bluuebunny/crossref_metadata_2025 huggingface dataset:
A co-assembly platform engaging macrophage scavenger receptor A for lysosome-targeting protein degradation
Authors: Wang Qian , Yang Xingyue , Yuan Ruixin , Shen Ao , Wang Pushu , Li Haoting , Zhang Jun , Tian Chao , Jiang Zhujun , Li Wenzhe , Dong Suwei
Published: February 2024

Targeted degradation of proteins has emerged as a powerful method for modulating protein homeostasis. Identification of suitable degraders is essential for achieving effective protein degradation. Here, we present a non-covalent degrader construction strategy, based on a modular supramolecular co-assembly system consisting of two self-assembling peptide ligands that bind cell membrane receptors and the protein of interest simultaneously, resulting in targeted protein degradation. The developed lysosome-targeting co-assemblies (LYTACAs) can induce lysosomal degradation of extracellular protein IL-17A and membrane protein PD-L1 in several scavenger receptor A-expressing cell lines. The IL-17A-degrading co-assembly has been applied in an imiquimod-induced psoriasis mouse model, where it decreases IL-17A levels in the skin lesion and alleviates psoriasis-like inflammation. Extending to asialoglycoprotein receptor-related protein degradation, LYTACAs have demonstrated the versatility and potential in streamlining degraders for extracellular and membrane proteins.
Silencing Parkinson’s risk allele Rit2 sex-specifically compromises motor function and dopamine neuron viability
Authors: Kearney Patrick J. , Zhang Yuanxi , Liang Marianna , Tan Yanglan , Kahuno Elizabeth , Conklin Tucker L. , Fagan Rita R. , Pavchinskiy Rebecca G. , Shaffer Scott A. , Yue Zhenyu , Melikian Haley E.
Published: February 2024

Parkinson’s disease (PD) is the second most prevalent neurodegenerative disease and arises from dopamine (DA) neuron death selectively in the substantia nigra pars compacta (SNc). Rit2 is a reported PD risk allele, and recent single cell transcriptomic studies identified a major RIT2 cluster in PD DA neurons, potentially linking Rit2 expression loss to a PD patient cohort. However, it is still unknown whether Rit2 loss itself impacts DA neuron function and/or viability. Here we report that conditional Rit2 silencing in mouse DA neurons drove motor dysfunction that occurred earlier in males than females and was rescued at early stages by either inhibiting the DA transporter (DAT) or with L-DOPA treatment. Motor dysfunction was accompanied by decreased DA release, striatal DA content, phenotypic DAergic markers, DA neurons, and DAergic terminals, with increased pSer129-alpha synuclein and pSer935-LRRK2 expression. These results provide clear evidence that Rit2 loss is causal for SNc cell death and motor dysfunction, and reveal key sex-specific differences in the response to Rit2 loss.
Tandem catalysis enables chlorine-containing waste as chlorination reagents
Authors: Liu Mingyang , Wu Xinbang , Dyson Paul J.
Published: February 2024

Chlorinated compounds are ubiquitous. However, accumulation of chlorine-containing waste has a negative impact on human health and the environment due to the inapplicability of common disposal methods, such as landfill and incineration. Here we report a sustainable approach to valorize chlorine-containing hydrocarbon waste, including solids (chlorinated polymers) and liquids (chlorinated solvents), based on copper and palladium catalysts with a NaNO3 promoter. In the process, waste is oxidized to release the chlorine in the presence of N-directing arenes to afford valuable aryl chlorides, such as the FDA-approved drug vismodegib. The remaining hydrocarbon component is mineralized to afford CO, CO2 and H2O. Moreover, the CO and CO2 generated could be further utilized directly. Thus, chlorine-containing hydrocarbon waste, including mixed waste, can serve as chlorination reagents that neither generate hazardous by-products nor involve specialty chlorination reagents. This tandem catalytic approach represents a promising method for the viable management of a wide and diverse range of chlorine-containing hydrocarbon wastes.
Chromosome-level genome assembly and annotation of the Yunling cattle with PacBio and Hi-C sequencing data
Authors: Wei Zaichao , Zhang Lilian , Gao Lutao , Chen Jian , Peng Lin , Yang Linnan
Published: February 2024

Yunling cattle is a new breed of beef cattle bred in Yunnan Province, China. It is bred by crossing the Brahman, the Murray Grey and the Yunnan Yellow cattle. Yunling cattle can adapt to the tropical and subtropical climate environment, and has good reproductive ability and growth speed under high temperature and high humidity conditions, it also has strong resistance to internal and external parasites and with good beef performance. In this study, we generated a high-quality chromosome-level genome assembly of a male Yunling cattle using a combination of short reads sequencing, PacBio HiFi sequencing and Hi-C scaffolding technologies. The genome assembly(3.09 Gb) is anchored to 31 chromosomes(29 autosomes plus one X and Y), with a contig N50 of 35.97 Mb and a scaffold N50 of 112.01 Mb. It contains 1.62 Gb of repetitive sequences and 20,660 protein-coding genes. This first construction of the Yunling cattle genome provides a valuable genetic resource that will facilitate further study of the genetic diversity of bovine species and accelerate Yunling cattle breeding efforts.
Quantitative description of six fish species’ gut contents and prey abundances in the Baltic Sea (1968–1978)
Authors: Gauzens Benoit , Kalinkat Gregor , Antunes Ana Carolina , Boy Thomas , O’Gorman Eoin J. , Jacob Ute , Jochum Malte , Kortsch Susanne , Rosenbaum Benjamin , Figueiredo Ludmilla , Brose Ulrich
Published: February 2024

The dataset presents a compilation of stomach contents from six demersal fish species from two functional groups inhabiting the Baltic Sea. It includes detailed information on prey identities, body masses, and biomasses recovered from both the fish’s digestive systems and their surrounding environment. Environmental parameters, such as salinity and temperature levels, have been integrated to enrich this dataset. The juxtaposition of information on prey found in stomachs and in the environment provides an opportunity to quantify trophic interactions across different environmental contexts and investigate how fish foraging behaviour adapts to changes in their environment, such as an increase in temperature. The compilation of body mass and taxonomic information for all species allows approaching these new questions using either a taxonomic (based on species identity) or functional trait (based on body mass) approach.
Speech emotion recognition via graph-based representations
Authors: Pentari Anastasia , Kafentzis George , Tsiknakis Manolis
Published: February 2024

Speech emotion recognition (SER) has gained an increased interest during the last decades as part of enriched affective computing. As a consequence, a variety of engineering approaches have been developed addressing the challenge of the SER problem, exploiting different features, learning algorithms, and datasets. In this paper, we propose the application of the graph theory for classifying emotionally-colored speech signals. Graph theory provides tools for extracting statistical as well as structural information from any time series. We propose to use the mentioned information as a novel feature set. Furthermore, we suggest setting a unique feature-based identity for each emotion belonging to each speaker. The emotion classification is performed by a Random Forest classifier in a Leave-One-Speaker-Out Cross Validation (LOSO-CV) scheme. The proposed method is compared with two state-of-the-art approaches involving well known hand-crafted features as well as deep learning architectures operating on mel-spectrograms. Experimental results on three datasets, EMODB (German, acted) and AESDD (Greek, acted), and DEMoS (Italian, in-the-wild), reveal that our proposed method outperforms the comparative methods in these datasets. Specifically, we observe an average UAR increase of almost $$18\%$$

18
%

, $$8\%$$

8
%

and $$13\%$$

13
%

, respectively.
Development of renewable energy fed three-level hybrid active filter for EV charging station load using Jaya grey wolf optimization
Authors: Srilakshmi Koganti , Santosh D. Teja , Ramadevi Alapati , Balachandran Praveen Kumar , Reddy Ganesh Prasad , Palanivelu Aravindhababu , Colak Ilhami , Dhanamjayulu C. , Chinthaginjala Ravi Kumar , Khan Baseem
Published: February 2024

This work develops a hybrid active power filter (HAPF) in this article to operate in conjunction with the energy storage system (ESS), wind power generation system (WPGS), and solar energy system (SES). It employs three level shunt voltage source converters (VSC) connected to the DC-bus. Optimization of the gain values of the fractional-order proportional integral derivative controller (FOPIDC) and parameter values of the HAPF is achieved using the Jaya grey wolf hybrid algorithm (GWJA). The primary objectives of this study, aimed at enhancing power quality (PQ), include: (1) ensuring swift stabilization of DC link capacitor voltage (DCLCV); (2) reducing harmonics and improving power factor (PF); (3) maintaining satisfactory performance under different combinations of loads like EV charging load, non linear load and solar irradiation conditions. The proposed controller's performance is evaluated through three test scenarios featuring different load configurations and irradiation levels. Additionally, the HAPF is subjected to design using other optimization algorithms such as genetic algorithm (GA), particle swarm optimization (PSO), and ant colony optimization (ACO) to assess their respective contributions to PQ improvement.
Metabolomic associations of impaired awareness of hypoglycaemia in type 1 diabetes
Authors: Varkevisser R. D. M. , Cecil A. , Prehn C. , Mul D. , Aanstoot H. J. , Paterson A. D. , Wolffenbuttel B. H. R. , van der Klauw M. M.
Published: February 2024

This study investigates impaired awareness of hypoglycaemia (IAH), a complication of insulin therapy affecting 20–40% of individuals with type 1 diabetes. The exact pathophysiology is unclear, therefore we sought to identify metabolic signatures in IAH to elucidate potential pathophysiological pathways. Plasma samples from 578 individuals of the Dutch type 1 diabetes biomarker cohort, 67 with IAH and 108 without IAH (NAH) were analysed using the targeted metabolomics Biocrates AbsoluteIDQ p180 assay. Eleven metabolites were significantly associated with IAH. Genome-wide association studies of these 11 metabolites identified significant single nucleotide polymorphisms (SNPs) in C22:1-OH and phosphatidylcholine diacyl C36:6. After adjusting for the SNPs, 11 sphingomyelins and phosphatidylcholines were significantly higher in the IAH group in comparison to NAH. These metabolites are important components of the cell membrane and have been implicated to play a role in cell signalling in diabetes. These findings demonstrate the potential role of phosphatidylcholine and sphingomyelins in IAH.
Comprehensive analyses of solute carrier family members identify SLC12A2 as a novel therapy target for colorectal cancer
Authors: Chen Dan-yang , Zhang Yang-yang , Nie Hai-hang , Wang Hai-zhou , Qiu Pei-shan , Wang Fan , Peng Ya-nan , Xu Fei , Zhao Qiu , Zhang Meng
Published: February 2024

As the largest transporter family impacting on tumor genesis and development, the prognostic value of solute carrier (SLC) members has not been elucidated in colorectal cancer (CRC). We aimed to identify a prognostic signature from the SLC members and comprehensively analyze their roles in CRC. Firstly, we downloaded transcriptome data and clinical information of CRC samples from GEO (GSE39582) and TCGA as training and testing dataset, respectively. We extracted the expression matrix of SLC genes and established a prognostic model by univariate and multivariate Cox regression. Afterwards, the low-risk and high-risk group were identified. Then, the differences of prognosis traits, transcriptome features, clinical characteristics, immune infiltration and drug sensitivity between the two groups were explored. Furthermore, molecular subtyping was also implemented by non-negative matrix factorization (NMF). Finally, we studied the expression of the screened SLC genes in CRC tumor tissues and normal tissues as well as investigated the role of SLC12A2 by loss of function and gain of function. As a result, we developed a prognostic risk model based on the screened 6-SLC genes (SLC39A8, SLC2A3, SLC39A13, SLC35B1, SLC4A3, SLC12A2). Both in the training and testing sets, CRC patients in the high-risk group had the poorer prognosis and were in the more advanced pathological stage. What’s more, the high-risk group were enriched with CRC progression signatures and immune infiltration. Two groups showed different drug sensitivity. On the other hand, two distinct subclasses (C1 and C2) were identified based on the 6 SLC genes. CRC patients in the high-risk group and C1 subtype had a worse prognosis. Furthermore, we found and validated that SLC12A2 was steadily upregulated in CRC. A loss-of-function study showed that knockdown of SLC12A2 expression restrained proliferation and stemness of CRC cells while a gain-of-function study showed the contrary results. Hence, we provided a 6-SLC gene signature for prognosis prediction of CRC patients. At the same time, we identified that SLC12A2 could promote tumor progression in CRC, which may serve as a potential therapeutic target.
Prolonged culturing of colonic epithelial organoids derived from healthy individuals and ulcerative colitis patients results in the decrease of LINE-1 methylation level
Authors: Inciuraite Ruta , Steponaitiene Ruta , Raudze Odeta , Kulokiene Ugne , Kiudelis Vytautas , Lukosevicius Rokas , Ugenskiene Rasa , Adamonis Kestutis , Kiudelis Gediminas , Jonaitis Laimas Virginijus , Kupcinskas Juozas , Skieceviciene Jurgita
Published: February 2024

Patient-derived human intestinal organoids are becoming an indispensable tool for the research of digestive system in health and disease. However, very little is still known about the long-term culturing effect on global genomic methylation level in colonic epithelial organoids derived from healthy individuals as well as active and quiescent ulcerative colitis (UC) patients. In this study, we aimed to evaluate the epigenetic stability of these organoids by assessing the methylation level of LINE-1 during prolonged culturing. We found that LINE-1 region of both healthy control and UC patient colon tissues as well as corresponding epithelial organoids is highly methylated (exceeding 60%). We also showed that long-term culturing of colonic epithelial organoids generated from stem cells of healthy and diseased (both active and quiescent UC) individuals results in decrease of LINE-1 (up to 8%) methylation level, when compared to tissue of origin and short-term cultures. Moreover, we revealed that LINE-1 methylation level in sub-cultured organoids decreases at different pace depending on the patient diagnosis (healthy control, active or quiescent UC). Therefore, we propose LINE-1 as a potential and convenient biomarker for reliable assessment of global methylation status of patient-derived intestinal epithelial organoids in routine testing of ex vivo cultures.
UroPredict: Machine learning model on real-world data for prediction of kidney cancer recurrence (UroCCR-120)
Authors: Margue Gaëlle , Ferrer Loïc , Etchepare Guillaume , Bigot Pierre , Bensalah Karim , Mejean Arnaud , Roupret Morgan , Doumerc Nicolas , Ingels Alexandre , Boissier Romain , Pignot Géraldine , Parier Bastien , Paparel Philippe , Waeckel Thibaut , Colin Thierry , Bernhard Jean-Christophe
Published: February 2024

Renal cell carcinoma (RCC) is most often diagnosed at a localized stage, where surgery is the standard of care. Existing prognostic scores provide moderate predictive performance, leading to challenges in establishing follow-up recommendations after surgery and in selecting patients who could benefit from adjuvant therapy. In this study, we developed a model for individual postoperative disease-free survival (DFS) prediction using machine learning (ML) on real-world prospective data. Using the French kidney cancer research network database, UroCCR, we analyzed a cohort of surgically treated RCC patients. Participating sites were randomly assigned to either the training or testing cohort, and several ML models were trained on the training dataset. The predictive performance of the best ML model was then evaluated on the test dataset and compared with the usual risk scores. In total, 3372 patients were included, with a median follow-up of 30 months. The best results in predicting DFS were achieved using Cox PH models that included 24 variables, resulting in an iAUC of 0.81 [IC95% 0.77–0.85]. The ML model surpassed the predictive performance of the most commonly used risk scores while handling incomplete data in predictors. Lastly, patients were stratified into four prognostic groups with good discrimination (iAUC = 0.79 [IC95% 0.74–0.83]). Our study suggests that applying ML to real-world prospective data from patients undergoing surgery for localized or locally advanced RCC can provide accurate individual DFS prediction, outperforming traditional prognostic scores.
Fungal polysaccharides from Inonotus obliquus are agonists for Toll-like receptors and induce macrophage anti-cancer activity
Authors: Wold Christian Winther , Christopoulos Panagiotis F. , Arias Maykel A. , Dzovor Deborah Elikplim , Øynebråten Inger , Corthay Alexandre , Inngjerdingen Kari Tvete
Published: February 2024

Fungal polysaccharides can exert immunomodulating activity by triggering pattern recognition receptors (PRRs) on innate immune cells such as macrophages. Here, we evaluate six polysaccharides isolated from the medicinal fungus Inonotus obliquus for their ability to activate mouse and human macrophages. We identify two water-soluble polysaccharides, AcF1 and AcF3, being able to trigger several critical antitumor functions of macrophages. AcF1 and AcF3 activate macrophages to secrete nitric oxide and the pro-inflammatory cytokines tumor necrosis factor-α (TNF-α) and interleukin-6 (IL-6). Combined with interferon-γ, the fungal polysaccharides trigger high production of IL-12p70, a central cytokine for antitumor immunity, and induce macrophage-mediated inhibition of cancer cell growth in vitro and in vivo. AcF1 and AcF3 are strong agonists of the PRRs Toll-like receptor 2 (TLR2) and TLR4, and weak agonists of Dectin-1. In comparison, two prototypical particulate β-glucans, one isolated from I. obliquus and one from Saccharomyces cerevisiae (zymosan), are agonists for Dectin-1 but not TLR2 or TLR4, and are unable to trigger anti-cancer functions of macrophages. We conclude that the water-soluble polysaccharides AcF1 and AcF3 from I. obliquus have a strong potential for cancer immunotherapy by triggering multiple PRRs and by inducing potent anti-cancer activity of macrophages.
Transcript-dependent effects of the CALCA gene on the progression of post-traumatic osteoarthritis in mice
Authors: Jiang Shan , Xie Weixin , Knapstein Paul Richard , Donat Antonia , Albertsen Lilly-Charlotte , Sevecke Jan , Erdmann Cordula , Appelt Jessika , Fuchs Melanie , Hildebrandt Alexander , Maleitzke Tazio , Frosch Karl-Heinz , Baranowsky Anke , Keller Johannes
Published: February 2024

Osteoarthritis represents a chronic degenerative joint disease with exceptional clinical relevance. Polymorphisms of the CALCA gene, giving rise to either a procalcitonin/calcitonin (PCT/CT) or a calcitonin gene-related peptide alpha (αCGRP) transcript by alternative splicing, were reported to be associated with the development of osteoarthritis. The objective of this study was to investigate the role of both PCT/CT and αCGRP transcripts in a mouse model of post-traumatic osteoarthritis (ptOA). WT, αCGRP−/− and CALCA−/− mice were subjected to anterior cruciate ligament transection (ACLT) to induce ptOA of the knee. Mice were sacrificed 4 and 8 weeks post-surgery, followed by micro-CT and histological evaluation. Here we show that the expression of both PCT/CT and αCGRP transcripts is induced in ptOA knees. CALCA−/− mice show increased cartilage degeneration and subchondral bone loss with elevated osteoclast numbers compared to αCGRP−/− and WT mice. Osteophyte formation is reduced to the same extent in CALCA−/− and αCGRP−/− mice compared to WT controls, while a reduced synovitis score is noticed exclusively in mice lacking CALCA. Our data show that expression of the PCT/CT transcript protects from the progression of ptOA, while αCGRP promotes osteophyte formation, suggesting that CALCA-encoded peptides may represent novel targets for the treatment of ptOA.
In-silico testing of new pharmacology for restoring inhibition and human cortical function in depression
Authors: Guet-McCreight Alexandre , Chameh Homeira Moradi , Mazza Frank , Prevot Thomas D. , Valiante Taufik A. , Sibille Etienne , Hay Etay
Published: February 2024

Reduced inhibition by somatostatin-expressing interneurons is associated with depression. Administration of positive allosteric modulators of α5 subunit-containing GABAA receptor (α5-PAM) that selectively target this lost inhibition exhibit antidepressant and pro-cognitive effects in rodent models of chronic stress. However, the functional effects of α5-PAM on the human brain in vivo are unknown, and currently cannot be assessed experimentally. We modeled the effects of α5-PAM on tonic inhibition as measured in human neurons, and tested in silico α5-PAM effects on detailed models of human cortical microcircuits in health and depression. We found that α5-PAM effectively recovered impaired cortical processing as quantified by stimulus detection metrics, and also recovered the power spectral density profile of the microcircuit EEG signals. We performed an α5-PAM dose-response and identified simulated EEG biomarker candidates. Our results serve to de-risk and facilitate α5-PAM translation and provide biomarkers in non-invasive brain signals for monitoring target engagement and drug efficacy.
Markers of fertility in reproductive microbiomes of male and female endangered black-footed ferrets (Mustela nigripes)
Authors: Bornbusch Sally L. , Bamford Alexandra , Thacher Piper , Crosier Adrienne , Marinari Paul , Bortner Robyn , Garelle Della , Livieri Travis , Santymire Rachel , Comizzoli Pierre , Maslanka Michael , Maldonado Jesús E. , Koepfli Klaus-Peter , Muletz-Wolz Carly R. , DeCandia Alexandra L.
Published: February 2024

Reproductive microbiomes contribute to reproductive health and success in humans. Yet data on reproductive microbiomes, and links to fertility, are absent for most animal species. Characterizing these links is pertinent to endangered species, such as black-footed ferrets (Mustela nigripes), whose populations show reproductive dysfunction and rely on ex-situ conservation husbandry. To understand microbial contributions to animal reproductive success, we used 16S rRNA amplicon sequencing to characterize male (prepuce) and female (vaginal) microbiomes of 59 black-footed ferrets at two ex-situ facilities and in the wild. We analyzed variation in microbiome structure according to markers of fertility such as numbers of viable and non-viable offspring (females) and sperm concentration (males). Ferret vaginal microbiomes showed lower inter-individual variation compared to prepuce microbiomes. In both sexes, wild ferrets harbored potential soil bacteria, perhaps reflecting their fossorial behavior and exposure to natural soil microbiomes. Vaginal microbiomes of ex-situ females that produced non-viable litters had greater phylogenetic diversity and distinct composition compared to other females. In males, sperm concentration correlated with varying abundances of bacterial taxa (e.g., Lactobacillus), mirroring results in humans and highlighting intriguing dynamics. Characterizing reproductive microbiomes across host species is foundational for understanding microbial biomarkers of reproductive success and for augmenting conservation husbandry.
Codon language embeddings provide strong signals for use in protein engineering
Authors: Outeiral Carlos , Deane Charlotte M.
Published: February 2024

Protein representations from deep language models have yielded state-of-the-art performance across many tasks in computational protein engineering. In recent years, progress has primarily focused on parameter count, with recent models’ capacities surpassing the size of the very datasets they were trained on. Here we propose an alternative direction. We show that large language models trained on codons, instead of amino acid sequences, provide high-quality representations that outperform comparable state-of-the-art models across a variety of tasks. In some tasks, such as species recognition, prediction of protein and transcript abundance or melting point estimation, we show that a language model trained on codons outperforms every other published protein language model, including some that contain over 50 times more parameters. These results indicate that, in addition to commonly studied scale and model complexity, the information content of biological data provides an orthogonal direction to improve the power of machine learning in biology.
Barnacle cement protein as an efficient bioinspired corrosion inhibitor
Authors: Bui My Hanh , Hiew Shu Hui , Salim Teddy , Saw Wan Geok , Webster Richard D. , Grüber Gerhard , Mu Yuguang , Miserez Ali
Published: February 2024

To prevent corrosion damage in aggressive environments such as seawater, metallic surfaces are coated with corrosion inhibitors usually made of organic molecules. Unfortunately, these inhibitors often exhibit environmental toxicity and are hazardous to natural habitats. Thus, developing greener and effective corrosion inhibitors is desirable. Here, we present an alternative green inhibitor, the recombinant protein rMrCP20 derived from the adhesive cement of the barnacle Megabalanus rosa and show that it efficiently protects mild steel against corrosion under high salt conditions mimicking the marine environment. We reveal that these anti-corrosion properties are linked to the protein’s biophysical properties, namely its strong adsorption to surfaces combined with its interaction with Fe ions released by steel substrates, which forms a stable layer that increases the coating’s impedance and delays corrosion. Our findings highlight the synergistic action of rMrCP20 in preventing corrosion and provide molecular-level guidelines to develop alternative green corrosion inhibitor additives.
Multi-scale V-net architecture with deep feature CRF layers for brain extraction
Authors: Park Jong Sung , Fadnavis Shreyas , Garyfallidis Eleftherios
Published: February 2024

Background

Brain extraction is a computational necessity for researchers using brain imaging data. However, the complex structure of the interfaces between the brain, meninges and human skull have not allowed a highly robust solution to emerge. While previous methods have used machine learning with structural and geometric priors in mind, with the development of Deep Learning (DL), there has been an increase in Neural Network based methods. Most proposed DL models focus on improving the training data despite the clear gap between groups in the amount and quality of accessible training data between.

Methods

We propose an architecture we call Efficient V-net with Additional Conditional Random Field Layers (EVAC+). EVAC+ has 3 major characteristics: (1) a smart augmentation strategy that improves training efficiency, (2) a unique way of using a Conditional Random Fields Recurrent Layer that improves accuracy and (3) an additional loss function that fine-tunes the segmentation output. We compare our model to state-of-the-art non-DL and DL methods.

Results

Results show that even with limited training resources, EVAC+ outperforms in most cases, achieving a high and stable Dice Coefficient and Jaccard Index along with a desirable lower Surface (Hausdorff) Distance. More importantly, our approach accurately segmented clinical and pediatric data, despite the fact that the training dataset only contains healthy adults.

Conclusions

Ultimately, our model provides a reliable way of accurately reducing segmentation errors in complex multi-tissue interfacing areas of the brain. We expect our method, which is publicly available and open-source, to be beneficial to a wide range of researchers.
Introduction
Authors: Cornelissen Germaine , Otsuka Kuniaki , Hirota Tsuyoshi
Published: February 2024

As new tools in molecular biology and genetics have made it possible to better understand the mechanisms of endogenous biological clocks and their interactions with other important molecular pathways, it is timely to ask experts in their respective fields to describe past achievements and offer their perspective on future avenues of research. Understanding biological timing at multiple levels of molecular, cellular, and neural organization will be important for translating findings made in the laboratory to clinical applications. The now widely recognized bidirectional association between circadian disruption and disease risk has led to a wide range of chronotherapeutic approaches and to the consideration of rhythm characteristics as important novel biomarkers aimed at prevention as well as treatment. As discussed throughout this book, among the remaining challenges (including the role of emotion, resilience, and well-being in many contexts of human life), a personalized approach to health maintenance is paramount, which can be achieved through a two-pronged approach focusing on a better understanding of molecular mechanisms and the chronobiological interpretation of longitudinal monitoring. Technological advances have contributed to the rapid evolution of the field, with far-reaching applications now within reach.
Circadian Clocks in Mammals: General Aspects of Oscillating Systems and Roles in Medicine
Authors: Honma Ken-ichi
Published: February 2024

The circadian system generates about 24-hour rhythms in body functions to adjust their performances to cyclic environments, thereby ensuring survival. Misalignment of internal periodicities and environmental cycles eventually leads to both mental and physical malfunctions. To gain insight into misalignment, it is absolutely necessary to understand the principle of entrainment, especially in relation to the light–dark (LD) cycle. Non-parametric and parametric entrainments are basic concepts and two coupled oscillators are likely involved in stable entrainment and its seasonal changes. It is critical to understand the molecular mechanism of the circadian system to comprehend the regulation of the system. The discovery of clock genes has greatly increased our knowledge but we are now grappling with the complexity of the system. The suprachiasmatic nucleus in the hypothalamus serves as the central clock, which entrains to the LD cycle and regulates the peripheral clocks located in almost all tissues and organs. Modern society is chaotic in terms of time structure, where the circadian system is easily disrupted. Understanding the mechanism underlying circadian disorders is important for their prevention and treatment. The concept of chronomedicine, which was proposed several decades ago, is now ready to be materialized with the advent of molecular chronobiology.
The Nervous System
Authors: Honma Sato
Published: February 2024

The mammalian circadian system comprises a master clock, located in the hypothalamic suprachiasmatic nucleus (SCN), and peripheral clocks situated throughout the body, including extra-SCN brain tissues. Individual cells have their own molecular circadian clock machinery, namely, transcriptional and translational feedback loops composed of several clock genes and their protein products. The SCN orchestrates peripheral clocks to carry out their physiological functions, meaning that the SCN does not merely drive the circadian signal but synchronizes the cell-based and peripheral clocks. The SCN itself is composed of multiple networks of oscillator cells in which both neurons and glia are involved. The hierarchical multi-oscillator system, both within the SCN and throughout the body, enables temporally coordinated functions, which are crucial for good health.
Circadian Rhythms and the Gastrointestinal System
Authors: Cassone Vincent M.
Published: February 2024

Circadian organization comprises both hierarchical and distributed pacemakers, as well as peripheral oscillators that are coordinated by the hypothalamic suprachiasmatic nuclei (SCN). Among the peripheral tissues that are coordinated by the SCN is the gastrointestinal system via the sympathetic nervous system. At each level of gastrointestinal function, circadian clocks regulate the homeostatic functions of consuming, breaking down, digesting and absorbing nutrients. This system contains a semi-independent circadian clock capable of producing endogenously generated rhythms in gene expression, motility, and absorption both in vivo and in vitro, and capable of entraining directly to timed meals. Within the gastrointestinal lumen, a vibrant ecosystem of microorganisms, known as the gastrointestinal microbiome is regulated by the gastrointestinal clock through the presentation of nutrients, hormones, and changes in body temperature (TB), among other signals. Some of these bacteria directly respond to the host signals, while others, possessing endogenous circadian clocks themselves, may entrain to the host’s Zeitgebers, and still others may respond to signals generated by other members of the gut microbiome itself. Disruption of the circadian system may be critical in exacerbating or even causing pathological processes and diseases, including deleterious effects of aging, cancer, and inflammatory bowel disease, among others.
Quo Vadis
Authors: Cornelissen Germaine , Hirota Tsuyoshi
Published: February 2024

Ubiquitous and prominent circadian rhythms are only one component of a rich inter-modulating multi-frequency time structure. While a molecular mechanism underlying circadian rhythms has been uncovered, a molecular basis for other rhythmic components is now emerging. Evidence for a partially endogenous broader-than-circadian time structure awaits further investigation into the underlying mechanisms since it may offer added chronotherapeutic applications in the clinic, as already shown empirically. Much attention is devoted to the discovery and applications of small molecules targeting the circadian clock directly, representing another area that is rapidly evolving and offering a novel approach to treat a host of different conditions where the restoration of a well-functioning circadian system plays a central role.
Advances in MXene-based luminescence sensing strategies
Authors: Gao Lingfeng , He Chiyang
Published: February 2024

MXene-based luminescence sensing strategies include fluorescence, electrochemiluminescence and chemiluminescence sensors. Their performance are summarized, and their challenges and application perspectives are discussed.
Biomaterial engineering strategies for B cell immunity modulations
Authors: Zareein Ali , Mahmoudi Mina , Jadhav Shruti Sunil , Wilmore Joel , Wu Yaoying
Published: February 2024

Biomaterials enhance B cell immunity by modulating the delivery approach, crosslinking B cell receptors, and promoting T cell help, while inhibitory co-receptor engagement via biomaterial design suppresses B cell function.
Electronic structure modification of SnO2 to accelerate CO2 reduction towards formate
Authors: Li Lulu , Wu Shican , Cheng Dongfang , Zhao Zhi-Jian , Gong Jinlong
Published: February 2024

Electronic modification of SnO2 using doping to enhance electrocatalytic CO2 reduction to formate.
Coordination-triggered redox activity of early and late lanthanide calix[4]arene complexes
Authors: Jiao Yushu , Sanz Sergio , Koláčná Lucie , van Leusen Jan , Izarova Natalya V. , Sarwar Sidra , Ludvík Jiří , Kögerler Paul
Published: February 2024

Two families of mononuclear lanthanide compounds based on calix[4]arene exhibit electrochemical (quasi-)reversible behavior triggered by coordination to lanthanides.
Ag–Ru interface for highly efficient hydrazine assisted water electrolysis
Authors: Fu Xiaoyang , Cheng Dongfang , Zhang Ao , Zhou Jingxuan , Wang Sibo , Zhao Xun , Chen Jun , Sautet Philippe , Huang Yu , Duan Xiangfeng
Published: February 2024

Ru decorated Ag nanoparticles are designed as highly effective bifunctional electrocatalysts for hydrazine oxidation and hydrogen evolution reactions, enabling a hydrazine assisted water electrolyser with greatly increased current density.
Peracetic acid to reduce disinfection by-product formation in drinking water
Authors: Mondal Subhajit , Mackey Erin , Hofmann Ron
Published: February 2024

A 5 mg L−1 PAA/H2O2 (mixture) pre-oxidation decreased the DBP formation potential by up to 40%.
Layer-coupled corner states in two-dimensional topological multiferroics
Authors: Li Runhan , Zou Xiaorong , Bai Yingxi , Chen Zhiqi , Huang Baibiao , Dai Ying , Niu Chengwang
Published: February 2024

In two-dimensional multiferroics, a new class of higher-order topological insulator materials realize layer-polarized topological corner states through ferroelectric polarization.
Guanidine-centred reactivity of CNN Pd(ii) pincer complexes including carboxylate-assisted N–H activation and –CH2– → –C(O)– oxygenation
Authors: Sinha Nitish Kumar , Khan Hilal Ahmad , Sivasankar Chinnappan , Thirupathi Natesan
Published: February 2024

Guanidinate(1−) Pd(ii) pincer complex A smoothly transforms into oxygenated guanidinate(2−) CNN Pd(ii) pincer complex Dvia a range of intermediates, which were either isolated and structurally characterized or modelled using DFT calculations.
UV-modification of Ag nanoparticles on α-MoCx for interface polarization engineering in electromagnetic wave absorption
Authors: Zhu Pengyuan , Kang Yifan , Li Xinglong , Yu Haoquan , Liu Tong , Song Ming , Zhang Yanan , Zhou Lifan , Zhao Ping , Huang Wenhuan
Published: February 2024

Based on bimetallic HZIF-ZnMo, a high-performance electromagnetic wave absorbing material with comprehensive conductivity loss, polarization loss and dielectric loss was obtained by graphiting and UV-modified silver nanoparticles.
Aggregation induced emission and volatile acid vapour sensing in acridine appended poly (aryl ether) based low molecular weight organogelator
Authors: Patra Srikanta Kumar , Mahato Malay Krishna , Prasad Edamana
Published: February 2024

An acridine-core poly(aryl ether) dendron (APD) molecular probe forms a long-range self-assembled AIE gel exhibit a selective sensory response towards volatile acids with a low detection limit down to 0.22 ppm with a rapid response time of 0.04 s.
Ab initioinvestigations of the structure-stability, mechanical, electronic, thermodynamic and optical properties of Ti2FeAs Heusler alloy
Authors: Kumari Anjali , Mishra Abhishek Kumar , Sharma Ramesh , Al-Qaisi Samah , Moayad A. J. A. , Alshomrany Ali S. , Sfina N. , Dar Sajad Ahmed , Srivastava Vipul
Published: February 2024

To study the structural, electronic, and magnetic characteristics of the Ti2FeAs alloy adopting the Hg2CuTi-type structure based on the DFT. The results imply that the Ti2FeAs alloy can soon be a viable material for application in optoelectronic devices such as UV absorbers and spintronics devices.
Organic pollutant degradation for micro-molecule product emission over SiO2 layers-coated g-C3N4 photocatalysts
Authors: Ma Yongning , Wu Peihan , Ku Mengting , Guo Mingyuan , Yang Yuhao , Li Xiaolong , Chen Haiyong
Published: February 2024

In this study, a SiO2 layer-coated g-C3N4 catalyst was prepared by a sol–gel method to overcome the poor adsorption ability and high recombination rate of charge carriers of pristine g-C3N4.
RAFT step-growth polymerization via the Z-group approach and deconstruction by RAFT interchange
Authors: Li Jiajia , Tanaka Joji , Li Qing , Jing Wang Claire Jing , Sheiko Sergei , Clouthier Samantha Marie , Zhu Jian , You Wei
Published: February 2024

RAFT step-growth polymerization via the Z-group approach was developed, offering a facile method to prepare deconstructable (multiblock) polymers by combining RAFT chain-growth polymerization and RAFT interchange.
Enhancing the stability of photocatalytic systems for hydrogen evolution in water by using a tris-phenyl-phenanthroline sulfonate ruthenium photosensitizer
Authors: Camara Fakourou , Aguirre-Araque Juan S. , Fortage Jérôme , Collomb Marie-Noëlle
Published: February 2024

Using the water-soluble Ru-tris-phenyl phenanthroline sulfonate photosensitizer versus regular Ru-tris-bipyridine improves the efficiency of H2 production in water.
A Mo–salicylaldehyde-linker (Mo–Tp) based 2D MOF as a single-atom catalyst for the nitrogen reduction reaction
Authors: Alhadidi Almheiri Hassan A. , Singh Nirpendra , Shetty Dinesh , Polychronopoulou Kyriaki , Alhammadi Ali A.
Published: February 2024

This work investigates a Mo–Tp 2D MOF screened from a number of different transition-metal-based 2D MOFs. After exfoliation, the Mo–Tp 2D MOF produces ammonia via the distal pathway at a very low limiting potential of −0.38 V.
Bionic inspired multifunctional modular energetic materials: an exploration of new generation of application-oriented energetic materials
Authors: Wen Yujia , Wen Linyuan , Tan Bojun , Dou Jinkang , Xu Minghui , Liu Yingzhe , Wang Bozhou , Liu Ning
Published: February 2024

Aiming to balance the pertinence and universality of energetic materials, this study proposes a new concept of bionic inspired multifunctional modular energetic materials and seeks out potential monomers via a high-throughput screening strategy.
Like-charge attraction between two identical dielectric spheres in a uniform electric field: a theoretical study via a multiple-image method and an effective-dipole approach
Authors: Li Xin , Li Changhao , Gao Xin , Huang Decai
Published: February 2024

A multiple-image method is developed as an accurate numerical approach to calculate the electrostatic interaction between two like-charged dielectric spheres in a uniform electric field.
Highly lubricative, self-healing, chemically degradable, anti-flaming and anti-irradiating magnetic gels simply prepared from binary mixtures of Fe3O4 nanoparticles and water
Authors: Hu Lulin , Yu Weiyan , Liu Jian , Yang Yi , Hao Jingcheng , Xu Lu
Published: February 2024

Magnetic gels are usually organic polymer–inorganic particle hybrids. We show that magnetic gels with high lubricity, self-healing, chemical degradability, and flame and irradiation resistances can be prepared solely with Fe3O4 particles and water.
Stimuli-free Zn/soda-lime glass/CuO-based MIS device for sensing human skin moisture
Authors: Kumar Kanhai , Rachna Devi Hemam , Raj Gokul , Kar Nanda Karuna
Published: February 2024

A highly sensitive, self-biased, and room temperature operational proximity sensor for sensing human skin moisture.
A Lewis-base-based antisolvent method for fabricating triple-cation perovskite solar cells
Authors: Liu Xuewen , Lee Eun-Cheol
Published: February 2024

The incorporation of tetrahydrofuran into ethyl acetate enhances the power conversion efficiency of the perovskite solar cell, primarily due to an elevation in the short-circuit current.
Metal cation detection based on a stable n-channel accumulation organic electrochemical transistor
Authors: Shi Cheng , Jiang Xingyu , Wang Qi , Dong Xinyu , Xiang Chuan , Wang Zi , Chi Lifeng , Huang Lizhen
Published: February 2024

An n-channel high-performance, stable OECT device by using a highly crystalline fullerene derivative film as the channel layer has been prepared and has demonstrated promising potential for metal cation detection.
Palladium-catalyzed enantioselective arylation of trichloro- or tri-/difluoroacetaldimine precursors
Authors: Wei Jian , Du Zhongjian , Wang Xu , Ji Chenlei , Li Longji , You Yang’en
Published: February 2024

A palladium-catalyzed asymmetric α-arylation of N-carbamoyl imines precursors containing CCl3, CF3 and CF2H has been developed, affording a series of chiral α-aryl amines bearing various functional groups, with good results (up to 99% ee).
Redox-neutral zinc-catalyzed cascade [1,4]-H shift/annulation of diaziridines with donor–acceptor aziridines
Authors: Samantaray Swati , Maharana Prabhat Kumar , Kar Subhradeep , Saha Sharajit , Punniyamurthy Tharmalingam
Published: February 2024

A Zn(ii)-catalyzed (3+2)-annulation of diaziridines with DA aziridines has been accomplished via 1,4-hydride shift to furnish imidazo[1,5-b]pyrazole-4,4-dicarboxylates under mild reaction conditions.
Construction of a redox pathway through a polyoxometalate and covalent organic framework for H2O2 photosynthesis
Authors: Gong Yin , Ren Hongda , Sang Xiaojing , Zhu Haotian , Zhang Jingzhen , Li Sifan , Lang Zhongling , Li Jiansheng
Published: February 2024

A novel electron donor–acceptor system was constructed from a covalent organic framework and a polyoxometalate, which exhibited good photocatalytic performance for H2O2 production in pure water.
Growth of single-crystalline SrNbO2N micron particles and assembling of particulate photoanodes
Authors: Huang Hezhou , Liu Xiaoli , Ma Jianguo , Zhang Jingsheng , Zhang Yifan , Kang Jiahao , Zhu Ting , Gong Chaoxiu , Luo Mingbiao , Xiong Feng-Qiang
Published: February 2024

SrNbO2N crystal growth and control of defects were optimized by adjusting excess SrO in the flux-assisted thermal ammonolysis process.
High-throughput screening of the transport behavior of tetragonal perovskites
Authors: Chen Yuanyuan , Xiao Lu , Shi Libin , Qian Ping
Published: February 2024

Halide perovskites have attracted attention due to their low cost and excellent optoelectronic properties.
Correction: Photoelectrochemical NADH regeneration on a polymer semiconductor-based photocathode
Authors: Li Nanxin , You Jia , Huang Lanlan , Zhang Haoran , Wang Xianlong , He Lihua , Gong Chunli , Lin Shiwei , Zhang Bingqing
Published: February 2024

Correction for ‘Photoelectrochemical NADH regeneration on a polymer semiconductor-based photocathode’ by Nanxin Li et al., Green Chem., 2023, 25, 5247–5256, https://doi.org/10.1039/D3GC00559C.
Multi-component liquid-infused systems: a new approach to functional coatings
Authors: Applebee Zachary , Howell Caitlin
Published: February 2024

Adding a secondary component to a liquid coating results in new and synergistic properties.
A MnS/MnO-coated S,N-doped carbon anode obtained from a Mn(ii)-coordinated polymer for long-cycle life Li-ion batteries
Authors: Shim Kyubin , Kim Hyun Woo , Park Sungwoo , Seo Kyeong-Deok , Kim Chang-Yeon , Lee Jin Bae , Bae Jong Seong , Kim Hae Jin
Published: February 2024

A MnS/MnO-decorated S,N-doped carbon electrode was synthesized for advanced LIBs. This shows excellent cycling stability, with the material exhibiting superior performance. In situ XRD and XPS provided a fundamental understanding of the material.
Honeycomb-like micro-/nano-hierarchical porous germanium for high-performance lithium-ion battery anodes
Authors: Zheng Ya , Li Xiaocheng , Liu Juan , Zhao Xiaoyu , Ding Nengwen , Zhang Qian , Zhong Shengwen
Published: February 2024

The synthesized honeycomb-like micro-/nano-hierarchical porous Ge (hp-Ge) anode demonstrates comparable capacity to that of pristine solid Ge microparticles but with an enhanced ICE, better rate capability and more excellent cyclability.
Bio-inspired carbon electrodes for metal-ion batteries
Authors: Yang Yihan , Zhou Jiang , Rao Apparao M. , Lu Bingan
Published: February 2024

This mini-review highlights advances in multi-dimensional carbon electrodes with bio-inspired principles for metal-ion batteries.
Origin of site-selectivity of hydrogen atom transfer in carbohydrate C–H alkylations via photoredox catalysis
Authors: Ji Yujie , Hu Lingfei , Gao Han , Wu Yan-Bo , Lv Xiangying , Lu Gang
Published: February 2024

Two major factors, i.e., C–H σ orbital energy and C–H BDE, account for the HAT site-selectivity of carbohydrates with the quinuclidine radical cation.
Total syntheses of certain asperversiamides, linearly-fused and prenylated indole alkaloids
Authors: Xu Zhongnan , Liang Xin-Ting , Lan Ping , Banwell Martin G.
Published: February 2024

Biogenetically-patterned total syntheses of seven prenylated alkaloids embodying the pyrano[3,2-f]indole framework have been realised alongside the preparation of several potential natural products.