bluuebunny/crossref_metadata_2025_split huggingface dataset:
MAGinator enables accurate profiling of de novo MAGs with strain-level phylogenies
Authors: Zachariasen Trine , Russel Jakob , Petersen Charisse , Vestergaard Gisle A. , Shah Shiraz , Atienza Lopez Pablo , Passali Moschoula , Turvey Stuart E. , Sørensen Søren J. , Lund Ole , Stokholm Jakob , Brejnrod Asker , Thorsen Jonathan 
Published: July 2024

AbstractMetagenomic sequencing has provided great advantages in the characterisation of microbiomes, but currently available analysis tools lack the ability to combine subspecies-level taxonomic resolution and accurate abundance estimation with functional profiling of assembled genomes. To define the microbiome and its associations with human health, improved tools are needed to enable comprehensive understanding of the microbial composition and elucidation of the phylogenetic and functional relationships between the microbes. Here, we present MAGinator, a freely available tool, tailored for profiling of shotgun metagenomics datasets. MAGinator provides de novo identification of subspecies-level microbes and accurate abundance estimates of metagenome-assembled genomes (MAGs). MAGinator utilises the information from both gene- and contig-based methods yielding insight into both taxonomic profiles and the origin of genes and genetic content, used for inference of functional content of each sample by host organism. Additionally, MAGinator facilitates the reconstruction of phylogenetic relationships between the MAGs, providing a framework to identify clade-level differences.
Topologically controlled synthesis of active colloidal bipeds
Authors: Elschner Jonas , Farrokhzad Farzaneh , Kuświk Piotr , Urbaniak Maciej , Stobiecki Feliks , Akhundzada Sapida , Ehresmann Arno , de las Heras Daniel , Fischer Thomas M. 
Published: July 2024

AbstractTopological growth control allows to produce a narrow distribution of outgrown colloidal rods with defined and adjustable length. We use an external magnetic field to assemble paramagnetic colloidal spheres into colloidal rods of a chosen length. The rods reside above a metamorphic hexagonal magnetic pattern. The periodic repetition of specific loops of the orientation of an applied external field renders paramagnetic colloidal particles and their assemblies into active bipeds that walk on the pattern. The metamorphic patterns allow the robust and controlled polymerization of single colloids to bipeds of a desired length. The colloids are exposed to this fixed external control loop that causes multiple simultaneous responses: Small bipeds and single colloidal particles interpret the external magnetic loop as an order to walk toward the active zone, where they assemble and polymerize. Outgrown bipeds interpret the same loop as an order to walk away from the active zone. The topological transition occurs solely for the growing biped and nothing is changed in the environment nor in the magnetic control loop. As in many biological systems the decision of a biped that reached its outgrown length to walk away from the reaction site is made internally, not externally.
Leukocyte immunoglobulin-like receptor B1 (LILRB1) protects human multiple myeloma cells from ferroptosis by maintaining cholesterol homeostasis
Authors: Xian Miao , Wang Qiang , Xiao Liuling , Zhong Ling , Xiong Wei , Ye Lingqun , Su Pan , Zhang Chuanchao , Li Yabo , Orlowski Robert Z. , Zhan Fenghuang , Ganguly Siddhartha , Zu Youli , Qian Jianfei , Yi Qing 
Published: July 2024

AbstractMultiple myeloma (MM) is a hematologic malignancy characterized by uncontrolled proliferation of plasma cells in the bone marrow. MM patients with aggressive progression have poor survival, emphasizing the urgent need for identifying new therapeutic targets. Here, we show that the leukocyte immunoglobulin-like receptor B1 (LILRB1), a transmembrane receptor conducting negative immune response, is a top-ranked gene associated with poor prognosis in MM patients. LILRB1 deficiency inhibits MM progression in vivo by enhancing the ferroptosis of MM cells. Mechanistic studies reveal that LILRB1 forms a complex with the low-density lipoprotein receptor (LDLR) and LDLR adapter protein 1 (LDLRAP1) to facilitate LDL/cholesterol uptake. Loss of LILRB1 impairs cholesterol uptake but activates the de novo cholesterol synthesis pathway to maintain cellular cholesterol homeostasis, leading to the decrease of anti-ferroptotic metabolite squalene. Our study uncovers the function of LILRB1 in regulating cholesterol metabolism and protecting MM cells from ferroptosis, implicating LILRB1 as a promising therapeutic target for MM patients.
Metabolic reprograming mediated by tumor cell-intrinsic type I IFN signaling is required for CD47-SIRPα blockade efficacy
Authors: Zhou Hang , Wang Wenjun , Xu Hairong , Liang Yong , Ding Jiyu , Lv Mengjie , Ren Boyang , Peng Hua , Fu Yang-Xin , Zhu Mingzhao 
Published: July 2024

AbstractType I interferons have been well recognized for their roles in various types of immune cells during tumor immunotherapy. However, their direct effects on tumor cells are less understood. Oxidative phosphorylation is typically latent in tumor cells. Whether oxidative phosphorylation can be targeted for immunotherapy remains unclear. Here, we find that tumor cell responsiveness to type I, but not type II interferons, is essential for CD47-SIRPα blockade immunotherapy in female mice. Mechanistically, type I interferons directly reprogram tumor cell metabolism by activating oxidative phosphorylation for ATP production in an ISG15-dependent manner. ATP extracellular release is also promoted by type I interferons due to enhanced secretory autophagy. Functionally, tumor cells with genetic deficiency in oxidative phosphorylation or autophagy are resistant to CD47-SIRPα blockade. ATP released upon CD47-SIRPα blockade is required for antitumor T cell response induction via P2X7 receptor-mediated dendritic cell activation. Based on this mechanism, combinations with inhibitors of ATP-degrading ectoenzymes, CD39 and CD73, are designed and show synergistic antitumor effects with CD47-SIRPα blockade. Together, these data reveal an important role of type I interferons on tumor cell metabolic reprograming for tumor immunotherapy and provide rational strategies harnessing this mechanism for enhanced efficacy of CD47-SIRPα blockade.
Synergism of primary and secondary interactions in a crystalline hydrogen peroxide complex with tin
Authors: Medvedev Alexander G. , Egorov Pavel A. , Mikhaylov Alexey A. , Belyaev Evgeny S. , Kirakosyan Gayane A. , Gorbunova Yulia G. , Filippov Oleg A. , Belkova Natalia V. , Shubina Elena S. , Brekhovskikh Maria N. , Kirsanova Anna A. , Babak Maria V. , Lev Ovadia , Prikhodchenko Petr V. 
Published: July 2024

AbstractDespite the significance of H2O2-metal adducts in catalysis, materials science and biotechnology, the nature of the interactions between H2O2 and metal cations remains elusive and debatable. This is primarily due to the extremely weak coordinating ability of H2O2, which poses challenges in characterizing and understanding the specific nature of these interactions. Herein, we present an approach to obtain H2O2–metal complexes that employs neat H2O2 as both solvent and ligand. SnCl4 effectively binds H2O2, forming a SnCl4(H2O2)2 complex, as confirmed by 119Sn and 17O NMR spectroscopy. Crystalline adducts, SnCl4(H2O2)2·H2O2·18-crown-6 and 2[SnCl4(H2O2)(H2O)]·18-crown-6, are isolated and characterized by X-ray diffraction, providing the complete characterization of the hydrogen bonding of H2O2 ligands including geometric parameters and energy values. DFT analysis reveals the synergy between a coordinative bond of H2O2 with metal cation and its hydrogen bonding with a second coordination sphere. This synergism of primary and secondary interactions might be a key to understanding H2O2 reactivity in biological systems.
Context-invariant beliefs are supported by dynamic reconfiguration of single unit functional connectivity in prefrontal cortex of male macaques
Authors: Noel Jean-Paul , Balzani Edoardo , Savin Cristina , Angelaki Dora E. 
Published: July 2024

AbstractNatural behaviors occur in closed action-perception loops and are supported by dynamic and flexible beliefs abstracted away from our immediate sensory milieu. How this real-world flexibility is instantiated in neural circuits remains unknown. Here, we have male macaques navigate in a virtual environment by primarily leveraging sensory (optic flow) signals, or by more heavily relying on acquired internal models. We record single-unit spiking activity simultaneously from the dorsomedial superior temporal area (MSTd), parietal area 7a, and the dorso-lateral prefrontal cortex (dlPFC). Results show that while animals were able to maintain adaptive task-relevant beliefs regardless of sensory context, the fine-grain statistical dependencies between neurons, particularly in 7a and dlPFC, dynamically remapped with the changing computational demands. In dlPFC, but not 7a, destroying these statistical dependencies abolished the area’s ability for cross-context decoding. Lastly, correlational analyses suggested that the more unit-to-unit couplings remapped in dlPFC, and the less they did so in MSTd, the less were population codes and behavior impacted by the loss of sensory evidence. We conclude that dynamic functional connectivity between neurons in prefrontal cortex maintain a stable population code and context-invariant beliefs during naturalistic behavior.
Deoxycholic acid inducing chronic atrophic gastritis with colonic mucosal lesion correlated to mucosal immune dysfunction in rats
Authors: Cheng Yuqin , Wang Shuaishuai , Zhu Wenfei , Xu Zijing , Xiao Ling , Wu Jianping , Meng Yufen , Zhang Junfeng , Cheng Chun 
Published: July 2024

AbstractThe present study aimed to explore the underlying mechanism of bile reflux-inducing chronic atrophic gastritis (CAG) with colonic mucosal lesion. The rat model of CAG with colonic mucosal lesion was induced by free-drinking 20 mmol/L sodium deoxycholate to simulate bile reflux and 2% cold sodium salicylate for 12 weeks. In comparison to the control group, the model rats had increased abundances of Bacteroidetes and Firmicutes but had decreased abundances of Proteobacteria and Fusobacterium. Several gut bacteria with bile acids transformation ability were enriched in the model group, such as Blautia, Phascolarctobacter, and Enterococcus. The cytotoxic deoxycholic acid and lithocholic acid were significantly increased in the model group. Transcriptome analysis of colonic tissues presented that the down-regulated genes enriched in T cell receptor signaling pathway, antigen processing and presentation, Th17 cell differentiation, Th1 and Th2 cell differentiation, and intestinal immune network for IgA production in the model group. These results suggest that bile reflux-inducing CAG with colonic mucosal lesion accompanied by gut dysbacteriosis, mucosal immunocompromise, and increased gene expressions related to repair of intestinal mucosal injury.
Three-dimensional convolutional neural network-based classification of chronic kidney disease severity using kidney MRI
Authors: Nagawa Keita , Hara Yuki , Inoue Kaiji , Yamagishi Yosuke , Koyama Masahiro , Shimizu Hirokazu , Matsuura Koichiro , Osawa Iichiro , Inoue Tsutomu , Okada Hirokazu , Kobayashi Naoki , Kozawa Eito 
Published: July 2024

AbstractA three-dimensional convolutional neural network model was developed to classify the severity of chronic kidney disease (CKD) using magnetic resonance imaging (MRI) Dixon-based T1-weighted in-phase (IP)/opposed-phase (OP)/water-only (WO) imaging. Seventy-three patients with severe renal dysfunction (estimated glomerular filtration rate [eGFR] < 30 mL/min/1.73 m2, CKD stage G4–5); 172 with moderate renal dysfunction (30 ≤ eGFR < 60 mL/min/1.73 m2, CKD stage G3a/b); and 76 with mild renal dysfunction (eGFR ≥ 60 mL/min/1.73 m2, CKD stage G1–2) participated in this study. The model was applied to the right, left, and both kidneys, as well as to each imaging method (T1-weighted IP/OP/WO images). The best performance was obtained when using bilateral kidneys and IP images, with an accuracy of 0.862 ± 0.036. The overall accuracy was better for the bilateral kidney models than for the unilateral kidney models. Our deep learning approach using kidney MRI can be applied to classify patients with CKD based on the severity of kidney disease.
Experimental study of the effects of the void located at the pile tip on the load capacity of rock-socketed piles
Authors: Zhao Xiaolin , Melentijevic Svetlana , Shen Yupeng , Sun Zengkui , Wang Kaiyuan , Xu Jincui , Li Zhiqiang 
Published: July 2024

AbstractTo address the design challenge of the rock-socketed piles posed by the void located below the pile tip, the physical laboratory model tests were designed and performed to simulate rock socketed piles using similar materials. The study investigates the behavior of the single pile under axial loading with the void located at varying distances from the pile tip. Through multi-level load tests, the variations of unit pile side friction, pile tip resistance, pile axial force and pile settlement are obtained for different positions of the void from the pile tip, as well as after grouting. Its comparison to the rock-socketed pile without void is performed as a reference to quantify the reduction in its bearing capacity. The results are presented in the form of graphs for different void positions and its grouting shows the influence on pile bearing capacity and emphasizes the importance of its detailed cautious investigation and introduction in the analysis. The 2D finite element modeling of the model pile-the void based on ABAQUS is performed to further investigate the influence of the void below pile tip on the bearing capacity of model pile, applying the Mohr Coulomb model as the constitutive model of rock mass behavior. The critical distance of the void below the pile tip is determined.
Preparation of 3D printed silicon nitride bioceramics by microwave sintering
Authors: Zeng Xiaofeng , Sipaut Coswald Stephen , Ismail Noor Maizura , Liu Yuandong , Farm Yan yan , Peng Bo , He Jiayu 
Published: July 2024

AbstractSilicon nitride (Si3N4) is a bioceramic material with potential applications. Customization and high reliability are the foundation for the widespread application of Si3N4 bioceramics. This study constructed a new microwave heating structure and successfully prepared 3D printed dense Si3N4 materials, overcoming the adverse effects of a large amount of 3D printed organic forming agents on degreasing and sintering processes, further improving the comprehensive performance of Si3N4 materials. Compared with control materials, the 3D printed Si3N4 materials by microwave sintering have the best mechanical performance: bending strength is 928 MPa, fracture toughness is 9.61 MPa·m1/2. Meanwhile, it has the best biocompatibility and antibacterial properties, and cells exhibit the best activity on the material surface. Research has shown that the excellent mechanical performance and biological activity of materials are mainly related to the high-quality degreasing, high cleanliness sintering environment, and high-quality liquid-phase sintering of materials in microwave environments.
Neural correlates of depression-related smartphone language use in adolescents
Authors: McNeilly Elizabeth A. , Teresi Giana I. , Coury Saché , Bajwa Zia , Kahn Lauren E. , Crowley Ryann , Allen Nicholas B. , Ho Tiffany C. 
Published: July 2024

AbstractMagnetic resonance imaging has provided pathophysiological insights into adolescent depression but is a relatively inaccessible technology. Generating scalable indicators of depression that are informed by neuroscience is therefore critical for providing solutions that allow us to detect and treat this devastating disorder. In this preregistered study, we investigated whether passively acquired smartphone-based language usage represents such an indicator of depression and explored whether the neural correlates of depression mediate or moderate this association. Forty adolescents (ages 14–18 years) with (n = 26) and without (n = 14) depression completed clinical assessments and a resting-state fMRI scan, prior to downloading a passive mobile sensing app to their smartphones. Linguistic features derived from over 1.2 million words (319,364 messages) across all smartphone apps were used to examine word usage patterns. Independent components analysis followed by dual regression was used to derive intrinsic networks commonly associated with depression: central executive network (CEN), default mode network (DMN), and salience network (SN). Depression was associated with more negative emotion word usage and fewer future-focus word usage on a daily basis (all ps < 0.05). Higher depressive symptoms and brain networks DMN and CEN were associated with greater first-person pronoun usage (all ps < 0.04). Accounting for CEN connectivity amplified the positive association between depressive symptoms and first-person pronoun usage. Lower SN–CEN connectivity moderated the association between depression and negative emotion word usage. Depression in adolescents is associated with naturalistic language usage during smartphone activities and may represent neurocognitive biases that are candidate treatment targets for interventions.
The IRE1α/XBP1 signaling axis drives myoblast fusion in adult skeletal muscle
Authors: Joshi Aniket S , Tomaz da Silva Meiricris , Roy Anirban , Koike Tatiana E , Wu Mingfu , Castillo Micah B , Gunaratne Preethi H , Liu Yu , Iwawaki Takao , Kumar Ashok 
Published: July 2024

AbstractSkeletal muscle regeneration involves a signaling network that regulates the proliferation, differentiation, and fusion of muscle precursor cells to injured myofibers. IRE1α, one of the arms of the unfolded protein response, regulates cellular proteostasis in response to ER stress. Here, we demonstrate that inducible deletion of IRE1α in satellite cells of mice impairs skeletal muscle regeneration through inhibiting myoblast fusion. Knockdown of IRE1α or its downstream target, X-box protein 1 (XBP1), also inhibits myoblast fusion during myogenesis. Transcriptome analysis revealed that knockdown of IRE1α or XBP1 dysregulates the gene expression of molecules involved in myoblast fusion. The IRE1α-XBP1 axis mediates the gene expression of multiple profusion molecules, including myomaker (Mymk). Spliced XBP1 (sXBP1) transcription factor binds to the promoter of Mymk gene during myogenesis. Overexpression of myomaker in IRE1α-knockdown cultures rescues fusion defects. Inducible deletion of IRE1α in satellite cells also inhibits myoblast fusion and myofiber hypertrophy in response to functional overload. Collectively, our study demonstrates that IRE1α promotes myoblast fusion through sXBP1-mediated up-regulation of the gene expression of multiple profusion molecules, including myomaker.
Anti‐interference lithium‐ion battery intelligent perception for thermal fault detection and localization
Authors: Tian Luyu , Dong Chaoyu , Wang Rui , Mu Yunfei , Jia Hongjie 
Published: July 2024

AbstractLithium‐ion batteries are widely employed in electric vehicles, power grid energy storage, and other fields. Thermal fault diagnostics for battery packs is crucial to preventing thermal runaway from impairing the safe operation and extended cycle service life of batteries. Therefore, a lithium‐ion battery thermal fault diagnosis model based on deep learning algorithms is presented, which includes three parts: autoencoder denoising network, coarse mask generator, and mask precise adjustment. Autoencoder denoising network can reduce data noise during thermal imaging acquisition, improve the anti‐interference ability of diagnostic models, and ensure the accuracy of thermal runaway diagnosis. A two‐stage diagnostic structure is then formulated by the coarse mask generator and mask precise adjustment, which enable quick identification, categorisation, and localisation of thermal fault battery cells. According to the test results, the segmentation boundary is more distinct and is capable of matching the original image's level. The recognition accuracy of the thermal diagnosis model for faulty batteries is close to 100%. After denoising by the autoencoder, the prediction results improved by 22% compared to non‐local mean denoising and by about 32% compared to noisy images.
The politics of suspension suspended: the curious case of a cryopreserved cell product
Authors: Liburkina Ruzana 
Published: July 2024

AbstractFollowing recent discussions around suspended life, this paper focuses on an endeavor that sought to arrest biological material in time and space and render it available on demand. It depicts the attempt to establish a collection of cryopreserved donated cells. The study offers rare insights into how this initiative was at odds with familiar politics significant in its field, those of innovation and preparedness, and therefore was suspended itself. In identifying parallels with accounts of unsuccessful biobanks, the paper makes a case for the analytical value of considering ill-fated projects of suspension along with those that prosper and attract public attention. The case of a novel cryo-collection, in particular, demonstrates how the idea and practice of suspension only gathers political momentum when it serves other well-established rationales. As such, it prompts two important conclusions. First, the power to arrest life as it comes with cryotechnologies is much more likely to unravel in entrenched constellations than to carry transformative or disruptive potential. Second, however, the paper also exemplifies that projects of suspension are not necessarily doomed to serve hegemonic ways of governing life. It advocates for preventing such mismatches from falling into oblivion.
Calotropis procera (Apocynaceae) shrub intrusion on wildlife foraging rangelands in the Ruaha National Park
Authors: Bukombe John , Kavana Pius , Marealle Wilfred , Sanare John , Wanzara Norbert , Sagari Wolfgang , Kiwango Halima , Efraim Joely , Mein’gataki Godwell Ole , Lobora Alex 
Published: July 2024

The relationships between the encroachment of Calotropis procera (Apocynaceae) and understorey herbaceous cover and various environmental variables of recipient grasslands were studied in the north-eastern Ruaha National Park in southern Tanzania. Three hypotheses were investigated. (1) C. procera exerts a negative influence on the cover of understorey herbaceous plants. (2) C. procera exerts a negative influence on environmental variables (humidity, light intensity, soil pH, air temperature, and soil temperature). (3) The native shrub canopy exerts a negative influence on understorey herbaceous plant cover and the environmental variables. We identified two sampling areas, one encroached by C. procera, the other with only native tree/shrub species. In each area, 21 5 m × 5 m subplots were established, and within each, two 1 m × 1 m sample plots were established, one 20 cm from the stem of a C. procera or native trees/shrub, the other at 5 m distance, and herbaceous plant cover and environmental variables were measured. Variables were measured on three occasions (December 2022, March, and July 2023) on the 42 subplots in each sampling area. Results demonstrated a negative influence of C. procera on understorey herbaceous cover, with a significantly lower percentage (16 ± 1.7) of herbaceous cover for plots at 20 cm than 5 m (72.4 ± 1.4) from C. procera stems. Moreover, soil pH was significantly lower at 20 cm than at 5 m distance from the stems in the encroached area, whereas in the non-encroached area, there was no recorded difference in the environmental variables. These results emphasised the necessity for a prompt intervention to contain the spread of C. procera in suitable grazing areas. A detailed study to find out the most practical and cost-effective control approaches appears warranted.