultivars into three distinct clusters with eight, ten, and two genotypes. Our study revealed the nutritional richness of these specialty Joha rice cultivars and sufficient scope for yield enhancement through their interbreeding to keep quality intact.
Risk factors affecting patients survival with colorectal cancer in Morocco: survival analysis using an interpretable machine learning approach
Authors: El Badisy Imad , BenBrahim Zineb , Khalis Mohamed , Elansari Soukaina , ElHitmi Youssef , Abbass Fouad , Mellas Nawfal , EL Rhazi Karima
Published: February 2024

The aim of our study was to assess the overall survival rates for colorectal cancer at 3 years and to identify associated strong prognostic factors among patients in Morocco through an interpretable machine learning approach. This approach is based on a fully non-parametric survival random forest (RSF), incorporating variable importance and partial dependence effects. The data was povided from a retrospective study of 343 patients diagnosed and followed at Hassan II University Hospital. Covariate selection was performed using the variable importance based on permutation and partial dependence plots were displayed to explore in depth the relationship between the estimated partial effect of a given predictor and survival rates. The predictive performance was measured by two metrics, the Concordance Index (C-index) and the Brier Score (BS). Overall survival rates at 1, 2 and 3 years were, respectively, 87% (SE = 0.02; CI-95% 0.84–0.91), 77% (SE = 0.02; CI-95% 0.73–0.82) and 60% (SE = 0.03; CI-95% 0.54–0.66). In the Cox model after adjustment for all covariates, sex, tumor differentiation had no significant effect on prognosis, but rather tumor site had a significant effect. The variable importance obtained from RSF strengthens that surgery, stage, insurance, residency, and age were the most important prognostic factors. The discriminative capacity of the Cox PH and RSF was, respectively, 0.771 and 0.798 for the C-index while the accuracy of the Cox PH and RSF was, respectively, 0.257 and 0.207 for the BS. This shows that RSF had both better discriminative capacity and predictive accuracy. Our results show that patients who are older than 70, living in rural areas, without health insurance, at a distant stage and who have not had surgery constitute a subgroup of patients with poor prognosis.
Real-time study of spatio-temporal dynamics (4D) of physiological activities in alive biological specimens with different FOVs and resolutions simultaneously
Authors: K. S. Aiswarya , Sarkar Sohela , Vishnu Smitha , S. R. Rinsa , Negi Simran , Narendradev Nikhil Dev , Arora Rishica Harish , Sanam Sreelakshmi , P. V. Anu , Sharma Rahul , Khurana Satish , Varghese Jishy , Srinivasula Srinivasa Murty , Singh Mayanglambam Suheshkumar
Published: February 2024

This article reports the development of a microscopy imaging system that gives feasibility for studying spatio-temporal dynamics of physiological activities of alive biological specimens (over entire volume not only for a particular section, i.e., in 4D). The imaging technology facilitates to obtain two image frames of a section of the larger specimen ($$\sim \text {mm}$$

∼
mm

) with different FOVs at different resolutions or magnifications simultaneously in real-time (in addition to recovery of 3D (volume) information). Again, this imaging system addresses the longstanding challenges of housing multiple light sources (6 at the maximum till date) in microscopy (in general) and light sheet fluorescence microscopy (LSFM) (in particular), by using a tuneable pulsed laser source (with an operating wavelength in the range $$\sim 420$$

∼
420

–670 nm) in contrast to the conventional CW laser source being adopted for inducing photo-excitation of tagged fluorophores. In the present study, we employ four wavelengths ($$\sim$$
∼
488 nm, 585 nm, 590 nm, and 594 nm). Our study also demonstrates quantitative characterization of spatio-temporal dynamics (velocity—both amplitude and direction) of organelles (mitochondria) and their mutual correlationships. Mitochondria close to the nucleus (or in clustered cells) are observed to possess a lower degree of freedom in comparison to that at the cellular periphery (or isolated cells). In addition, the study demonstrates real-time observation and recording of the development and growth of all tracheal branches during the entire period ($$\sim 95$$

∼
95

min) of embryonic development (Drosophila). The experimental results—with experiments being conducted in various and diversified biological specimens (Drosophila melanogaster, mouse embryo, and HeLa cells)—demonstrate that the study is of great scientific impact both from the aspects of technology and biological sciences.
Lytic activity of phages against bacterial pathogens infecting diabetic foot ulcers
Authors: Kifelew Legesse Garedew , Warner Morgyn S. , Morales Sandra , Gordon David L. , Thomas Nicky , Mitchell James G. , Speck Peter G.
Published: February 2024

Complications of diabetes, such as diabetic foot ulcers (DFUs), are common, multifactorial in origin, and costly to treat. DFUs are the cause of nearly 90% of limb amputations among persons with diabetes. In most chronic infections such as DFU, biofilms are involved. Bacteria in biofilms are 100–1000 times more resistant to antibiotics than their planktonic counterparts. Multidrug-resistant (MDR) Staphylococcus aureus and Pseudomonas aeruginosa infections in DFUs may require alternative therapeutic agents such as bacteriophages ("phages"). This study describes the lytic activity of phage cocktails AB-SA01 (3-phage cocktail) and AB-PA01 (4-phage cocktail), which target S. aureus and P. aeruginosa, respectively. The host range and lytic effect of AB-SA01 and AB-PA01 on a planktonic culture, single-species biofilm, and mixed-species biofilm were evaluated. In vitro testing showed that 88.7% of S. aureus and 92.7% of P. aeruginosa isolates were susceptible to AB-SA01 and AB-PA01, respectively, in the planktonic state. The component phages of AB-SA01 and AB-PA01 infected 66% to 94.3% of the bacterial isolates tested. Furthermore, AB-SA01 and AB-PA01 treatment significantly (p < 0.05) reduced the biofilm biomass of their hosts, regardless of the antibiotic-resistant characteristics of the isolates and the presence of a non-susceptible host. In conclusion, the strong lytic activity, broad host range, and significant biofilm biomass reduction of AB-SA01 and AB-PA01 suggest the considerable potential of phages in treating antibiotic-resistant S. aureus and P. aeruginosa infections alone or as coinfections in DFUs.
A transcriptomic time-series reveals differing trajectories during pre-floral development in the apex and leaf in winter and spring varieties of Brassica napus
Authors: Jones D. Marc , Hepworth Jo , Wells Rachel , Pullen Nick , Trick Martin , Morris Richard J.
Published: February 2024

Oilseed rape (Brassica napus) is an important global oil crop, with spring and winter varieties grown commercially. To understand the transcriptomic differences between these varieties, we collected transcriptomes from apex and leaf tissue from a spring variety, Westar, and a winter variety, Tapidor, before, during, and after vernalisation treatment, until the plants flowered. Large transcriptomic differences were noted in both varieties during the vernalisation treatment because of temperature and day length changes. Transcriptomic alignment revealed that the apex transcriptome reflects developmental state, whereas the leaf transcriptome is more closely aligned to the age of the plant. Similar numbers of copies of genes were expressed in both varieties during the time series, although key flowering time genes exhibited expression pattern differences.BnaFLCcopies on A2 and A10 are the best candidates for the increased vernalisation requirement of Tapidor. OtherBnaFLCcopies show tissue-dependent reactivation of expression post-cold, with these dynamics suggesting some copies have retained or acquired a perennial nature.BnaSOC1genes, also related to the vernalisation pathway, have expression profiles which suggest tissue subfunctionalisation. This understanding may help to breed varieties with more consistent or robust vernalisation responses, of special importance due to the milder winters resulting from climate change.
Navigating the nuances: comparative analysis and hyperparameter optimisation of neural architectures on contrast-enhanced MRI for liver and liver tumour segmentation
Authors: Quinton Felix , Presles Benoit , Leclerc Sarah , Nodari Guillaume , Lopez Olivier , Chevallier Olivier , Pellegrinelli Julie , Vrigneaud Jean-Marc , Popoff Romain , Meriaudeau Fabrice , Alberini Jean-Louis
Published: February 2024

In medical imaging, accurate segmentation is crucial to improving diagnosis, treatment, or both. However, navigating the multitude of available architectures for automatic segmentation can be overwhelming, making it challenging to determine the appropriate type of architecture and tune the most crucial parameters during dataset optimisation. To address this problem, we examined and refined seven distinct architectures for segmenting the liver, as well as liver tumours, with a restricted training collection of 60 3D contrast-enhanced magnetic resonance images (CE-MRI) from the ATLAS dataset. Included in these architectures are convolutional neural networks (CNNs), transformers, and hybrid CNN/transformer architectures. Bayesian search techniques were used for hyperparameter tuning to hasten convergence to the optimal parameter mixes while also minimising the number of trained models. It was unexpected that hybrid models, which typically exhibit superior performance on larger datasets, would exhibit comparable performance to CNNs. The optimisation of parameters contributed to better segmentations, resulting in an average increase of 1.7% and 5.0% in liver and tumour segmentation Dice coefficients, respectively. In conclusion, the findings of this study indicate that hybrid CNN/transformer architectures may serve as a practical substitute for CNNs even in small datasets. This underscores the significance of hyperparameter optimisation.
The metabolism-related lncRNA signature predicts the prognosis of breast cancer patients
Authors: Ge Xin , Lei Shu , Wang Panliang , Wang Wenkang , Wang Wendong
Published: February 2024

Long non-coding RNAs (lncRNAs) involved in metabolism are recognized as significant factors in breast cancer (BC) progression. We constructed a novel prognostic signature for BC using metabolism-related lncRNAs and investigated their underlying mechanisms. The training and validation cohorts were established from BC patients acquired from two public sources: The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO). The prognostic signature of metabolism-related lncRNAs was constructed using the least absolute shrinkage and selection operator (LASSO) cox regression analysis. We developed and validated a new prognostic risk model for BC using the signature of metabolism-related lncRNAs (SIRLNT, SIAH2-AS1, MIR205HG, USP30-AS1, MIR200CHG, TFAP2A-AS1, AP005131.2, AL031316.1, C6orf99). The risk score obtained from this signature was proven to be an independent prognostic factor for BC patients, resulting in a poor overall survival (OS) for individuals in the high-risk group. The area under the curve (AUC) for OS at three and five years were 0.67 and 0.65 in the TCGA cohort, and 0.697 and 0.68 in the GEO validation cohort, respectively. The prognostic signature demonstrated a robust association with the immunological state of BC patients. Conventional chemotherapeutics, such as docetaxel and paclitaxel, showed greater efficacy in BC patients classified as high-risk. A nomogram with a c-index of 0.764 was developed to forecast the survival time of BC patients, considering their risk score and age. The silencing of C6orf99 markedly decreased the proliferation, migration, and invasion capacities in MCF-7 cells. Our study identified a signature of metabolism-related lncRNAs that predicts outcomes in BC patients and could assist in tailoring personalized prevention and treatment plans.
Early maladaptive schemas in female patients with migraine and tension-type headache
Authors: Yontar Gözde , Ozgan Esen
Published: February 2024

Chronic headache is a serious clinical problem in women which psychological factors play major role and requires an approach with bio-psycho-social integrity. Psychiatric comorbidities such as anxiety disorder and major depression are frequent. Young described Early Maladaptive Schemas (EMS) as maladaptive and dysfunctional patterns that appear due to unpleasant situations occurred between patient and people who were important to him. EMS affect perception, emotions, thoughts and behaviors that makes a basis for many disorders. EMS are found to be related with depression, anxiety and somatization within recent literature. In literature, chronic pain and migraine’s relationship with EMS were studied before in a few separate articles. However, there is a lack of data that compares the relationship between EMS and clearly distinguished headache types: migraine (MH) and tension-type headache (TTH) especially in female patients who are more prone to somatic complaints/findings. Our study directly compared three groups, migraine and tension type headache and healthy controls. 150 female patients with chronic headache were enrolled for study in consecutive fashion. Exclusion criteria were as follows: age < 18 or > 60 years, male gender, existence of comorbidity affecting central nervous system, headache due to drug/substance abuse, previous diagnosis of migraine with aura, previous diagnosis of psychotic disease, mental retardation, cognitive disorders, being in delirium state. Patients were grouped into two categories according to type of headache and a third control group. All patients were evaluated with Young Schema Questionnaire (YSQ) and their scores were noted and categorized in related schema domains. Sociodemographic data were comparable among groups. However, there were significant differences in terms of previous psychiatric diagnosis and psychiatric drug usage. When we compared YSQ scores, groups differed in many schema categories. MH group showed significantly higher scores in dependency/incompetency, unrelenting standards and punitiveness schemas when compared to remaining two groups. TTH group had significantly more points in emotional deprivation, vulnerability to harm or illness schemas among all groups. On the other hand, control group had significantly higher scores in insufficient self-discipline and entitlement/grandiosity schemas when compared to both MH and TTH groups. Presence of EMS in female patients with headache significantly differed from control group. Types of EMS were also significantly different between patients with MH and TTH among this whole headache group. We suggest that a comprehensive psychotherapeutic approach that targets to improve coping methods for distinct EMS in distinct headache types would provide critical aid to general treatment of headaches especially in resistant cases.
Effects of radiofrequency field from 5G communication on fecal microbiome and metabolome profiles in mice
Authors: Wang Xing , Zhou Guiqiang , Lin Jiajin , Qin Tongzhou , Du Junze , Guo Ling , Lai Panpan , jing Yuntao , Zhang Zhaowen , Zhou Yan , Ding Guirong
Published: February 2024

With the rapid development of 5G networks, the influence of the radiofrequency field (RF) generated from 5G communication equipment on human health is drawing increasing attention in public. The study aimed at assessing the effects of long-term exposure to 4.9 GHz (one of the working frequencies of 5G communication) RF field on fecal microbiome and metabolome profiles in adult male C57BL/6 mice. The animals were divided into Sham group and radiofrequency group (RF group). For RF group, the mice were whole body exposed to 4.9 GHz RF field for three weeks, 1 h/d, at average power density (PD) of 50 W/m2. After RF exposure, the mice fecal samples were collected to detect gut microorganisms and metabolites by 16S rRNA gene sequencing and LC–MS method, respectively. The results showed that intestinal microbial compositions were altered in RF group, as evidenced by reduced microbial diversity and changed microbial community distribution. Metabolomics profiling identified 258 significantly differentially abundant metabolites in RF group, 57 of which can be classified to Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Besides, functional correlation analysis showed that changes in gut microbiota genera were significantly correlated with changes in fecal metabolites. In summary, the results suggested that altered gut microbiota and metabolic profile are associated with 4.9 GHz radiofrequency exposure.
A framework based on subject-specific musculoskeletal models and Monte Carlo simulations to personalize muscle coordination retraining
Authors: Kainz Hans , Koller Willi , Wallnöfer Elias , Bader Till R. , Mindler Gabriel T. , Kranzl Andreas
Published: February 2024

Excessive loads at lower limb joints can lead to pain and degenerative diseases. Altering joint loads with muscle coordination retraining might help to treat or prevent clinical symptoms in a non-invasive way. Knowing how much muscle coordination retraining can reduce joint loads and which muscles have the biggest impact on joint loads is crucial for personalized gait retraining. We introduced a simulation framework to quantify the potential of muscle coordination retraining to reduce joint loads for an individuum. Furthermore, the proposed framework enables to pinpoint muscles, which alterations have the highest likelihood to reduce joint loads. Simulations were performed based on three-dimensional motion capture data of five healthy adolescents (femoral torsion 10°–29°, tibial torsion 19°–38°) and five patients with idiopathic torsional deformities at the femur and/or tibia (femoral torsion 18°–52°, tibial torsion 3°–50°). For each participant, a musculoskeletal model was modified to match the femoral and tibial geometry obtained from magnetic resonance images. Each participant’s model and the corresponding motion capture data were used as input for a Monte Carlo analysis to investigate how different muscle coordination strategies influence joint loads. OpenSim was used to run 10,000 simulations for each participant. Root-mean-square of muscle forces and peak joint contact forces were compared between simulations. Depending on the participant, altering muscle coordination led to a maximum reduction in hip, knee, patellofemoral and ankle joint loads between 5 and 18%, 4% and 45%, 16% and 36%, and 2% and 6%, respectively. In some but not all participants reducing joint loads at one joint increased joint loads at other joints. The required alteration in muscle forces to achieve a reduction in joint loads showed a large variability between participants. The potential of muscle coordination retraining to reduce joint loads depends on the person’s musculoskeletal geometry and gait pattern and therefore showed a large variability between participants, which highlights the usefulness and importance of the proposed framework to personalize gait retraining.
Machine learning driven methodology for enhanced nylon microplastic detection and characterization
Authors: Yang Cihang , Xie Junhao , Gowen Aoife , Xu Jun-Li
Published: February 2024

In recent years, the field of microplastic (MP) research has evolved significantly; however, the lack of a standardized detection methodology has led to incomparability across studies. Addressing this gap, our current study innovates a reliable MP detection system that synergizes sample processing, machine learning, and optical photothermal infrared (O-PTIR) spectroscopy. This approach includes examining high-temperature filtration and alcohol treatment for reducing non-MP particles and utilizing a support vector machine (SVM) classifier focused on key wavenumbers that could discriminate between nylon MPs and non-nylon MPs (1077, 1541, 1635, 1711 cm−1 were selected based on the feature importance of SVM-Full wavenumber model) for enhanced MP identification. The SVM model built from key wavenumbers demonstrates a high accuracy rate of 91.33%. Results show that alcohol treatment is effective in minimizing non-MP particles, while filtration at 70 °C has limited impact. Additionally, this method was applied to assess MPs released from commercial nylon teabags, revealing an average release of 106 particles per teabag. This research integrates machine learning with O-PTIR spectroscopy, paving the way for potential standardization in MP detection methodologies and providing vital insights into their environmental and health implications.
Frequency pushing enhanced by an exceptional point in an atom–cavity coupled system
Authors: Lee Joohye , Kim Jinuk , An Kyungwon
Published: February 2024

We observed the frequency pushing of the cavity resonance as a result of the coupling of the cavity field with the ground state 138Ba in a high-Q cavity. A weak probe laser propagated along the axis of a Fabry–Pérot cavity while ground-state barium atoms traversed the cavity mode perpendicularly. By operating the atom–cavity composite in the vicinity of an exceptional point, we could observe a greatly enhanced frequency shift of the cavity transmission peak, which was pushed away from the atomic resonance, resulting in up to 41 ± 7 kHz frequency shift per atom from the empty cavity resonance. We analyzed our results by using the Maxwell–Schrödinger equation and obtained good agreement with the measurements.
Microbial butyrate capacity is reduced in inflamed mucosa in patients with ulcerative colitis
Authors: Jangi Sushrut , Moyer John , Sandlow Sarah , Fu May , Chen Hannah , Shum Ann , Hsia Katie , Cersosimo Laura , Yeliseyev Vladimir , Zhao Naisi , Bry Lynn , Michaud Dominique S
Published: February 2024

Reduced butyrate-production capacity has been reported in fecal microbial communities in patients with active ulcerative colitis. However, the butyrate-production capacity of the mucosal microbiome from active vs quiescent mucosa in ulcerative colitis has been unexplored. We sought to determine the diversity and relative abundance of mucosal bacterial and fungal communities from endoscopically active vs quiescent mucosa in patients with UC, and aimed to predict contributions of mucosal microbial communities to butyrate synthesis. Systematic, segmental right- and left-sided biopsies were obtained from endoscopically active (n = 13) or quiescent (n = 17) colonic mucosa, among 15 patients with pan-colonic ulcerative colitis. Dietary fiber intake of patients was performed using the validated five-item FiberScreen questionnaire. Amplicon sequencing of mucosal bacteria and fungi was performed. The diversity and relative abundance of mucosal bacterial and fungal taxa were quantified, and predicted contributions to butyrate synthesis were ascertained. Bacterial alpha and beta diversity were similar between active vs quiescent mucosa. Butyrogenic taxa were significantly increased in quiescence, includingButyricimonas,Subdoligranulum, andAlistipes. Predicted butyrate kinase activity was significantly and concomitantly increased in quiescent mucosa. Fiber intake was positively correlated with butyrogenic microbes. Compared to mucosal bacterial prevalence, mucosal fungi were detected in low prevalence. Butyrogenic microbes are relatively increased in quiescent mucosa in ulcerative colitis, and may be related to increased fiber intake during quiescence. Manipulation of the mucosal microbiome towards butyrate-producing bacteria may be associated with endoscopic quiescence.
Functional BRI2-TREM2 interactions in microglia: implications for Alzheimer’s and related dementias
Authors: Yin Tao , Yesiltepe Metin , D’Adamio Luciano
Published: February 2024

ITM2B/BRI2 mutations cause Alzheimer’s Disease (AD)-related dementias. We observe heightened ITM2B/BRI2 expression in microglia, a pivotal cell type in AD due to risk-increasing variants in the microglial gene TREM2. Single-cell RNA-sequencing demonstrates a Trem2/Bri2-dependent microglia cluster, underscoring their functional interaction. α-secretase cleaves TREM2 into TREM2-CTF and sTREM2. As BRI2 hinders α-secretase cleavage of the AD-related Aβ-Precursor-Protein, we probed whether BRI2 influences TREM2 processing. Our findings indicate a BRI2-TREM2 interaction that inhibits TREM2 processing in heterologous cells. Recombinant BRI2 and TREM2 proteins demonstrate a direct, cell-free BRI2-TREM2 ectodomain interaction. Constitutive and microglial-specific Itm2b-Knock-out mice, and Itm2b-Knock-out primary microglia provide evidence that Bri2 reduces Trem2 processing, boosts Trem2 mRNA expression, and influences Trem2 protein levels through α-secretase-independent pathways, revealing a multifaceted BRI2-TREM2 functional interaction. Moreover, a mutant Itm2b dementia mouse model exhibits elevated Trem2-CTF and sTrem2, mirroring sTREM2 increases in AD patients. Lastly, Bri2 deletion reduces phagocytosis similarly to a pathogenic TREM2 variant that enhances processing. Given BRI2’s role in regulating Aβ-Precursor-Protein and TREM2 functions, it holds promise as a therapeutic target for AD and related dementias.
RNA polymerase II promotes the organization of chromatin following DNA replication
Authors: Bandau Susanne , Alvarez Vanesa , Jiang Hao , Graff Sarah , Sundaramoorthy Ramasubramanian , Gierlinski Marek , Toman Matt , Owen-Hughes Tom , Sidoli Simone , Lamond Angus , Alabert Constance
Published: February 2024

Understanding how chromatin organisation is duplicated on the two daughter strands is a central question in epigenetics. In mammals, following the passage of the replisome, nucleosomes lose their defined positioning and transcription contributes to their re-organisation. However, whether transcription plays a greater role in the organization of chromatin following DNA replication remains unclear. Here we analysed protein re-association with newly replicated DNA upon inhibition of transcription using iPOND coupled to quantitative mass spectrometry. We show that nucleosome assembly and the re-establishment of most histone modifications are uncoupled from transcription. However, RNAPII acts to promote the re-association of hundreds of proteins with newly replicated chromatin via pathways that are not observed in steady-state chromatin. These include ATP-dependent remodellers, transcription factors and histone methyltransferases. We also identify a set of DNA repair factors that may handle transcription-replication conflicts during normal transcription in human non-transformed cells. Our study reveals that transcription plays a greater role in the organization of chromatin post-replication than previously anticipated.
Ni0.5Co0.5S nano-chains: a high-performing intercalating pseudocapacitive electrode in asymmetric supercapacitor (ASC) mode for the development of large-scale energy storage devices
Authors: Kushwaha Vishal , Mandal K. D. , Gupta Asha , Singh Preetam
Published: February 2024

The Ni0.5Co0.5S nano-chain electrode showed a capacitance of 2001.6 F g−1 at 1 mV s−1 scan rate and a specific capacity of 267 mA h g−1 (1920 F g−1) at a current rate of 1 A g−1 in 4 M KOH aqueous electrolyte.
New insights into tunnel-type NaxMnO2−yFy with high performance and excellent cycling stability: the impact of F-doping
Authors: Ruiz Rafaela , Pérez-Vicente Carlos , Alcántara Ricardo
Published: February 2024

Easy diffusion of sodium in tunnel-type NaxMnO2−yFy electrode materials.
Phospholipid-rich krill oil promotes intestinal health by strengthening beneficial gut microbial interactions in an infectious colitis model
Authors: Liu Fang , Smith Allen D. , Wang Thomas T. Y. , Pham Quynhchi , Hou Pengfen , Cheung Lumei , Yang Haiyan , Li Robert W.
Published: February 2024

Phospholipid-rich krill oil decreases intestinal hyperplasia and curbs excessive inflammation via multiple targets.
The impact of moisture on the stability and degradation of perovskites in solar cells
Authors: Kore Bhushan P. , Jamshidi Mahboubeh , Gardner James M.
Published: February 2024

Efficiency and stability are the two most important factors in commercially scalable solar cells.
Effective correction of dissolved organic carbon interference in nitrate detection using ultraviolet spectroscopy combined with the equivalent concentration offset method
Authors: Dong Jing , Tang Junwu , Wu Guojun , Xin Yu , Li Ruizhuo , Li Yahui
Published: February 2024

A simple and rapid method for DOC interference correction based on an equivalent concentration offset method was proposed to address the challenging issue of DOC interference in nitrate detection in aquatic environments.
Photoinduced deformation behavior of poly(aryl ether)s with different azobenzene groups in the side chain
Authors: Yi Jie , Yang Yajing , Song Xi-ming , Zhang Yuxuan
Published: February 2024

Two novel azobenzene-functionalised poly(aryl ether)s were synthesized, and their photoresponsive properties studied. The photoinduced motion of the polymers was faster. Poly(aryl ether)s containing azobenzene groups in the side chain showed highly stable photoinduced deformation.
Multi-site isomerization of synergistically regulated stimuli-responsive AIE materials toward multi-level decryption
Authors: Zhong Weiren , Zhang Jianyu , Lin Yuting , Li Shouji , Yang Yalan , Wang Wen-Jin , Si Chuanling , Kühn Fritz E. , Zhao Zheng , Cai Xu-Min , Tang Ben Zhong
Published: February 2024

The utilization of multi-site modifications brings about the manipulation of excited-state processes and multi-stimuli responses of salicylaldehyde Schiff base isomers, which can be successfully applied in multi-level decryption.
A Siamese neural network framework for glass transition recognition
Authors: Osiecka-Drewniak Natalia , Deptuch Aleksandra , Urbańska Magdalena , Juszyńska-Gałązka Ewa
Published: February 2024

A Siamese neural network, a deep learning technique, was utilized to distinguish selected liquid crystal phases (antiferroelectric smectic CA*, smectic I, and smectic G) from their corresponding glasses.
Correction: Impact of temperature-dependent non-PAN peroxynitrate formation, RO2NO2, on nighttime atmospheric chemistry
Authors: Färber Michelle , Vereecken Luc , Fuchs Hendrik , Gkatzelis Georgios I. , Rohrer Franz , Wedel Sergej , Wahner Andreas , Novelli Anna
Published: February 2024

Correction for ‘Impact of temperature-dependent non-PAN peroxynitrate formation, RO2NO2, on nighttime atmospheric chemistry’ by Michelle Färber et al., Phys. Chem. Chem. Phys., 2024, https://doi.org/10.1039/d3cp04163h.
Mesoporous Mo-doped PtBi intermetallic metallene superstructures to enable the complete electrooxidation of ethylene glycol
Authors: Yang Xiaotong , Yuan Qiang , Sheng Tian , Wang Xun
Published: February 2024

Novel freestanding M-PtBiMo IMSs were achieved via a simple and effective one-step wet chemical method. The M-PtBiMo IMSs as highly efficient anode electrocatalysts boosted the activity and stability toward the EGOR and actual DEGFCs.
Automatic optimal design of field plate for silicon on insulator lateral double‐diffused metal oxide semiconductor using simulated annealing algorithm
Authors: Chen Jing , Xia Renji , You Jinwen , Yao Qing , Dai Yuxuan , Zhang Jun , Yao Jiafei , Guo Yufeng
Published: February 2024

Field plate (FP) technology has been widely used due to its simple structure and process compatibility. Through introducing the interface charge to suppress the electric field peak at the junction region, the breakdown performance can be improved. However, designing an appropriate FP for semiconductor power devices is challenging and time‐consuming. In this paper, the authors propose a fully automated FP optimal design method based on simulated annealing algorithm (SA) for silicon on insulator lateral double‐diffused metal oxide semiconductor. By using an automatic iterative process to obtain the minimum value of the objective function, the parameters related to the FP can be effectively provided. Numerical results show that when the breakdown occurs at the N+N or PN junction, the breakdown voltage can be optimized by an average of 18.6% and 45.5%, respectively. Moreover, compared with the existing methods, the proposed approach is highly efficient with a runtime that does not exceed 12 s. The authors believe that this method can greatly accelerate the power device design process.
Cover Image
Authors: Pang Lei , Ding Zijun , Bian Xiaodong , Shuang Weibing
Published: February 2024

The cover image is based on the Original Article Research on symptoms composition, time series evolution, and network visualisation of interstitial cystitis based on complex network community discovery algorithm by Lei Pang et al., https://doi.org/10.1049/syb2.12083

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Searching for cold gas traced by MgII quasar absorbers in massive X-ray-selected galaxy clusters
Authors: Fresco A. , Péroux C. , Merloni A. , Comparat J. , Szakacs R. , Weng S.
Published: February 2024

Context. Almost 50% of galaxies in the local Universe are in clusters or groups coexisting with both hot and cold gas components. In the present study, we observationally probed the cold-gas content of X-ray-selected massive galaxy clusters with spectroscopic redshift measured from the SDSS/SPIDERS survey. This paper focuses on the most massive structures: galaxy clusters with a mean mass of M500c = 2.7 × 1014 M⊙.

Aims. We used a large number of background quasar optical spectra from SDSS DR16 to probe the diffuse T = 104 K gas in their intracluster medium.

Methods. We first analysed a sample of spectra with known MgII absorbers, and then blindly stacked about 16 000 archival spectra at the redshifts of the foreground galaxy clusters.

Results. We tentatively (3.7σ significance) detect MgII in the clusters with an equivalent width EW(MgII λ2796) of 0.056 ± 0.015 Å, corresponding to a column density of log [N(MgII)/cm−2] = 12.12 ± 0.1. We tested our methodology by generating 22 000 mock SDSS spectra with MgII absorbers from Illustris-TNG50 cosmological magnetohydrodynamical simulations, combining photo-ionisation modelling and ray tracing. We also performed bootstrapping stacking at different cluster redshifts and stacked quasar spectra with no intervening clusters in the line of sight to measure the significance of our detection.

Conclusions. These results are in line with the findings of recent, similar observational studies but challenge predictions from Illustris-TNG simulations. Together, our findings indicate that large amounts of cold gas may be found in the most massive structures of the Universe.
The spectroastrometric detectability of nearby Solar System-like exomoons
Authors: van Woerkom Q. B. , Kleisioti E.
Published: February 2024

Context. Though efforts to detect them have been made with a variety of methods, no technique can claim a successful, confirmed detection of a moon outside the Solar System yet. Moon detection methods are restricted in capability to detecting moons of masses beyond what formation models would suggest, or they require surface temperatures exceeding what tidal heating simulations allow.

Aims. We expand upon spectroastrometry, a method that makes use of the variation of the centre of light with wavelength as the result of an unresolved companion, which has previously been shown to be capable of detecting Earth-analogue moons around nearby exo-Jupiters, with the aim to place bounds on the types of moons detectable using this method.

Methods. We derived a general, analytic expression for the spectroastrometric signal of a moon in any closed Keplerian orbit, as well as a new set of estimates on the noise due to photon noise, pointing inaccuracies, background and instrument noise, and a pixelated detector. This framework was consequently used to derive bounds on the temperature required for Solar System-like moons to be observable around super-Jupiters in nearby systems, with∈Indi Ab as an archetype.

Results. We show that such a detection is possible with the ELT for Solar System-like moons of moderate temperatures (150–300 K) in line with existing literature on tidal heating, and that the detection of large (Mars-sized or greater) icy moons of temperatures such as those observed in our Solar System in the very nearest systems may be feasible.
SN 2022jli: The ultraluminous birth of a low-mass X-ray binary
Authors: King Andrew , Lasota Jean-Pierre
Published: February 2024

Observations show that the 12.4 d binary system descending from the recent supernova SN 2022jli closely fits hypotheses of how low-mass X-ray binaries form, but requires an apparently super-Eddington accretion luminosity from the accreting component. We show that this agrees very well with the type of accretion-induced beaming found in ultraluminous X-ray sources, as recently strongly confirmed by X-ray polarimetry of the X-ray binary Cyg X-3. Beaming in the SN 2022jli binary system occurs because of the very high mass-transfer rate induced by the violent effect of the supernova on the binary geometry. This explains the very soft nature of the accretion luminosity, its distinctive periodic light curve, and its luminosity decay on a ∼250 day timescale. A test of this picture is that the system’s orbital period should increase on a 105 year timescale.