bluuebunny/crossref_metadata_2025_split huggingface dataset:
The E3 ubiquitin ligase MARCH2 protects against myocardial ischemia-reperfusion injury through inhibiting pyroptosis via negative regulation of PGAM5/MAVS/NLRP3 axis
Authors: Liu Shuolin , Bi Yaguang , Han Tianting , Li Yiran E. , Wang Qihang , Wu Ne Natalie , Xu Chenguo , Ge Junbo , Hu Ronggui , Zhang Yingmei 
Published: February 2024

AbstractInflammasome activation and pyroptotic cell death are known to contribute to the pathogenesis of cardiovascular diseases, such as myocardial ischemia-reperfusion (I/R) injury, although the underlying regulatory mechanisms remain poorly understood. Here we report that expression levels of the E3 ubiquitin ligase membrane-associated RING finger protein 2 (MARCH2) were elevated in ischemic human hearts or mouse hearts upon I/R injury. Genetic ablation of MARCH2 aggravated myocardial infarction and cardiac dysfunction upon myocardial I/R injury. Single-cell RNA-seq analysis suggested that loss of MARCH2 prompted activation of NLRP3 inflammasome in cardiomyocytes. Mechanistically, phosphoglycerate mutase 5 (PGAM5) was found to act as a novel regulator of MAVS-NLRP3 signaling by forming liquid-liquid phase separation condensates with MAVS and fostering the recruitment of NLRP3. MARCH2 directly interacts with PGAM5 to promote its K48-linked polyubiquitination and proteasomal degradation, resulting in reduced PGAM5–MAVS co-condensation, and consequently inhibition of NLRP3 inflammasome activation and cardiomyocyte pyroptosis. AAV-based re-introduction of MARCH2 significantly ameliorated I/R-induced mouse heart dysfunction. Altogether, our findings reveal a novel mechanism where MARCH2-mediated ubiquitination negatively regulates the PGAM5/MAVS/NLRP3 axis to protect against cardiomyocyte pyroptosis and myocardial I/R injury.
People quasi-randomly assigned to farm rice are more collectivistic than people assigned to farm wheat
Authors: Talhelm Thomas , Dong Xiawei 
Published: February 2024

AbstractThe rice theory of culture argues that the high labor demands and interdependent irrigation networks of paddy rice farming makes cultures more collectivistic than wheat-farming cultures. Despite prior evidence, proving causality is difficult because people are not randomly assigned to farm rice. In this study, we take advantage of a unique time when the Chinese government quasi-randomly assigned people to farm rice or wheat in two state farms that are otherwise nearly identical. The rice farmers show less individualism, more loyalty/nepotism toward a friend over a stranger, and more relational thought style. These results rule out confounds in tests of the rice theory, such as temperature, latitude, and historical events. The differences suggest rice-wheat cultural differences can form in a single generation.
Chemoenzymatic indican for light-driven denim dyeing
Authors: Bidart Gonzalo Nahuel , Teze David , Jansen Charlotte Uldahl , Pasutto Eleonora , Putkaradze Natalia , Sesay Anna-Mamusu , Fredslund Folmer , Lo Leggio Leila , Ögmundarson Olafur , Sukumara Sumesh , Qvortrup Katrine , Welner Ditte Hededam 
Published: February 2024

AbstractBlue denim, a billion-dollar industry, is currently dyed with indigo in an unsustainable process requiring harsh reducing and alkaline chemicals. Forming indigo directly in the yarn through indican (indoxyl-β-glucoside) is a promising alternative route with mild conditions. Indican eliminates the requirement for reducing agent while still ending as indigo, the only known molecule yielding the unique hue of blue denim. However, a bulk source of indican is missing. Here, we employ enzyme and process engineering guided by techno-economic analyses to develop an economically viable drop-in indican synthesis technology. Rational engineering of PtUGT1, a glycosyltransferase from the indigo plant, alleviated the severe substrate inactivation observed with the wildtype enzyme at the titers needed for bulk production. We further describe a mild, light-driven dyeing process. Finally, we conduct techno-economic, social sustainability, and comparative life-cycle assessments. These indicate that the presented technologies have the potential to significantly reduce environmental impacts from blue denim dyeing with only a modest cost increase.
Comparative transcriptomics coupled to developmental grading via transgenic zebrafish reporter strains identifies conserved features in neutrophil maturation
Authors: Kirchberger Stefanie , Shoeb Mohamed R. , Lazic Daria , Wenninger-Weinzierl Andrea , Fischer Kristin , Shaw Lisa E. , Nogueira Filomena , Rifatbegovic Fikret , Bozsaky Eva , Ladenstein Ruth , Bodenmiller Bernd , Lion Thomas , Traver David , Farlik Matthias , Schöfer Christian , Taschner-Mandl Sabine , Halbritter Florian , Distel Martin 
Published: February 2024

AbstractNeutrophils are evolutionarily conserved innate immune cells playing pivotal roles in host defense. Zebrafish models have contributed substantially to our understanding of neutrophil functions but similarities to human neutrophil maturation have not been systematically characterized, which limits their applicability to studying human disease. Here we show, by generating and analysing transgenic zebrafish strains representing distinct neutrophil differentiation stages, a high-resolution transcriptional profile of neutrophil maturation. We link gene expression at each stage to characteristic transcription factors, including C/ebp-β, which is important for late neutrophil maturation. Cross-species comparison of zebrafish, mouse, and human samples confirms high molecular similarity of immature stages and discriminates zebrafish-specific from pan-species gene signatures. Applying the pan-species neutrophil maturation signature to RNA-sequencing data from human neuroblastoma patients reveals association between metastatic tumor cell infiltration in the bone marrow and an overall increase in mature neutrophils. Our detailed neutrophil maturation atlas thus provides a valuable resource for studying neutrophil function at different stages across species in health and disease.
Finite-momentum Cooper pairing in proximitized altermagnets
Authors: Zhang Song-Bo , Hu Lun-Hui , Neupert Titus 
Published: February 2024

AbstractFinite-momentum Cooper pairing is an unconventional form of superconductivity that is widely believed to require finite magnetization. Altermagnetism is an emerging magnetic phase with highly anisotropic spin-splitting of specific symmetries, but zero net magnetization. Here, we study Cooper pairing in metallic altermagnets connected to conventional s-wave superconductors. Remarkably, we find that the Cooper pairs induced in the altermagnets acquire a finite center-of-mass momentum, despite the zero net magnetization in the system. This anomalous Cooper-pair momentum strongly depends on the propagation direction and exhibits unusual symmetric patterns. Furthermore, it yields several unique features: (i) highly orientation-dependent oscillations in the order parameter, (ii) controllable 0-π transitions in the Josephson supercurrent, (iii) large-oblique-angle Cooper-pair transfer trajectories in junctions parallel with the direction where spin splitting vanishes, and (iv) distinct Fraunhofer patterns in junctions oriented along different directions. Finally, we discuss the implementation of our predictions in candidate materials such as RuO2 and KRu4O8.
Deaggregation of mutant Plasmodium yoelii de-ubiquitinase UBP1 alters MDR1 localization to confer multidrug resistance
Authors: Xu Ruixue , Lin Lirong , Jiao Zhiwei , Liang Rui , Guo Yazhen , Zhang Yixin , Shang Xiaoxu , Wang Yuezhou , Wang Xu , Yao Luming , Liu Shengfa , Deng Xianming , Yuan Jing , Su Xin-zhuan , Li Jian 
Published: February 2024

AbstractMutations in a Plasmodium de-ubiquitinase UBP1 have been linked to antimalarial drug resistance. However, the UBP1-mediated drug-resistant mechanism remains unknown. Through drug selection, genetic mapping, allelic exchange, and functional characterization, here we show that simultaneous mutations of two amino acids (I1560N and P2874T) in the Plasmodium yoelii UBP1 can mediate high-level resistance to mefloquine, lumefantrine, and piperaquine. Mechanistically, the double mutations are shown to impair UBP1 cytoplasmic aggregation and de-ubiquitinating activity, leading to increased ubiquitination levels and altered protein localization, from the parasite digestive vacuole to the plasma membrane, of the P. yoelii multidrug resistance transporter 1 (MDR1). The MDR1 on the plasma membrane enhances the efflux of substrates/drugs out of the parasite cytoplasm to confer multidrug resistance, which can be reversed by inhibition of MDR1 transport. This study reveals a previously unknown drug-resistant mechanism mediated by UBP1 through altered MDR1 localization and substrate transport direction in a mouse model, providing a new malaria treatment strategy.
Q586B2 is a crucial virulence factor during the early stages of Trypanosoma brucei infection that is conserved amongst trypanosomatids
Authors: Stijlemans Benoit , De Baetselier Patrick , Van Molle Inge , Lecordier Laurence , Hendrickx Erika , Romão Ema , Vincke Cécile , Baetens Wendy , Schoonooghe Steve , Hassanzadeh-Ghassabeh Gholamreza , Korf Hannelie , Wallays Marie , Pinto Torres Joar E. , Perez-Morga David , Brys Lea , Campetella Oscar , Leguizamón María S. , Claes Mathieu , Hendrickx Sarah , Mabille Dorien , Caljon Guy , Remaut Han , Roelants Kim , Magez Stefan , Van Ginderachter Jo A. , De Trez Carl 
Published: February 2024

AbstractHuman African trypanosomiasis or sleeping sickness, caused by the protozoan parasite Trypanosoma brucei, is characterized by the manipulation of the host’s immune response to ensure parasite invasion and persistence. Uncovering key molecules that support parasite establishment is a prerequisite to interfere with this process. We identified Q586B2 as a T. brucei protein that induces IL-10 in myeloid cells, which promotes parasite infection invasiveness. Q586B2 is expressed during all T. brucei life stages and is conserved in all Trypanosomatidae. Deleting the Q586B2-encoding Tb927.6.4140 gene in T. brucei results in a decreased peak parasitemia and prolonged survival, without affecting parasite fitness in vitro, yet promoting short stumpy differentiation in vivo. Accordingly, neutralization of Q586B2 with newly generated nanobodies could hamper myeloid-derived IL-10 production and reduce parasitemia. In addition, immunization with Q586B2 delays mortality upon a challenge with various trypanosomes, including Trypanosoma cruzi. Collectively, we uncovered a conserved protein playing an important regulatory role in Trypanosomatid infection establishment.
Mesoscopic fluctuations in entanglement dynamics
Authors: Lim Lih-King , Lou Cunzhong , Tian Chushun 
Published: February 2024

AbstractUnderstanding fluctuation phenomena plays a dominant role in the development of many-body physics. The time evolution of entanglement is essential to a broad range of subjects in many-body physics, ranging from exotic quantum matter to quantum thermalization. Stemming from various dynamical processes of information, fluctuations in entanglement evolution differ conceptually from out-of-equilibrium fluctuations of traditional physical quantities. Their studies remain elusive. Here we uncover an emergent random structure in the evolution of the many-body wavefunction in two classes of integrable—either interacting or noninteracting—lattice models. It gives rise to out-of-equilibrium entanglement fluctuations which fall into the paradigm of mesoscopic fluctuations of wave interference origin. Specifically, the entanglement entropy variance obeys a universal scaling law in each class, and the full distribution displays a sub-Gaussian upper and a sub-Gamma lower tail. These statistics are independent of both the system’s microscopic details and the choice of entanglement probes, and broaden the class of mesoscopic universalities. They have practical implications for controlling entanglement in mesoscopic devices.
Rapid genomic sequencing for genetic disease diagnosis and therapy in intensive care units: a review
Authors: Kingsmore Stephen F. , Nofsinger Russell , Ellsworth Kasia 
Published: February 2024

AbstractSingle locus (Mendelian) diseases are a leading cause of childhood hospitalization, intensive care unit (ICU) admission, mortality, and healthcare cost. Rapid genome sequencing (RGS), ultra-rapid genome sequencing (URGS), and rapid exome sequencing (RES) are diagnostic tests for genetic diseases for ICU patients. In 44 studies of children in ICUs with diseases of unknown etiology, 37% received a genetic diagnosis, 26% had consequent changes in management, and net healthcare costs were reduced by $14,265 per child tested by URGS, RGS, or RES. URGS outperformed RGS and RES with faster time to diagnosis, and higher rate of diagnosis and clinical utility. Diagnostic and clinical outcomes will improve as methods evolve, costs decrease, and testing is implemented within precision medicine delivery systems attuned to ICU needs. URGS, RGS, and RES are currently performed in <5% of the ~200,000 children likely to benefit annually due to lack of payor coverage, inadequate reimbursement, hospital policies, hospitalist unfamiliarity, under-recognition of possible genetic diseases, and current formatting as tests rather than as a rapid precision medicine delivery system. The gap between actual and optimal outcomes in children in ICUs is currently increasing since expanded use of URGS, RGS, and RES lags growth in those likely to benefit through new therapies. There is sufficient evidence to conclude that URGS, RGS, or RES should be considered in all children with diseases of uncertain etiology at ICU admission. Minimally, diagnostic URGS, RGS, or RES should be ordered early during admissions of critically ill infants and children with suspected genetic diseases.
Biological study of skin wound treated with Alginate/Carboxymethyl cellulose/chorion membrane, diopside nanoparticles, and Botox A
Authors: Mahheidari Naimeh , Kamalabadi-Farahani Mohammad , Nourani Mohammad Reza , Atashi Amir , Alizadeh Morteza , Aldaghi Niloofar , Salehi Majid 
Published: February 2024

AbstractA hydrogel-based wound dressing with desirable properties is necessary for achieving functional skin integrity post-injury. This study focuses on preparing a hydrogel using Alginate/Carboxymethyl cellulose (Alg/CMC) as a base material. To evaluate its regenerative effects on full-thickness wounds, diopside nanoparticles and Botulinum toxin A (BTX-A) were incorporated into the hydrogel along with chorion membrane. The diopside nanoparticles (DNPs) act as a proangiogenic factor, promoting proliferation and regulating inflammation, while the chorion membrane facilitates these processes. Additionally, BTX-A prevents scar formation and aids in wound closure. The nanoparticles and hydrogel were characterized using various techniques, and their cytocompatibility was assessed. In vivo studies and quantitative polymerase chain reaction analysis showed that wound area reduction was significant after two weeks of treatment with the Alg/CMC/ChNPs/DNPs/BTX-A hydrogel. Overall, this scaffold demonstrated potential for promoting tissue regeneration and new epithelization formation, making it a promising candidate for enhancing skin restoration in wound treatments.
Drinkable in situ-forming tough hydrogels for gastrointestinal therapeutics
Authors: Liu Gary W. , Pickett Matthew J. , Kuosmanen Johannes L. P. , Ishida Keiko , Madani Wiam A. M. , White Georgia N. , Jenkins Joshua , Park Sanghyun , Feig Vivian R. , Jimenez Miguel , Karavasili Christina , Lal Nikhil B. , Murphy Matt , Lopes Aaron , Morimoto Joshua , Fitzgerald Nina , Cheah Jaime H. , Soule Christian K. , Fabian Niora , Hayward Alison , Langer Robert , Traverso Giovanni 
Published: February 2024

AbstractPills are a cornerstone of medicine but can be challenging to swallow. While liquid formulations are easier to ingest, they lack the capacity to localize therapeutics with excipients nor act as controlled release devices. Here we describe drug formulations based on liquid in situ-forming tough (LIFT) hydrogels that bridge the advantages of solid and liquid dosage forms. LIFT hydrogels form directly in the stomach through sequential ingestion of a crosslinker solution of calcium and dithiol crosslinkers, followed by a drug-containing polymer solution of alginate and four-arm poly(ethylene glycol)-maleimide. We show that LIFT hydrogels robustly form in the stomachs of live rats and pigs, and are mechanically tough, biocompatible and safely cleared after 24 h. LIFT hydrogels deliver a total drug dose comparable to unencapsulated drug in a controlled manner, and protect encapsulated therapeutic enzymes and bacteria from gastric acid-mediated deactivation. Overall, LIFT hydrogels may expand access to advanced therapeutics for patients with difficulty swallowing.
Pan-chloroplast genomes for accession-specific marker development in Hibiscus syriacus
Authors: Go Sangjin , Koo Hyunjin , Jung Minah , Hong Seongmin , Yi Gibum , Kim Yong-Min 
Published: February 2024

AbstractHibiscus syriacus L. is a renowned ornamental plant. We constructed 95 chloroplast genomes of H. syriacus L. cultivars using a short-read sequencing platform (Illumina) and a long-read sequencing platform (Oxford Nanopore Technology). The following genome assembly, we delineate quadripartite structures encompassing large single-copy, small single-copy, and inverted repeat (IRa and IRb) regions, from 160,231 bp to 161,041 bp. Our comprehensive analyses confirmed the presence of 79 protein-coding genes, 30 tRNA genes, and 4 rRNA genes in the pan-chloroplast genome, consistent with prior research on the H. syriacus chloroplast genome. Subsequent pangenome analysis unveiled widespread genome sequence conservation alongside unique cultivar-specific variant patterns consisting of 193 single-nucleotide polymorphisms and 61 insertions or deletions. The region containing intra-species variant patterns, as identified in this study, has the potential to develop accession-specific molecular markers, enhancing precision in cultivar classification. These findings are anticipated to drive advancements in breeding strategies, augment biodiversity, and unlock the agricultural potential inherent in H. syriacus.
High-quality genome assembly of a C. crossoptilon and related functional and genetics data resources
Authors: Wu Siwen , Wang Kun , Dou Tengfei , Yuan Sisi , Wu Dong-Dong , Ge Changrong , Jia Junjing , Su Zhengchang 
Published: February 2024

AbstractThere are four species in the Crossoptilon genus inhibiting at from very low to very high altitudes across China, and they are in varying levels of danger of extinction. To better understand the genetic basis of adaptation to high altitudes and genetic changes due to bottleneck, we assembled the genome (~1.02 Gb) of a white eared pheasant (WT) (Crossoptilon crossoptilon) inhibiting at high altitudes (3,000~7,000 m) in northwest of Yunnan province, China, using a combination of Illumina short reads, PacBio long reads and Hi-C reads, with a contig N50 of 19.63 Mb and only six gaps. To further provide resources for gene annotation as well as functional and population genetics analyses, we sequenced transcriptomes of 20 major tissues of the WT individual and re-sequenced another 10 WT individuals and a blue eared pheasant (Crossoptilon auritum) individual inhabiting at intermediate altitudes (1,500~3,000 m). Our assembled WT genome, transcriptome data, and DNA sequencing data can be valuable resources for studying the biology, evolution and developing conservation strategies of these endangered species.
Synergistic activity of Limosilactobacillus reuteri KUB-AC5 and water-based plants against Salmonella challenge in a human in vitro gut model
Authors: Mok Kevin , Honwichit Orranich , Funnuam Thanyakan , Charoensiddhi Suvimol , Nitisinprasert Sunee , Nielsen Dennis Sandris , Nakphaichit Massalin 
Published: February 2024

AbstractA synbiotic is a combination of live microorganisms and specific substrates that are selectively utilized by host microorganisms, resulting in health benefits for the host. Previous studies have demonstrated the protective effects of L. reuteri KUB-AC5 against Salmonella infection in chicken and mouse models. The probiotic activity of L. reuteri KUB-AC5 in these hosts was influenced by nutritional supplements. Water-based plants contain significant amounts of carbohydrates, particularly dietary fiber and proteins, making them potential prebiotic substrates. In this study, four water-based plants (Ulva rigida, Caulerpa lentillifera, Wolffia globosa, and Gracillaria fisheri) were screened for their ability to support the growth of L. reuteri KUB-AC5. Under monoculture testing, U. rigida exhibited the highest capacity to support the growth of L. reuteri KUB-AC5 and the production of organic acids, including acetic acid, lactic acid, and propionic acid (p ≤ 0.05). In co-culture experiments, the synbiotic combination of U. rigida and L. reuteri KUB-AC5 demonstrated the potential to eliminate Salmonella Typhimurium DMST 48437 when inoculated at 104 CFU/mL within 9 h. The synbiotic activities of U. rigida and L. reuteri KUB-AC5 were further investigated using an in vitro human gut model. Compared to the probiotic treatment, the synbiotic combination of L. reuteri KUB-AC5 and U. rigida showed significantly higher levels of L. reuteri KUB-AC5 (5.1 log copies/mL) and a reduction of S. Typhimurium by 0.8 log (CFU/ml) after 24 h (p ≤ 0.05). Synbiotic treatment also significantly promoted the production of short-chain fatty acids (SCFAs), including butyric acid, propionic acid, and acetic acid, compared to prebiotic and probiotic treatments alone (p ≤ 0.05). Furthermore, the synbiotic formulation modulated the in vitro simulated gut microbiome, enhancing putatively beneficial gut microbes, including lactobacilli, Faecalibacterium, and Blautia. Our findings demonstrated that L. reuteri KUB-AC5, in combination with U. rigida, exhibited synergistic activity, as indicated by increased viability, higher anti-pathogenicity toward Salmonella, and the ability to modulate the gut microbiome.
Association of adverse childhood experiences with anemia in older Chinese: Guangzhou Biobank Cohort Study
Authors: He Shao Yi , Zhang Wei Sen , Jiang Chao Qiang , Jin Ya Li , Lam Tai Hing , Cheng Kar Keung , Xu Lin 
Published: February 2024

AbstractTo examine the association of adverse childhood experiences (ACEs) with anemia among older people. 24,116 participants aged 50 years or above were recruited. Multivariable linear and logistic regression was used to assess the associations of self-reported ACEs number with hemoglobin concentrations (g/dL) and presence of anemia. Older individuals with two or more ACEs, versus no ACEs, showed lower hemoglobin concentrations (β =  − 0.08 g/dL, 95% confidence intervals (CI) − 0.12 to − 0.03) and higher odds of anemia (odds ratio = 1.26, 95% CI 1.01–1.59). A more pronounced association between ACEs and anemia in the lower education group was found, while the association became non-significant in those with higher education (P for ACEs-education interaction = 0.02). ACEs was associated with anemia in older people, and the association was stronger in those with lower education, highlighting the significance of early-life psychological stressors assessment and consideration of education background in geriatric care.