bluuebunny/crossref_metadata_2025_split huggingface dataset:
Targeted immunotherapy: harnessing the immune system to battle multiple myeloma
Authors: Xu Limei , Wen Caining , Xia Jiang , Zhang Hao , Liang Yujie , Xu Xiao 
Published: January 2024

AbstractMultiple myeloma (MM) remains an incurable hematological malignancy disease characterized by the progressive dysfunction of the patient’s immune system. In this context, immunotherapy for MM has emerged as a prominent area of research in recent years. Various targeted immunotherapy strategies, such as monoclonal antibodies, antibody-drug conjugates, bispecific antibodies, chimeric antigen receptor T cells/natural killer (NK) cells, and checkpoint inhibitors have been developed for MM. This review aims to discuss promising experimental and clinical evidence as well as the mechanisms of action underlying these immunotherapies. Specifically, we will explore the design of exosome-based bispecific monoclonal antibodies that offer cell-free immunotherapy options. The treatment landscape for myeloma continues to evolve with the development of numerous emerging immunotherapies. Given their significant advantages in modulating the MM immune environment through immune-targeted therapy, these approaches provide novel perspectives in selecting cutting-edge treatments for MM.
Despite structural identity, ace-1 heterogenous duplication resistance alleles are quite diverse in Anopheles mosquitoes
Authors: Claret Jean-Loup , Di-Liegro Marion , Namias Alice , Assogba Benoit , Makoundou Patrick , Koffi Alphonsine , Pennetier Cédric , Weill Mylène , Milesi Pascal , Labbé Pierrick 
Published: January 2024

AbstractAnopheles gambiae s.l. has been the target of intense insecticide treatment since the mid-20th century to try and control malaria. A substitution in the ace-1 locus has been rapidly selected for, allowing resistance to organophosphate and carbamate insecticides. Since then, two types of duplication of the ace-1 locus have been found in An. gambiae s.l. populations: homogeneous duplications that are composed of several resistance copies, or heterogeneous duplications that contain both resistance and susceptible copies. The substitution induces a trade-off between resistance in the presence of insecticides and disadvantages in their absence: the heterogeneous duplications allow the fixation of the intermediate heterozygote phenotype. So far, a single heterogeneous duplication has been described in An. gambiae s.l. populations (in contrast with the multiple duplicated alleles found in Culex pipiens mosquitoes). We used a new approach, combining long and short-read sequencing with Sanger sequencing to precisely identify and describe at least nine different heterogeneous duplications, in two populations of An. gambiae s.l. We show that these alleles share the same structure as the previously identified heterogeneous and homogeneous duplications, namely 203-kb tandem amplifications with conserved breakpoints. Our study sheds new light on the origin and maintenance of these alleles in An. gambiae s.l. populations, and their role in mosquito adaptation.
Rising rainfall intensity induces spatially divergent hydrological changes within a large river basin
Authors: Wu Yiping , Yin Xiaowei , Zhou Guoyi , Bruijnzeel L. Adrian , Dai Aiguo , Wang Fan , Gentine Pierre , Zhang Guangchuang , Song Yanni , Zhou Decheng 
Published: January 2024

AbstractDroughts or floods are usually attributed to precipitation deficits or surpluses, both of which may become more frequent and severe under continued global warming. Concurring large-scale droughts in the Southwest and flooding in the Southeast of China in recent decades have attracted considerable attention, but their causes and interrelations are not well understood. Here, we examine spatiotemporal changes in hydrometeorological variables and investigate the mechanism underlying contrasting soil dryness/wetness patterns over a 54-year period (1965–2018) across a representative mega-watershed in South China—the West River Basin. We demonstrate that increasing rainfall intensity leads to severe drying upstream with decreases in soil water storage, water yield, and baseflow, versus increases therein downstream. Our study highlights a simultaneous occurrence of increased drought and flooding risks due to contrasting interactions between rainfall intensification and topography across the river basin, implying increasingly vulnerable water and food security under continued climate change.
Trajectory inference across multiple conditions with condiments
Authors: Roux de Bézieux Hector , Van den Berge Koen , Street Kelly , Dudoit Sandrine 
Published: January 2024

AbstractIn single-cell RNA sequencing (scRNA-Seq), gene expression is assessed individually for each cell, allowing the investigation of developmental processes, such as embryogenesis and cellular differentiation and regeneration, at unprecedented resolution. In such dynamic biological systems, cellular states form a continuum, e.g., for the differentiation of stem cells into mature cell types. This process is often represented via a trajectory in a reduced-dimensional representation of the scRNA-Seq dataset. While many methods have been suggested for trajectory inference, it is often unclear how to handle multiple biological groups or conditions, e.g., inferring and comparing the differentiation trajectories of wild-type and knock-out stem cell populations. In this manuscript, we presentcondiments, a method for the inference and downstream interpretation of cell trajectories across multiple conditions. Our framework allows the interpretation of differences between conditions at the trajectory, cell population, and gene expression levels. We start by integrating datasets from multiple conditions into a single trajectory. By comparing the cell’s conditions along the trajectory’s path, we can detect large-scale changes, indicative of differential progression or fate selection. We also demonstrate how to detect subtler changes by finding genes that exhibit different behaviors between these conditions along a differentiation path.
Global distribution of surface soil organic carbon in urban greenspaces
Authors: Guo Hongbo , Du Enzai , Terrer César , Jackson Robert B. 
Published: January 2024

AbstractUrban greenspaces continue to grow with global urbanization. The global distribution and stock of soil organic carbon (SOC) in urban greenspaces remain largely undescribed and missing in global carbon (C) budgets. Here, we synthesize data of 420 observations from 257 cities in 52 countries to evaluate the global pattern of surface SOC density (0–20 cm depth) in urban greenspaces. Surface SOC density in urban greenspaces increases significantly at higher latitudes and decreases significantly with higher mean annual temperature, stronger temperature and precipitation seasonality, as well as lower urban greenness index. By mapping surface SOC density using a random forest model, we estimate an average SOC density of 55.2 (51.9–58.6) Mg C ha−1 and a SOC stock of 1.46 (1.37–1.54) Pg C in global urban greenspaces. Our findings present a comprehensive assessment of SOC in global urban greenspaces and provide a baseline for future urban soil C assessment under continuing urbanization.
Intensifying rice production to reduce imports and land conversion in Africa
Authors: Yuan Shen , Saito Kazuki , van Oort Pepijn A. J. , van Ittersum Martin K. , Peng Shaobing , Grassini Patricio 
Published: January 2024

AbstractAfrica produces around 60% of the rice the continent consumes, relying heavily on rice imports to fulfill the rest of the domestic demand. Over the past 10 years, the rice-agricultural area increased nearly 40%, while average yield remained stagnant. Here we used a process-based crop simulation modelling approach combined with local weather, soil, and management datasets to evaluate the potential to increase rice production on existing cropland area in Africa and assess cropland expansion and rice imports by year 2050 for different scenarios of yield intensification. We find that Africa can avoid further increases in rice imports, and even reduce them, through a combination of cropland expansion following the historical trend together with closure of the current exploitable yield gap by half or more. Without substantial increase in rice yields, meeting future rice demand will require larger rice imports and/or land conversion than now.
Three-dimensional covalent organic frameworks with nia nets for efficient separation of benzene/cyclohexane mixtures
Authors: Chang Jianhong , Chen Fengqian , Li Hui , Suo Jinquan , Zheng Haorui , Zhang Jie , Wang Zitao , Zhu Liangkui , Valtchev Valentin , Qiu Shilun , Fang Qianrong 
Published: January 2024

AbstractThe synthesis of three-dimensional covalent organic frameworks with highly connected building blocks presents a significant challenge. In this study, we report two 3D COFs with the nia topology, named JUC-641 and JUC-642, by introducing planar hexagonal and triangular prism nodes. Notably, our adsorption studies and breakthrough experiments reveal that both COFs exhibit exceptional separation capabilities, surpassing previously reported 3D COFs and most porous organic polymers, with a separation factor of up to 2.02 for benzene and cyclohexane. Additionally, dispersion-corrected density functional theory analysis suggests that the good performance of these 3D COFs can be attributed to the incorporation of highly aromatic building blocks and the presence of extensive pore structures. Consequently, this research not only expands the diversity of COFs but also highlights the potential of functional COF materials as promising candidates for environmentally-friendly separation applications.
Sexual dimorphism in melanocyte stem cell behavior reveals combinational therapeutic strategies for cutaneous repigmentation
Authors: An Luye , Kim Dahihm , Donahue Leanne R. , Mejooli Menansili Abraham , Eom Chi-Yong , Nishimura Nozomi , White Andrew C. 
Published: January 2024

AbstractVitiligo is an autoimmune skin disease caused by cutaneous melanocyte loss. Although phototherapy and T cell suppression therapy have been widely used to induce epidermal re-pigmentation, full pigmentation recovery is rarely achieved due to our poor understanding of the cellular and molecular mechanisms governing this process. Here, we identify unique melanocyte stem cell (McSC) epidermal migration rates between male and female mice, which is due to sexually dimorphic cutaneous inflammatory responses generated by ultra-violet B exposure. Using genetically engineered mouse models, and unbiased bulk and single-cell mRNA sequencing approaches, we determine that manipulating the inflammatory response through cyclooxygenase and its downstream prostaglandin product regulates McSC proliferation and epidermal migration in response to UVB exposure. Furthermore, we demonstrate that a combinational therapy that manipulates both macrophages and T cells (or innate and adaptive immunity) significantly promotes epidermal melanocyte re-population. With these findings, we propose a novel therapeutic strategy for repigmentation in patients with depigmentation conditions such as vitiligo.
Mitophagy curtails cytosolic mtDNA-dependent activation of cGAS/STING inflammation during aging
Authors: Jiménez-Loygorri Juan Ignacio , Villarejo-Zori Beatriz , Viedma-Poyatos Álvaro , Zapata-Muñoz Juan , Benítez-Fernández Rocío , Frutos-Lisón María Dolores , Tomás-Barberán Francisco A. , Espín Juan Carlos , Area-Gómez Estela , Gomez-Duran Aurora , Boya Patricia 
Published: January 2024

AbstractMacroautophagy decreases with age, and this change is considered a hallmark of the aging process. It remains unknown whether mitophagy, the essential selective autophagic degradation of mitochondria, also decreases with age. In our analysis of mitophagy in multiple organs in the mito-QC reporter mouse, mitophagy is either increased or unchanged in old versus young mice. Transcriptomic analysis shows marked upregulation of the type I interferon response in the retina of old mice, which correlates with increased levels of cytosolic mtDNA and activation of the cGAS/STING pathway. Crucially, these same alterations are replicated in primary human fibroblasts from elderly donors. In old mice, pharmacological induction of mitophagy with urolithin A attenuates cGAS/STING activation and ameliorates deterioration of neurological function. These findings point to mitophagy induction as a strategy to decrease age-associated inflammation and increase healthspan.
In-situ-sprayed therapeutic hydrogel for oxygen-actuated Janus regulation of postsurgical tumor recurrence/metastasis and wound healing
Authors: Chen Shuiling , Luo Yang , He Yang , Li Ming , Liu Yongjian , Zhou Xishen , Hou Jianwen , Zhou Shaobing 
Published: January 2024

AbstractSurgery is the mainstay of treatment modality for malignant melanoma. However, the deteriorative hypoxic microenvironment after surgery is recognized as a stemming cause for tumor recurrence/metastasis and delayed wound healing. Here we design and construct a sprayable therapeutic hydrogel (HIL@Z/P/H) encapsulating tumor-targeted nanodrug and photosynthetic cyanobacteria (PCC 7942) to prevent tumor recurrence/metastasis while promote wound healing. In a postsurgical B16F10 melanoma model in female mice, the nanodrug can disrupt cellular redox homeostasis via the photodynamic therapy-induced cascade reactions within tumor cells. Besides, the photosynthetically generated O2 by PCC 7942 can not only potentiate the oxidative stress-triggered cell death to prevent local recurrence of residual tumor cells, but also block the signaling pathway of hypoxia-inducible factor 1α to inhibit their distant metastasis. Furthermore, the long-lasting O2 supply and PCC 7942-secreted extracellular vesicles can jointly promote angiogenesis and accelerate the wound healing process. Taken together, the developed HIL@Z/P/H capable of preventing tumor recurrence/metastasis while promoting wound healing shows great application potential for postsurgical cancer therapy.
Hydrogen bond unlocking-driven pore structure control for shifting multi-component gas separation function
Authors: Yang Rong , Wang Yu , Cao Jian-Wei , Ye Zi-Ming , Pham Tony , Forrest Katherine A. , Krishna Rajamani , Chen Hongwei , Li Libo , Ling Bo-Kai , Zhang Tao , Gao Tong , Jiang Xue , Xu Xiang-Ou , Ye Qian-Hao , Chen Kai-Jie 
Published: January 2024

AbstractPurification of ethylene (C2H4) as the most extensive and output chemical, from complex multi-components is of great significance but highly challenging. Herein we demonstrate that precise pore structure tuning by controlling the network hydrogen bonds in two highly-related porous coordination networks can shift the efficient C2H4 separation function from C2H2/C2H4/C2H6 ternary mixture to CO2/C2H2/C2H4/C2H6 quaternary mixture system. Single-crystal X-ray diffraction revealed that the different amino groups on the triazolate ligands resulted in the change of the hydrogen bonding in the host network, which led to changes in the pore shape and pore chemistry. Gas adsorption isotherms, adsorption kinetics and gas-loaded crystal structure analysis indicated that the coordination network Zn-fa-atz (2) weakened the affinity for three C2 hydrocarbons synchronously including C2H4 but enhanced the CO2 adsorption due to the optimized CO2-host interaction and the faster CO2 diffusion, leading to effective C2H4 production from the CO2/C2H2/C2H4/C2H6 mixture in one step based on the experimental and simulated breakthrough data. Moreover, it can be shaped into spherical pellets with maintained porosity and separation performance.
Reconstitution of human PDAC using primary cells reveals oncogenic transcriptomic features at tumor onset
Authors: Xu Yi , Nipper Michael H. , Dominguez Angel A. , Ye Zhenqing , Akanuma Naoki , Lopez Kevin , Deng Janice J. , Arenas Destiny , Sanchez Ava , Sharkey Francis E. , Court Colin M. , Singhi Aatur D. , Wang Huamin , Fernandez-Zapico Martin E. , Sun Lu-Zhe , Zheng Siyuan , Chen Yidong , Liu Jun , Wang Pei 
Published: January 2024

AbstractAnimal studies have demonstrated the ability of pancreatic acinar cells to transform into pancreatic ductal adenocarcinoma (PDAC). However, the tumorigenic potential of human pancreatic acinar cells remains under debate. To address this gap in knowledge, we expand sorted human acinar cells as 3D organoids and genetically modify them through introduction of common PDAC mutations. The acinar organoids undergo dramatic transcriptional alterations but maintain a recognizable DNA methylation signature. The transcriptomes of acinar organoids are similar to those of disease-specific cell populations. Oncogenic KRAS alone do not transform acinar organoids. However, acinar organoids can form PDAC in vivo after acquiring the four most common driver mutations of this disease. Similarly, sorted ductal cells carrying these genetic mutations can also form PDAC, thus experimentally proving that PDACs can originate from both human acinar and ductal cells. RNA-seq analysis reveal the transcriptional shift from normal acinar cells towards PDACs with enhanced proliferation, metabolic rewiring, down-regulation of MHC molecules, and alterations in the coagulation and complement cascade. By comparing PDAC-like cells with normal pancreas and PDAC samples, we identify a group of genes with elevated expression during early transformation which represent potential early diagnostic biomarkers.
BacPE: a versatile prime-editing platform in bacteria by inhibiting DNA exonucleases
Authors: Zhang Hongyuan , Ma Jiacheng , Wu Zhaowei , Chen Xiaoyang , Qian Yangyang , Chen Weizhong , Wang Zhipeng , Zhang Ya , Zhu Huanhu , Huang Xingxu , Ji Quanjiang 
Published: January 2024

AbstractPrime editing allows precise installation of any single base substitution and small insertions and deletions without requiring homologous recombination or double-strand DNA breaks in eukaryotic cells. However, the applications in bacteria are hindered and the underlying mechanisms that impede efficient prime editing remain enigmatic. Here, we report the determination of vital cellular factors that affect prime editing in bacteria. Genetic screening of 129 Escherichia coli transposon mutants identified sbcB, a 3ʹ→5ʹ DNA exonuclease, as a key genetic determinant in impeding prime editing in E. coli, combinational deletions of which with two additional 3ʹ→5ʹ DNA exonucleases, xseA and exoX, drastically enhanced the prime editing efficiency by up to 100-fold. Efficient prime editing in wild-type E. coli can be achieved by simultaneously inhibiting the DNA exonucleases via CRISPRi. Our results pave the way for versatile applications of prime editing for bacterial genome engineering.
Consistent stoichiometric long-term relationships between nutrients and chlorophyll-a across shallow lakes
Authors: Graeber Daniel , McCarthy Mark J. , Shatwell Tom , Borchardt Dietrich , Jeppesen Erik , Søndergaard Martin , Lauridsen Torben L. , Davidson Thomas A. 
Published: January 2024

AbstractAquatic ecosystems are threatened by eutrophication from nutrient pollution. In lakes, eutrophication causes a plethora of deleterious effects, such as harmful algal blooms, fish kills and increased methane emissions. However, lake-specific responses to nutrient changes are highly variable, complicating eutrophication management. These lake-specific responses could result from short-term stochastic drivers overshadowing lake-independent, long-term relationships between phytoplankton and nutrients. Here, we show that strong stoichiometric long-term relationships exist between nutrients and chlorophyll a (Chla) for 5-year simple moving averages (SMA, median R² = 0.87) along a gradient of total nitrogen to total phosphorus (TN:TP) ratios. These stoichiometric relationships are consistent across 159 shallow lakes (defined as average depth < 6 m) from a cross-continental, open-access database. We calculate 5-year SMA residuals to assess short-term variability and find substantial short-term Chla variation which is weakly related to nutrient concentrations (median R² = 0.12). With shallow lakes representing 89% of the world’s lakes, the identified stoichiometric long-term relationships can globally improve quantitative nutrient management in both lakes and their catchments through a nutrient-ratio-based strategy.
Bioinspired light-driven chloride pump with helical porphyrin channels
Authors: Li Chao , Zhai Yi , Jiang Heming , Li Siqi , Liu Pengxiang , Gao Longcheng , Jiang Lei 
Published: January 2024

AbstractHalorhodopsin, a light-driven chloride pump, utilizes photonic energy to drive chloride ions across biological membranes, regulating the ion balance and conveying biological information. In the light-driven chloride pump process, the chloride-binding chromophore (protonated Schiff base) is crucial, able to form the active center by absorbing light and triggering the transport cycle. Inspired by halorhodopsin, we demonstrate an artificial light-driven chloride pump using a helical porphyrin channel array with excellent photoactivity and specific chloride selectivity. The helical porphyrin channels are formed by a porphyrin-core star block copolymer, and the defects along the channels can be effectively repaired by doping a small number of porphyrins. The well-repaired porphyrin channel exhibits the light-driven Cl− migration against a 3-fold concentration gradient, showing the ion pumping behavior. The bio-inspired artificial light-driven chloride pump provides a prospect for designing bioinspired responsive ion channel systems and high-performance optogenetics.
Phase transitions associated with magnetic-field induced topological orbital momenta in a non-collinear antiferromagnet
Authors: Deng Sihao , Gomonay Olena , Chen Jie , Fischer Gerda , He Lunhua , Wang Cong , Huang Qingzhen , Shen Feiran , Tan Zhijian , Zhou Rui , Hu Ze , Šmejkal Libor , Sinova Jairo , Wernsdorfer Wolfgang , Sürgers Christoph 
Published: January 2024

AbstractResistivity measurements are widely exploited to uncover electronic excitations and phase transitions in metallic solids. While single crystals are preferably studied to explore crystalline anisotropies, these usually cancel out in polycrystalline materials. Here we show that in polycrystalline Mn3Zn0.5Ge0.5N with non-collinear antiferromagnetic order, changes in the diagonal and, rather unexpected, off-diagonal components of the resistivity tensor occur at low temperatures indicating subtle transitions between magnetic phases of different symmetry. This is supported by neutron scattering and explained within a phenomenological model which suggests that the phase transitions in magnetic field are associated with field induced topological orbital momenta. The fact that we observe transitions between spin phases in a polycrystal, where effects of crystalline anisotropy are cancelled suggests that they are only controlled by exchange interactions. The observation of an off-diagonal resistivity extends the possibilities for realising antiferromagnetic spintronics with polycrystalline materials.