bluuebunny/crossref_metadata_2025_split huggingface dataset:
Spatially-resolved transcriptomics reveal macrophage heterogeneity and prognostic significance in diffuse large B-cell lymphoma
Authors: Liu Min , Bertolazzi Giorgio , Sridhar Shruti , Lee Rui Xue , Jaynes Patrick , Mulder Kevin , Syn Nicholas , Hoppe Michal Marek , Fan Shuangyi , Peng Yanfen , Thng Jocelyn , Chua Reiya , Jayalakshmi  , Batumalai Yogeshini , De Mel Sanjay , Poon Limei , Chan Esther Hian Li , Lee Joanne , Hue Susan Swee-Shan , Chang Sheng-Tsung , Chuang Shih-Sung , Chandy K. George , Ye Xiaofei , Pan-Hammarström Qiang , Ginhoux Florent , Chee Yen Lin , Ng Siok-Bian , Tripodo Claudio , Jeyasekharan Anand D. 
Published: March 2024

AbstractMacrophages are abundant immune cells in the microenvironment of diffuse large B-cell lymphoma (DLBCL). Macrophage estimation by immunohistochemistry shows varying prognostic significance across studies in DLBCL, and does not provide a comprehensive analysis of macrophage subtypes. Here, using digital spatial profiling with whole transcriptome analysis of CD68+ cells, we characterize macrophages in distinct spatial niches of reactive lymphoid tissues (RLTs) and DLBCL. We reveal transcriptomic differences between macrophages within RLTs (light zone /dark zone, germinal center/ interfollicular), and between disease states (RLTs/ DLBCL), which we then use to generate six spatially-derived macrophage signatures (MacroSigs). We proceed to interrogate these MacroSigs in macrophage and DLBCL single-cell RNA-sequencing datasets, and in gene-expression data from multiple DLBCL cohorts. We show that specific MacroSigs are associated with cell-of-origin subtypes and overall survival in DLBCL. This study provides a spatially-resolved whole-transcriptome atlas of macrophages in reactive and malignant lymphoid tissues, showing biological and clinical significance.
A persistent prefrontal reference frame across time and task rules
Authors: Muysers Hannah , Chen Hung-Ling , Hahn Johannes , Folschweiller Shani , Sigurdsson Torfi , Sauer Jonas-Frederic , Bartos Marlene 
Published: March 2024

AbstractBehavior can be remarkably consistent, even over extended time periods, yet whether this is reflected in stable or ‘drifting’ neuronal responses to task features remains controversial. Here, we find a persistently active ensemble of neurons in the medial prefrontal cortex (mPFC) of mice that reliably maintains trajectory-specific tuning over several weeks while performing an olfaction-guided spatial memory task. This task-specific reference frame is stabilized during learning, upon which repeatedly active neurons show little representational drift and maintain their trajectory-specific tuning across long pauses in task exposure and across repeated changes in cue-target location pairings. These data thus suggest a ‘core ensemble’ of prefrontal neurons forming a reference frame of task-relevant space for the performance of consistent behavior over extended periods of time.
A three-level regulatory mechanism of the aldo-keto reductase subfamily AKR12D
Authors: Xiao Zhihong , Zha Jinyin , Yang Xu , Huang Tingting , Huang Shuxin , Liu Qi , Wang Xiaozheng , Zhong Jie , Zheng Jianting , Liang Rubing , Deng Zixin , Zhang Jian , Lin Shuangjun , Dai Shaobo 
Published: March 2024

AbstractModulation of protein function through allosteric regulation is central in biology, but biomacromolecular systems involving multiple subunits and ligands may exhibit complex regulatory mechanisms at different levels, which remain poorly understood. Here, we discover an aldo-keto reductase termed AKRtyl and present its three-level regulatory mechanism. Specifically, by combining steady-state and transient kinetics, X-ray crystallography and molecular dynamics simulation, we demonstrate that AKRtyl exhibits a positive synergy mediated by an unusual Monod-Wyman-Changeux (MWC) paradigm of allosteric regulation at low concentrations of the cofactor NADPH, but an inhibitory effect at high concentrations is observed. While the substrate tylosin binds at a remote allosteric site with positive cooperativity. We further reveal that these regulatory mechanisms are conserved in AKR12D subfamily, and that substrate cooperativity is common in AKRs across three kingdoms of life. This work provides an intriguing example for understanding complex allosteric regulatory networks.
PMI-controlled mannose metabolism and glycosylation determines tissue tolerance and virus fitness
Authors: Liang Ronghui , Ye Zi-Wei , Qin Zhenzhi , Xie Yubin , Yang Xiaomeng , Sun Haoran , Du Qiaohui , Luo Peng , Tang Kaiming , Hu Bodan , Cao Jianli , Wong Xavier Hoi-Leong , Ling Guang-Sheng , Chu Hin , Shen Jiangang , Yin Feifei , Jin Dong-Yan , Chan Jasper Fuk-Woo , Yuen Kwok-Yung , Yuan Shuofeng 
Published: March 2024

AbstractHost survival depends on the elimination of virus and mitigation of tissue damage. Herein, we report the modulation of D-mannose flux rewires the virus-triggered immunometabolic response cascade and reduces tissue damage. Safe and inexpensive D-mannose can compete with glucose for the same transporter and hexokinase. Such competitions suppress glycolysis, reduce mitochondrial reactive-oxygen-species and succinate-mediated hypoxia-inducible factor-1α, and thus reduce virus-induced proinflammatory cytokine production. The combinatorial treatment by D-mannose and antiviral monotherapy exhibits in vivo synergy despite delayed antiviral treatment in mouse model of virus infections. Phosphomannose isomerase (PMI) knockout cells are viable, whereas addition of D-mannose to the PMI knockout cells blocks cell proliferation, indicating that PMI activity determines the beneficial effect of D-mannose. PMI inhibition suppress a panel of virus replication via affecting host and viral surface protein glycosylation. However, D-mannose does not suppress PMI activity or virus fitness. Taken together, PMI-centered therapeutic strategy clears virus infection while D-mannose treatment reprograms glycolysis for control of collateral damage.
Light-responsive and ultrapermeable two-dimensional metal-organic framework membrane for efficient ionic energy harvesting
Authors: Wang Jin , Song Zeyuan , He Miaolu , Qian Yongchao , Wang Di , Cui Zheng , Feng Yuan , Li Shangzhen , Huang Bo , Kong Xiangyu , Han Jinming , Wang Lei 
Published: March 2024

AbstractNanofluidic membranes offer exceptional promise for osmotic energy conversion, but the challenge of balancing ionic selectivity and permeability persists. Here, we present a bionic nanofluidic system based on two-dimensional (2D) copper tetra-(4-carboxyphenyl) porphyrin framework (Cu-TCPP). The inherent nanoporous structure and horizontal interlayer channels endow the Cu-TCPP membrane with ultrahigh ion permeability and allow for a power density of 16.64 W m−2, surpassing state of-the-art nanochannel membranes. Moreover, leveraging the photo-thermal property of Cu-TCPP, light-controlled ion active transport is realized even under natural sunlight. By combining solar energy with salinity gradient, the driving force for ion transport is reinforced, leading to further improvements in energy conversion performance. Notably, light could even eliminate the need for salinity gradient, achieving a power density of 0.82 W m−2 in a symmetric solution system. Our work introduces a new perspective on developing advanced membranes for solar/ionic energy conversion and extends the concept of salinity energy to a notion of ionic energy.
Machine learning predictor PSPire screens for phase-separating proteins lacking intrinsically disordered regions
Authors: Hou Shuang , Hu Jiaojiao , Yu Zhaowei , Li Dan , Liu Cong , Zhang Yong 
Published: March 2024

AbstractThe burgeoning comprehension of protein phase separation (PS) has ushered in a wealth of bioinformatics tools for the prediction of phase-separating proteins (PSPs). These tools often skew towards PSPs with a high content of intrinsically disordered regions (IDRs), thus frequently undervaluing potential PSPs without IDRs. Nonetheless, PS is not only steered by IDRs but also by the structured modular domains and interactions that aren’t necessarily reflected in amino acid sequences. In this work, we introduce PSPire, a machine learning predictor that incorporates both residue-level and structure-level features for the precise prediction of PSPs. Compared to current PSP predictors, PSPire shows a notable improvement in identifying PSPs without IDRs, which underscores the crucial role of non-IDR, structure-based characteristics in multivalent interactions throughout the PS process. Additionally, our biological validation experiments substantiate the predictive capacity of PSPire, with 9 out of 11 chosen candidate PSPs confirmed to form condensates within cells.
Proton-selective coating enables fast-kinetics high-mass-loading cathodes for sustainable zinc batteries
Authors: Guo Quanquan , Li Wei , Li Xiaodong , Zhang Jiaxu , Sabaghi Davood , Zhang Jianjun , Zhang Bowen , Li Dongqi , Du Jingwei , Chu Xingyuan , Chung Sein , Cho Kilwon , Nguyen Nguyen Ngan , Liao Zhongquan , Zhang Zhen , Zhang Xinxing , Schneider Grégory F. , Heine Thomas , Yu Minghao , Feng Xinliang 
Published: March 2024

AbstractThe pressing demand for sustainable energy storage solutions has spurred the burgeoning development of aqueous zinc batteries. However, kinetics-sluggish Zn2+ as the dominant charge carriers in cathodes leads to suboptimal charge-storage capacity and durability of aqueous zinc batteries. Here, we discover that an ultrathin two-dimensional polyimine membrane, featured by dual ion-transport nanochannels and rich proton-conduction groups, facilitates rapid and selective proton passing. Subsequently, a distinctive electrochemistry transition shifting from sluggish Zn2+-dominated to fast-kinetics H+-dominated Faradic reactions is achieved for high-mass-loading cathodes by using the polyimine membrane as an interfacial coating. Notably, the NaV3O8·1.5H2O cathode (10 mg cm−2) with this interfacial coating exhibits an ultrahigh areal capacity of 4.5 mAh cm−2 and a state-of-the-art energy density of 33.8 Wh m−2, along with apparently enhanced cycling stability. Additionally, we showcase the applicability of the interfacial proton-selective coating to different cathodes and aqueous electrolytes, validating its universality for developing reliable aqueous batteries.
Tick hemocytes have a pleiotropic role in microbial infection and arthropod fitness
Authors: Rolandelli Agustin , Laukaitis-Yousey Hanna J. , Bogale Haikel N. , Singh Nisha , Samaddar Sourabh , O’Neal Anya J. , Ferraz Camila R. , Butnaru Matthew , Mameli Enzo , Xia Baolong , Mendes M. Tays , Butler L. Rainer , Marnin Liron , Cabrera Paz Francy E. , Valencia Luisa M. , Rana Vipin S. , Skerry Ciaran , Pal Utpal , Mohr Stephanie E. , Perrimon Norbert , Serre David , Pedra Joao H. F. 
Published: March 2024

AbstractUncovering the complexity of systems in non-model organisms is critical for understanding arthropod immunology. Prior efforts have mostly focused on Dipteran insects, which only account for a subset of existing arthropod species in nature. Here we use and develop advanced techniques to describe immune cells (hemocytes) from the clinically relevant tick Ixodes scapularis at a single-cell resolution. We observe molecular alterations in hemocytes upon feeding and infection with either the Lyme disease spirochete Borrelia burgdorferi or the rickettsial agent Anaplasma phagocytophilum. We reveal hemocyte clusters exhibiting defined signatures related to immunity, metabolism, and proliferation. Depletion of phagocytic hemocytes affects hemocytin and astakine levels, two I. scapularis hemocyte markers, impacting blood-feeding, molting behavior, and bacterial acquisition. Mechanistically, astakine alters hemocyte proliferation, whereas hemocytin affects the c-Jun N-terminal kinase (JNK) signaling pathway in I. scapularis. Altogether, we discover a role for tick hemocytes in immunophysiology and provide a valuable resource for comparative biology in arthropods.
Novel protective effect of the FOXO3 longevity genotype on mechanisms of cellular aging in Okinawans
Authors: Torigoe Trevor H. , Willcox D. Craig , Shimabukuro Michio , Higa Moritake , Gerschenson Mariana , Andrukhiv Anastasia , Suzuki Makoto , Morris Brian J. , Chen Randi , Gojanovich Greg S. , Allsopp Richard C. , Willcox Bradley J. 
Published: March 2024

AbstractThe genetic association of FOXO3 genotypes with human longevity is well established, although the mechanism is not fully understood. We now report on the relationship of the FOXO3 longevity variant rs2802292 with telomere length, telomerase activity, FOXO3 expression, and inflammatory cytokine levels in men and women. In agreement with earlier work, the FOXO3 longevity variant conferred protection against telomere shortening of peripheral blood mononuclear cells from adults aged 55 years and older. This was accompanied by higher levels of telomerase activity in mononuclear cells for carriers of the longevity-associated FOXO3 G-allele of SNP rs2802292 (P = 0.015). FOXO3 mRNA expression increased slightly with age in both young (P = 0.02) and old (P = 0.08) G-allele carriers. Older female G-allele carriers displayed a modest decline in levels of pro-inflammatory cytokine IL-6 with age (P = 0.07). In contrast, older male G-allele carriers displayed an age-dependent increase in levels of anti-inflammatory cytokine IL-10 with age (P = 0.04). Thus, FOXO3 may act through several different pro-longevity mechanisms, which may differ by age and sex.
Nonlinear dynamics of directly coupled skyrmions in ferrimagnetic spin torque nano-oscillators
Authors: Shen Laichuan , Qiu Lei , Shen Ka 
Published: March 2024

AbstractNonlinear spin torque nano-oscillators have received substantial attentions due to their important applications in microwave communication and neuromorphic computing. Here we investigate the dynamical behaviors of directly coupled skyrmion oscillators in a synthetic ferrimagnet. We demonstrate through the micromagnetic simulation and Thiele’s equation that the skyrmion oscillators can present either synchronization or frequency comb, depending on the strength of interactions between the skyrmions. The underlying physics of the transition between the two scenarios are unveiled based on a quantitative analysis of the effective potentials, which also successfully interprets the dependence of the transition on parameters. By further demonstrating the tunability of the nonlinear dynamics by the driving current of the oscillators, our work reveals the great potentials of ferrimagnetic-skyrmion-based interacting oscillators for nonlinear applications.
BCG-booster vaccination with HSP90-ESAT-6-HspX-RipA multivalent subunit vaccine confers durable protection against hypervirulent Mtb in mice
Authors: Kwon Kee Woong , Choi Han-Gyu , Kim Kwang Sung , Park Shin Ae , Kim Hwa-Jung , Shin Sung Jae 
Published: March 2024

AbstractThe quest for effective and enhanced multiantigenic tuberculosis (TB) subunit vaccine necessitates the induction of a protective pathogen-specific immune response while circumventing detrimental inflammation within the lung milieu. In line with this goal, we engineered a modified iteration of the quadrivalent vaccine, namely HSP90-ESAT-6-HspX-RipA (HEHR), which was coupled with the TLR4 adjuvant, CIA09A. The ensuing formulation was subjected to comprehensive assessment to gauge its protective efficacy against the hypervirulent Mycobacterium tuberculosis (Mtb) Haarlem clinical strain M2, following a BCG-prime boost regimen. Regardless of vaccination route, both intramuscular and subcutaneous administration with the HEHR vaccine exhibited remarkable protective efficacy in significantly reducing the Mtb bacterial burden and pulmonary inflammation. This underscores its notably superior protective potential compared to the BCG vaccine alone or a former prototype, the HSP90-E6 subunit vaccine. In addition, this superior protective efficacy was confirmed when testing a tag-free version of the HEHR vaccine. Furthermore, the protective immune determinant, represented by durable antigen-specific CD4+IFN-γ+IL-17A+ T-cells expressing a CXCR3+KLRG1- cell surface phenotype in the lung, was robustly induced in HEHR-boosted mice at 12 weeks post-challenge. Collectively, our data suggest that the BCG-prime HEHR boost vaccine regimen conferred improved and long-term protection against hypervirulent Mtb strain with robust antigen-specific Th1/Th17 responses.
Reconfiguring hydrogel assemblies using a photocontrolled metallopolymer adhesive for multiple customized functions
Authors: Liu Jiahui , Huang Yun-Shuai , Liu Yazhi , Zhang Dachuan , Koynov Kaloian , Butt Hans-Jürgen , Wu Si 
Published: March 2024

AbstractStimuli-responsive hydrogels with programmable shape changes are promising materials for soft robots, four-dimensional printing, biomedical devices and artificial intelligence systems. However, these applications require the fabrication of hydrogels with complex, heterogeneous and reconfigurable structures and customizable functions. Here we report the fabrication of hydrogel assemblies with these features by reversibly gluing hydrogel units using a photocontrolled metallopolymer adhesive. The metallopolymer adhesive firmly attached individual hydrogel units via metal–ligand coordination and polymer chain entanglement. Hydrogel assemblies containing temperature- and pH-responsive hydrogel units showed controllable shape changes and motions in response to these external stimuli. To reconfigure their structures, the hydrogel assemblies were disassembled by irradiating the metallopolymer adhesive with light; the disassembled hydrogel units were then reassembled using the metallopolymer adhesive with heating. The shape change and structure reconfiguration abilities allow us to reprogramme the functions of hydrogel assemblies. The development of reconfigurable hydrogel assemblies using reversible adhesives provides a strategy for designing intelligent materials and soft robots with user-defined functions.
An experimental test of whether financial incentives constitute undue inducement in decision-making
Authors: Ambuehl Sandro 
Published: March 2024

AbstractAround the world, laws limit the incentives that can be paid for transactions such as human research participation, egg donation or gestational surrogacy. A key reason is concerns about ‘undue inducement’—the influential but empirically untested hypothesis that incentives can cause harm by distorting individual decision-making. Here I present two experiments (n = 671 and n = 406), including one based on a highly visceral transaction (eating insects). Incentives caused biased information search—participants offered a higher incentive to comply more often sought encouragement to do so. However, I demonstrate theoretically that such behaviour does not prove that incentives have harmful effects; it is consistent with Bayesian rationality. Empirically, although a substantial minority of participants made bad decisions, incentives did not magnify them in a way that would suggest allowing a transaction but capping incentives. Under the conditions of this experiment, there was no evidence that higher incentives could undermine welfare for transactions that are permissible at low incentives.
Extrinsic apoptosis participates to tail regression during the metamorphosis of the chordate Ciona
Authors: Krasovec Gabriel , Renaud Cécile , Quéinnec Éric , Sasakura Yasunori , Chambon Jean-Philippe 
Published: March 2024

AbstractApoptosis is a regulated cell death ubiquitous in animals defined by morphological features depending on caspases. Two regulation pathways are described, currently named the intrinsic and the extrinsic apoptosis. While intrinsic apoptosis is well studied and considered ancestral among metazoans, extrinsic apoptosis is poorly studied outside mammals. Here, we address extrinsic apoptosis in the urochordates Ciona, belonging to the sister group of vertebrates. During metamorphosis, Ciona larvae undergo a tail regression depending on tissue contraction, migration and apoptosis. Apoptosis begin at the tail tip and propagates towards the trunk as a polarized wave. We identified Ci-caspase 8/10 by phylogenetic analysis as homolog to vertebrate caspases 8 and 10 that are the specific initiator of extrinsic apoptosis. We detected Ci-caspase 8/10 expression in Ciona larvae, especially at the tail tip. We showed that chemical inhibition of Ci-caspase 8/10 leads to a delay of tail regression, and Ci-caspase 8/10 loss of function induced an incomplete tail regression. The specificity between apoptotic pathways and initiator caspase suggests that extrinsic apoptosis regulates cell death during the tail regression. Our study presents rare in vivo work on extrinsic apoptosis outside mammals, and contribute to the discussion on its evolutionary history in animals.
Association of dietary live microbe intake with various cognitive domains in US adults aged 60 years or older
Authors: Lv Jia-jie , Li Xin-yu , Wang Jing-bing , Yang Xi-tao , Yin Min-yi , Yang Cheng-hao 
Published: March 2024

AbstractThe purpose of this study was to explore whether dietary live microbe intake is associated with various cognitive domains using data from the National Health and Nutrition Examination Survey (NHANES) from 2011 to 2014. And the specific relationship between low, medium and high dietary live microbe intake groups and cognitive ability of the elderly. Dietary live microbe intake was calculated from 24-h diet recall interviews. Cognitive function was assessed using the number symbol substitution test (DSST, which measures processing speed), the animal fluency test (AFT, which measures executive function), the Alzheimer's Registry sub-test (CERAD, which measures memory), and the Composite Z-score, which adds the Z-values of individual tests. Multiple linear regression models and restricted cubic bar graphs were used to investigate the relationship between live microbe intake and cognitive performance. A total of 2,450 participants aged 60 or older were included. Live microbe intake was positively correlated with cognitive ability on the whole. Specifically, when the intake of low, medium and high live microbe was > 2640 g, > 39 g and > 0 g respectively, the CERAD, DSST, AFT and compositive-Z score of the subjects increased with the increase of microbial intake (P < 0.05). In American adults age 60 or older, higher intakes of live microbes were associated with better cognitive performance, especially after a certain amount was reached.
Pyrolysis temperature and time of rice husk biochar potentially control ammonia emissions and Chinese cabbage yield from urea-fertilized soils
Authors: Kang Yun-Gu , Chun Jin-Hyuk , Yun Yeo-Uk , Lee Jun-Yeong , Sung Jwakyung , Oh Taek-Keun 
Published: March 2024

AbstractCurrent agricultural practices are increasingly favoring the biochar application to sequester carbon, enhance crop growth, and mitigate various environmental pollutants resulting from nitrogen (N) loss. However, since biochar’s characteristics can vary depending on pyrolysis conditions, it is essential to determine the optimal standard, as they can have different effects on soil health. In this study, we categorized rice husk biochars basis on their pH levels and investigated the role of each rice husk biochar in reducing ammonia (NH3) emissions and promoting the growth of Chinese cabbage in urea-fertilized fields. The findings of this study revealed that the variation in pyrolysis conditions of rice husk biochars and N rates affected both the NH3 emissions and crop growth. The neutral (pH 7.10) biochar exhibited effective NH3 volatilization reduction, attributed to its high surface area (6.49 m2 g−1), outperforming the acidic (pH 6.10) and basic (pH 11.01) biochars, particularly under high N rates (640 kg N ha−1). Chinese cabbage yield was highest, reaching 4.00 kg plant−1, with the basic biochar application with high N rates. Therefore, the neutral rice husk biochar effectively mitigate the NH3 emissions from urea-treated fields, while the agronomic performance of Chinese cabbage enhanced in all biochar amendments.