bluuebunny/crossref_metadata_2025_split huggingface dataset:
Model Validation and Sensitivity Analysis of Coupled Non‐Equilibrium Heat and Mass Transfer in Porous Media With Application to Evaporation From Bare Soils
Authors: Talebi Ashkan , Sleep Brent E. , O'Carroll Denis M. 
Published: October 2023

AbstractMathematical models in engineering play an important role in understanding and predicting the behavior of a system. A mechanistic coupled liquid water, water vapor and heat transfer model incorporating kinetic phase change accounting for real‐time interfacial area between water and gas phases was developed to predict coupled subsurface processes and evaporation (drying) rates from bare soils. To enhance the model capability to predict evaporation rates, the air resistance associated with the viscous sublayer was implemented in energy and mass exchange across the soil‐air interface (the land‐atmosphere boundary condition [BC]). The atmospheric stability condition was also considered in the calculation of sensible heat and vapor fluxes at the ground surface. This comprehensive model was validated against measured field data from bare soil test plots from a green roof study, during temperate summer conditions in Canada, demonstrating that the model captured the main coupled processes in the subsurface of bare soil during drying periods. A sensitivity analysis was performed to determine the importance of various components of the comprehensive model. Removal of viscous sublayer resistance in the vapor transfer BC resulted in poorer predictions of evaporation (drying) rates. Incorporating the atmospheric stability function accounting for real‐time atmospheric conditions did not improve the predictive capability for the simulated drying events compared to the case when only a neutral atmospheric condition was implemented. Neglecting heat transfer associated with hydrodynamic dispersion of water vapor in the subsurface had limited impact on subsurface temperature predictions.
Brain proteomic atlas of alcohol use disorder in adult males
Authors: Teng Pang-ning , Barakat Waleed , Tran Sophie M. , Tran Zoe M. , Bateman Nicholas W. , Conrads Kelly A. , Wilson Katlin N. , Oliver Julie , Gist Glenn , Hood Brian L. , Zhou Ming , Maxwell G. Larry , Leggio Lorenzo , Conrads Thomas P. , Lee Mary R. 
Published: October 2023

AbstractAlcohol use disorder (AUD) affects transcriptomic, epigenetic and proteomic expression in several organs, including the brain. There has not been a comprehensive analysis of altered protein abundance focusing on the multiple brain regions that undergo neuroadaptations occurring in AUD. We performed a quantitative proteomic analysis using a liquid chromatography-tandem mass spectrometry (LC-MS/MS) analysis of human postmortem tissue from brain regions that play key roles in the development and maintenance of AUD, the amygdala (AMG), hippocampus (HIPP), hypothalamus (HYP), nucleus accumbens (NAc), prefrontal cortex (PFC) and ventral tegmental area (VTA). Brain tissues were from adult males with AUD (n = 11) and matched controls (n = 16). Across the two groups, there were >6000 proteins quantified with differential protein abundance in AUD compared to controls in each of the six brain regions. The region with the greatest number of differentially expressed proteins was the AMG, followed by the HYP. Pathways associated with differentially expressed proteins between groups (fold change > 1.5 and LIMMA p < 0.01) were analyzed by Ingenuity Pathway Analysis (IPA). In the AMG, adrenergic, opioid, oxytocin, GABA receptor and cytokine pathways were among the most enriched. In the HYP, dopaminergic signaling pathways were the most enriched. Proteins with differential abundance in AUD highlight potential therapeutic targets such as oxytocin, CSNK1D (PF-670462), GABAB receptor and opioid receptors and may lead to the identification of other potential targets. These results improve our understanding of the molecular alterations of AUD across brain regions that are associated with the development and maintenance of AUD. Proteomic data from this study is publicly available at www.lmdomics.org/AUDBrainProteomeAtlas/.
Adenosine A2A receptors control generalization of contextual fear in rats
Authors: Simões Ana P. , Portes Marina A. M. , Lopes Cátia R. , Vanz Felipe , Lourenço Vanessa S. , Pliássova Anna , Gaspar Ingride L. , Silva Henrique B. , Tomé Ângelo R. , Canas Paula M. , Prediger Rui D. , Cunha Rodrigo A. 
Published: October 2023

AbstractFear learning is essential to survival, but traumatic events may lead to abnormal fear consolidation and overgeneralization, triggering fear responses in safe environments, as occurs in post-traumatic stress disorder (PTSD). Adenosine A2A receptors (A2AR) control emotional memory and fear conditioning, but it is not known if they affect the consolidation and generalization of fear, which was now investigated. We now report that A2AR blockade through systemic administration of the A2AR antagonist SCH58261 immediately after contextual fear conditioning (within the consolidation window), accelerated fear generalization. Conversely, A2AR activation with CGS21680 decreased fear generalization. Ex vivo electrophysiological recordings of field excitatory post-synaptic potentials (fEPSPs) in CA3-CA1 synapses and of population spikes in the lateral amygdala (LA), showed that the effect of SCH58261 is associated with a reversion of fear conditioning-induced decrease of long-term potentiation (LTP) in the dorsal hippocampus (DH) and with increased amplitude of LA LTP in conditioned animals. These data suggest that A2AR are engaged during contextual fear consolidation, controlling long-term potentiation mechanisms in both DH and LA during fear consolidation, impacting on fear generalization; this supports targeting A2AR during fear consolidation to control aberrant fear processing in PTSD and other fear-related disorders.
Practical advice for successful clinical treatment with resin-bonded bridges
Authors: King Stephanie , Sood Banoo , Ashley Martin P. 
Published: October 2023

AbstractResin-bonded bridges are one of the main options for replacing missing teeth for hypodontia patients. This technique offers several advantages for these patients, who are often young, have unrestored abutment teeth, and have had tooth positions optimised by orthodontic treatment. However, the replacement of missing teeth can be challenging due to tooth positions and anomalies of abutment tooth shape and size.These patients are often young adults at the time of restoration, making the minimally invasive nature and predictable long-term success of resin-bonded bridges advantageous over other treatment methods.This paper in the hypodontia themed issue discusses the importance of case selection and gives practical advice for the design and provision of resin-bonded bridges.
Fertility-preserving myeloablative conditioning using single-dose CD117 antibody-drug conjugate in a rhesus gene therapy model
Authors: Uchida Naoya , Stasula Ulana , Demirci Selami , Germino-Watnick Paula , Hinds Malikiya , Le Anh , Chu Rebecca , Berg Alexander , Liu Xiong , Su Ling , Wu Xiaolin , Krouse Allen E. , Linde N. Seth , Bonifacino Aylin , Hong So Gun , Dunbar Cynthia E. , Lanieri Leanne , Bhat Anjali , Palchaudhuri Rahul , Bennet Bindu , Hoban Megan , Bertelsen Kirk , Olson Lisa M. , Donahue Robert E. , Tisdale John F. 
Published: October 2023

AbstractHematopoietic stem cell (HSC) gene therapy has curative potential; however, its use is limited by the morbidity and mortality associated with current chemotherapy-based conditioning. Targeted conditioning using antibody-drug conjugates (ADC) holds promise for reduced toxicity in HSC gene therapy. Here we test the ability of an antibody-drug conjugate targeting CD117 (CD117-ADC) to enable engraftment in a non-human primate lentiviral gene therapy model of hemoglobinopathies. Following single-dose CD117-ADC, a >99% depletion of bone marrow CD34 + CD90 + CD45RA- cells without lymphocyte reduction is observed, which results are not inferior to multi-day myeloablative busulfan conditioning. CD117-ADC, similarly to busulfan, allows efficient engraftment, gene marking, and vector-derived fetal hemoglobin induction. Importantly, ADC treatment is associated with minimal toxicity, and CD117-ADC-conditioned animals maintain fertility. In contrast, busulfan treatment commonly causes severe toxicities and infertility in humans. Thus, the myeloablative capacity of single-dose CD117-ADC is sufficient for efficient engraftment of gene-modified HSCs while preserving fertility and reducing adverse effects related to toxicity in non-human primates. This targeted conditioning approach thus provides the proof-of-principle to improve risk-benefit ratio in a variety of HSC-based gene therapy products in humans.
Cryo-electron microscopy of IgM-VAR2CSA complex reveals IgM inhibits binding of Plasmodium falciparum to Chondroitin Sulfate A
Authors: Akhouri Reetesh Raj , Goel Suchi , Skoglund Ulf 
Published: October 2023

AbstractPlacental malaria is caused by Plasmodium falciparum-infected erythrocytes (IEs) adhering to chondroitin sulfate proteoglycans in placenta via VAR2CSA-type PfEMP1. Human pentameric immunoglobulin M (IgM) binds to several types of PfEMP1, including VAR2CSA via its Fc domain. Here, a 3.6 Å cryo-electron microscopy map of the IgM-VAR2CSA complex reveals that two molecules of VAR2CSA bind to the Cµ4 of IgM through their DBL3X and DBL5ε domains. The clockwise and anti-clockwise rotation of the two VAR2CSA molecules on opposite faces of IgM juxtaposes C-termini of both VAR2CSA near the J chain, where IgM creates a wall between both VAR2CSA molecules and hinders its interaction with its receptor. To support this, we show when VAR2CSA is bound to IgM, its staining on IEs as well as binding of IEs to chondroitin sulfate A in vitro is severely compromised.
Genomic adaptation of giant viruses in polar oceans
Authors: Meng Lingjie , Delmont Tom O. , Gaïa Morgan , Pelletier Eric , Fernàndez-Guerra Antonio , Chaffron Samuel , Neches Russell Y. , Wu Junyi , Kaneko Hiroto , Endo Hisashi , Ogata Hiroyuki 
Published: October 2023

AbstractDespite being perennially frigid, polar oceans form an ecosystem hosting high and unique biodiversity. Various organisms show different adaptive strategies in this habitat, but how viruses adapt to this environment is largely unknown. Viruses of phylaNucleocytoviricotaandMirusviricotaare groups of eukaryote-infecting large and giant DNA viruses with genomes encoding a variety of functions. Here, by leveraging the Global Ocean Eukaryotic Viral database, we investigate the biogeography and functional repertoire of these viruses at a global scale. We first confirm the existence of an ecological barrier that clearly separates polar and nonpolar viral communities, and then demonstrate that temperature drives dramatic changes in the virus–host network at the polar–nonpolar boundary. Ancestral niche reconstruction suggests that adaptation of these viruses to polar conditions has occurred repeatedly over the course of evolution, with polar-adapted viruses in the modern ocean being scattered across their phylogeny. Numerous viral genes are specifically associated with polar adaptation, although most of their homologues are not identified as polar-adaptive genes in eukaryotes. These results suggest that giant viruses adapt to cold environments by changing their functional repertoire, and this viral evolutionary strategy is distinct from the polar adaptation strategy of their hosts.
KRAS G12V neoantigen specific T cell receptor for adoptive T cell therapy against tumors
Authors: Lu Dan , Chen Yuan , Jiang Min , Wang Jie , Li Yiting , Ma Keke , Sun Wenqiao , Zheng Xing , Qi Jianxun , Jin Wenjing , Chen Yu , Chai Yan , Zhang Catherine W. H. , Liang Hao , Tan Shuguang , Gao George F. 
Published: October 2023

AbstractKRAS mutations are broadly recognized as promising targets for tumor therapy. T cell receptors (TCRs) can specifically recognize KRAS mutant neoantigens presented by human lymphocyte antigen (HLA) and mediate T cell responses to eliminate tumor cells. In the present study, we identify two TCRs specific for the 9-mer KRAS-G12V mutant neoantigen in the context of HLA-A*11:01. The TCR-T cells are constructed and display cytokine secretion and cytotoxicity upon co-culturing with varied tumor cells expressing the KRAS-G12V mutation. Moreover, 1-2C TCR-T cells show anti-tumor activity in preclinical models in female mice. The 9-mer KRAS-G12V mutant peptide exhibits a distinct conformation from the 9-mer wildtype peptide and its 10-mer counterparts. Specific recognition of the G12V mutant by TCR depends both on distinct conformation from wildtype peptide and on direct interaction with residues from TCRs. Our study reveals the mechanisms of presentation and TCR recognition of KRAS-G12V mutant peptide and describes TCRs with therapeutic potency for tumor immunotherapy.
An early warning signal for grassland degradation on the Qinghai-Tibetan Plateau
Authors: Zhu Qiuan , Chen Huai , Peng Changhui , Liu Jinxun , Piao Shilong , He Jin-Sheng , Wang Shiping , Zhao Xinquan , Zhang Jiang , Fang Xiuqin , Jin Jiaxin , Yang Qi-En , Ren Liliang , Wang Yanfen 
Published: October 2023

AbstractIntense grazing may lead to grassland degradation on the Qinghai-Tibetan Plateau, but it is difficult to predict where this will occur and to quantify it. Based on a process-based ecosystem model, we define a productivity-based stocking rate threshold that induces extreme grassland degradation to assess whether and where the current grazing activity in the region is sustainable. We find that the current stocking rate is below the threshold in ~80% of grassland areas, but in 55% of these grasslands the stocking rate exceeds half the threshold. According to our model projections, positive effects of climate change including elevated CO2 can partly offset negative effects of grazing across nearly 70% of grasslands on the Plateau, but only in areas below the stocking rate threshold. Our analysis suggests that stocking rate that does not exceed 60% (within 50% to 70%) of the threshold may balance human demands with grassland protection in the face of climate change.
Proteogenetic drug response profiling elucidates targetable vulnerabilities of myelofibrosis
Authors: Wildschut Mattheus H. E. , Mena Julien , Dördelmann Cyril , van Oostrum Marc , Hale Benjamin D. , Settelmeier Jens , Festl Yasmin , Lysenko Veronika , Schürch Patrick M. , Ring Alexander , Severin Yannik , Bader Michael S. , Pedrioli Patrick G. A. , Goetze Sandra , van Drogen Audrey , Balabanov Stefan , Skoda Radek C. , Lopes Massimo , Wollscheid Bernd , Theocharides Alexandre P. A. , Snijder Berend 
Published: October 2023

AbstractMyelofibrosis is a hematopoietic stem cell disorder belonging to the myeloproliferative neoplasms. Myelofibrosis patients frequently carry driver mutations in either JAK2 or Calreticulin (CALR) and have limited therapeutic options. Here, we integrate ex vivo drug response and proteotype analyses across myelofibrosis patient cohorts to discover targetable vulnerabilities and associated therapeutic strategies. Drug sensitivities of mutated and progenitor cells were measured in patient blood using high-content imaging and single-cell deep learning-based analyses. Integration with matched molecular profiling revealed three targetable vulnerabilities. First, CALR mutations drive BET and HDAC inhibitor sensitivity, particularly in the absence of high Ras pathway protein levels. Second, an MCM complex-high proliferative signature corresponds to advanced disease and sensitivity to drugs targeting pro-survival signaling and DNA replication. Third, homozygous CALR mutations result in high endoplasmic reticulum (ER) stress, responding to ER stressors and unfolded protein response inhibition. Overall, our integrated analyses provide a molecularly motivated roadmap for individualized myelofibrosis patient treatment.
Ampere-hour-scale soft-package potassium-ion hybrid capacitors enabling 6-minute fast-charging
Authors: Li Huanxin , Gong Yi , Zhou Haihui , Li Jing , Yang Kai , Mao Boyang , Zhang Jincan , Shi Yan , Deng Jinhai , Mao Mingxuan , Huang Zhongyuan , Jiao Shuqiang , Kuang Yafei , Zhao Yunlong , Luo Shenglian 
Published: October 2023

AbstractExtreme fast charging of Ampere-hour (Ah)-scale electrochemical energy storage devices targeting charging times of less than 10 minutes are desired to increase widespread adoption. However, this metric is difficult to achieve in conventional Li-ion batteries due to their inherent reaction mechanism and safety hazards at high current densities. In this work, we report 1 Ah soft-package potassium-ion hybrid supercapacitors (PIHCs), which combine the merits of high-energy density of battery-type negative electrodes and high-power density of capacitor-type positive electrodes. The PIHC consists of a defect-rich, high specific surface area N-doped carbon nanotube-based positive electrode, MnO quantum dots inlaid spacing-expanded carbon nanotube-based negative electrode, carbonate-based non-aqueous electrolyte, and a binder- and current collector-free cell design. Through the optimization of the cell configuration, electrodes, and electrolyte, the full cells (1 Ah) exhibit a cell voltage up to 4.8 V, high full-cell level specific energy of 140 Wh kg−1 (based on the whole mass of device) with a full charge of 6 minutes. An 88% capacity retention after 200 cycles at 10 C (10 A) and a voltage retention of 99% at 25 ± 1 °C are also demonstrated.
Cascaded metasurfaces for high-purity vortex generation
Authors: Mei Feng , Qu Geyang , Sha Xinbo , Han Jing , Yu Moxin , Li Hao , Chen Qinmiao , Ji Ziheng , Ni Jincheng , Qiu Cheng-Wei , Song Qinghai , Kivshar Yuri , Xiao Shumin 
Published: October 2023

AbstractWe introduce a new paradigm for generating high-purity vortex beams with metasurfaces. By applying optical neural networks to a system of cascaded phase-only metasurfaces, we demonstrate the efficient generation of high-quality Laguerre-Gaussian (LG) vortex modes. Our approach is based on two metasurfaces where one metasurface redistributes the intensity profile of light in accord with Rayleigh-Sommerfeld diffraction rules, and then the second metasurface matches the required phases for the vortex beams. Consequently, we generate high-purity LGp,l optical modes with record-high Laguerre polynomial orders p = 10 and l = 200, and with the purity in p, l and relative conversion efficiency as 96.71%, 85.47%, and 70.48%, respectively. Our engineered cascaded metasurfaces suppress greatly the backward reflection with a ratio exceeding −17 dB. Such higher-order optical vortices with multiple orthogonal states can revolutionize next-generation optical information processing.
Floquet non-Abelian topological insulator and multifold bulk-edge correspondence
Authors: Li Tianyu , Hu Haiping 
Published: October 2023

AbstractTopological phases characterized by non-Abelian charges are beyond the scope of the paradigmatic tenfold way and have gained increasing attention recently. Here we investigate topological insulators with multiple tangled gaps in Floquet settings and identify uncharted Floquet non-Abelian topological insulators without any static or Abelian analog. We demonstrate that the bulk-edge correspondence is multifold and follows the multiplication rule of the quaternion group Q8. The same quaternion charge corresponds to several distinct edge-state configurations that are fully determined by phase-band singularities of the time evolution. In the anomalous non-Abelian phase, edge states appear in all bandgaps despite trivial quaternion charge. Furthermore, we uncover an exotic swap effect—the emergence of interface modes with swapped driving, which is a signature of the non-Abelian dynamics and absent in Floquet Abelian systems. Our work, for the first time, presents Floquet topological insulators characterized by non-Abelian charges and opens up exciting possibilities for exploring the rich and uncharted territory of non-equilibrium topological phases.
Integrated urban water management by coupling iron salt production and application with biogas upgrading
Authors: Hu Zhetai , Li Lanqing , Cen Xiaotong , Zheng Min , Hu Shihu , Wang Xiuheng , Song Yarong , Xu Kangning , Yuan Zhiguo 
Published: October 2023

AbstractIntegrated urban water management is a well-accepted concept for managing urban water. It requires efficient and integrated technological solutions that enable system-wide gains via a whole-of-system approach. Here, we create a solid link between the manufacturing of an iron salt, its application in an urban water system, and high-quality bioenergy recovery from wastewater. An iron-oxidising electrochemical cell is used to remove CO2 (also H2S and NH3) from biogas, thus achieving biogas upgrading, and simultaneously producing FeCO3. The subsequent dose of the electrochemically produced FeCO3 to wastewater and sludge removes sulfide and phosphate, and enhances sludge settleability and dewaterability, with comparable or superior performance compared to the imported and hazardous iron salts it substitutes (FeCl2, and FeCl3). The process enables water utilities to establish a self-reliant and more secure supply chain to meet its demand for iron salts, at lower economic and environmental costs, and simultaneously achieve recovery of high-quality bioenergy.
Palmitoylation-driven PHF2 ubiquitination remodels lipid metabolism through the SREBP1c axis in hepatocellular carcinoma
Authors: Jeong Do-Won , Park Jong-Wan , Kim Kyeong Seog , Kim Jiyoung , Huh June , Seo Jieun , Kim Ye Lee , Cho Joo-Youn , Lee Kwang-Woong , Fukuda Junji , Chun Yang-Sook 
Published: October 2023

AbstractPalmitic acid (PA) is the most common fatty acid in humans and mediates palmitoylation through its conversion into palmitoyl coenzyme A. Although palmitoylation affects many proteins, its pathophysiological functions are only partially understood. Here we demonstrate that PA acts as a molecular checkpoint of lipid reprogramming in HepG2 and Hep3B cells. The zinc finger DHHC-type palmitoyltransferase 23 (ZDHHC23) mediates the palmitoylation of plant homeodomain finger protein 2 (PHF2), subsequently enhancing ubiquitin-dependent degradation of PHF2. This study also reveals that PHF2 functions as a tumor suppressor by acting as an E3 ubiquitin ligase of sterol regulatory element-binding protein 1c (SREBP1c), a master transcription factor of lipogenesis. PHF2 directly destabilizes SREBP1c and reduces SREBP1c-dependent lipogenesis. Notably, SREBP1c increases free fatty acids in hepatocellular carcinoma (HCC) cells, and the consequent PA induction triggers the PHF2/SREBP1c axis. Since PA seems central to activating this axis, we suggest that levels of dietary PA should be carefully monitored in patients with HCC.
SUN1/2 controls macrophage polarization via modulating nuclear size and stiffness
Authors: Jiao Shi , Li Chuanchuan , Guo Fenghua , Zhang Jinjin , Zhang Hui , Cao Zhifa , Wang Wenjia , Bu Wenbo , Lin Mobin , Lü Junhong , Zhou Zhaocai 
Published: October 2023

AbstractAlteration of the size and stiffness of the nucleus triggered by environmental cues are thought to be important for eukaryotic cell fate and function. However, it remains unclear how context-dependent nuclear remodeling occurs and reprograms gene expression. Here we identify the nuclear envelope proteins SUN1/2 as mechano-regulators of the nucleus during M1 polarization of the macrophage. Specifically, we show that LPS treatment decreases the protein levels of SUN1/2 in a CK2-βTrCP-dependent manner to shrink and soften the nucleus, therefore altering the chromatin accessibility for M1-associated gene expression. Notably, the transmembrane helix of SUN1/2 is solely required and sufficient for the nuclear mechano-remodeling. Consistently, SUN1/2 depletion in macrophages facilitates their phagocytosis, tissue infiltration, and proinflammatory cytokine production, thereby boosting the antitumor immunity in mice. Thus, our study demonstrates that, in response to inflammatory cues, SUN1/2 proteins act as mechano-regulators to remodel the nucleus and chromatin for M1 polarization of the macrophage.