bluuebunny/crossref_metadata_2025_split huggingface dataset:
A Case Study Featuring the Time Evolution of a Fire‐Induced Plume Jet Over the Rum Creek Fire: Mechanisms, Processes, and Dynamical Interplay
Authors: Strobach E. J. , Carroll B. J. , Baidar S. , Brown S. S. , Ahmadov R. , Brewer W. A. , Pichugina Y. , Makowiecki A. , Peischl J. , Zuraski K. 
Published: May 2024

AbstractResults are presented from the Rum Creek fire during the California Fire Dynamics Experiment (CalFiDE). An instrumented payload aboard the NOAA Twin Otter (TO) aircraft, which included a scanning micro‐pulsed Doppler lidar (DL) and in situ chemistry packages, was used to address the evolution of a buoyant plume jet (BPJ) and transport dynamics over the southwest corner of the fire between 09/01/2022 and 09/02/2022. An approach previously developed to isolate updrafts was modified to account for the Gaussian core structure when addressing the evolution of the updraft, plume‐top entrainment, lateral entrainment, and the role of fire‐atmosphere interactions on the characteristics of the BPJ during four overpasses. A persistent cross‐valley flow leading up to the BPJ was observed for all four overpasses, with flow enhancement during the second overpass that coincided with changes in the BPJ structure and turbulence characteristics surrounding the BPJ. Length scales and entrainment rates were estimated at the lateral edges and the top of the plume. In the case of the latter, an analytical form of the BPJ profile above the vertical velocity maximum of the updraft was derived using a simplified form of the vertical momentum equation following a partial budget analysis that accounted for plume‐top entrainment and the boundary layer (BL) inversion. Velocity core strength and characteristics were analyzed away from the updraft with similar relationships between depth‐to‐widths of velocity cores found in a forthcoming study focused on wildfire plumes.
Evaluation of Land Surface Phenology in Northern Hemisphere Permafrost Regions
Authors: Zhao Yaohua , Peng Xiaoqing , Frauenfeld Oliver W. , Cui Xia , Bi Jian , Ma Xuanlong , Wei Gang , Mu Cuicui , Sun Hao , Sui Jia 
Published: May 2024

AbstractVegetation phenology interacts strongly with climate through the exchange of carbon, water, momentum, and energy between terrestrial ecosystem and atmosphere. These vegetation dynamics in Northern Hemisphere permafrost regions have substantial uncertainties in previous studies, partly due to differences in datasets. Thus, reliable land surface phenology (LSP) retrievals are crucial for understanding the effects of climate change on ecosystems and biosphere‐atmosphere‐hydrosphere interactions. We assessed various LSP datasets at different spatial resolutions for 2001–2014, generated by different methods based on different satellite observations. We also assessed the accuracy of LSP by comparing with CO2 flux phenology. For start of growing season (SOS), the comprehensive evaluation indicated MODIS phenology showed better consistency and higher accuracy with flux‐derived phenology observations (R = 0.54, RMSE = 36.2 days, bias<5 days). For end of growing season (EOS), we cannot conclusively determine which LSP performs best. In the Northern Hemisphere permafrost regions, SOS occurred at 100–150 days (April–May), and EOS occurred at 260–320 days (September–November). During 2001–2014, SOS occurred earlier by 0.33 ± 0.30 days/yr. Significant trends were observed for 6.4%–27.6% of pixels, averaging −1.30 ± 1.16 days/yr. EOS occurred earlier by 0.25 ± 0.43 days/yr, with significant trends averaging −0.52 ± 0.94 days/yr. Among LSPs, variability in EOS trends was significant, with even the direction of trends differing. This study may provide insights into LSP data selection and further understanding of vegetation dynamics and its mechanisms in permafrost regions.
Evaluating Apparent Temperature in the Contiguous United States From Four Reanalysis Products Using Artificial Neural Networks
Authors: Ibebuchi Chibuike Chiedozie , Lee Cameron C. , Silva Alindomar , Sheridan Scott C. 
Published: May 2024

AbstractReanalysis data sets are the products of data assimilation systems and while they exhibit consistency with the observed climate, they tend to be biased, especially at a local scale. In this study, we present an innovative approach for the assessment of the accuracy of four reanalysis data sets—European Center for Medium‐Range Weather Forecasts, Reanalysis 5 (ERA5), Modern‐Era Retrospective analysis for Research and Applications Version 2, North American Regional Reanalysis, and the Twentieth Century Reanalysis—in capturing daily and extreme observed apparent temperatures in over 300 stations in the contiguous United States (USA). We modeled the relationship between the reanalysis and observed data during a training period and subsequently used these models to predict daily observations during the test period. This process enabled potential adjustment of the biases in the reanalysis data sets (i.e., the predictors). For predictive modeling, the performance of a Feed‐Forward Neural Network (FFNN) and a linear regression (LR) were assessed. Our results show the data assimilations were closer to observations in the eastern parts compared to the western parts of the USA. Considering the number of stations with the lowest error and highest hit rate (for extreme events), FFNN outperformed LR except for extreme warm events where LR performed better. Among the reanalysis data sets, ERA5 consistently exhibited the highest performance in predicting both daily and extreme values of apparent temperature, with a larger margin of relative accuracy for cold extremes. Thus, ERA5 is more adept at accurately representing apparent temperatures in the USA.
Drag Coefficient of Emergent Vegetation in a Shallow Nonuniform Flow Over a Mobile Sand Bed
Authors: Zhang Yonggang , Cheng Jinhua , Hassan Marwan A. , Wang Ping , Wu Zi 
Published: May 2024

AbstractWidely distributed in natural rivers and coasts, vegetation interacts with fluid flows and sediments in a variable and complicated manner. Such interactions make it difficult to predict associated drag forces during sediment transport. This paper investigates the drag coefficient for an emergent vegetated patch area under nonuniform flow and mobile bed conditions, based on an analytical model solving the momentum equation following our previous work (Zhang et al., 2020, https://doi.org/10.1029/2020WR027613). Emergent vegetation was modeled with rigid cylinders arranged in staggered arrays of different vegetation coverage ∅. Laboratory flume tests were conducted to measure variations in both the water and bed surfaces along a vegetated patch on a sand bed. Based on the experimental and theoretical analyses, a dimensionless drag model integrating both terms of flow properties and bed effects is proposed to predict the drag coefficient Cd over a mobile bed. The calculated values of Cd exhibit two different trends, that is, nonmonotonically or monotonically increasing along the streamwise direction, due to the combined effect of water surface gradient and bed slope. The morphodynamic response of the mobile bed to nonuniform flow manifests as an evolution in the bed slope within the vegetated patch. Ongoing scouring directs the flow's energy toward overcoming the rising Cd and bed slope, leading to a relatively stable stage with a low sediment transport rate. This study advances the existing understanding of the drag coefficient's role over a mobile bed within nonuniform flows. It also enhances the applicability of vegetation drag models in riverine restoration.
Biophysical Modeling of Mangrove Seedling Establishment and Survival Across an Elevation Gradient With Forest Zones
Authors: Gijsman R. , Horstman E. M. , Swales A. , Balke T. , Willemsen P. W. J. M. , van der Wal D. , Wijnberg K. M. 
Published: May 2024

AbstractMangrove forest development critically depends on the establishment and survival of seedlings. Mechanistic insights into how water levels, waves and bed level dynamics influence the establishment process of individual mangrove seedlings are increasing. However, little is known about how spatial and temporal changes in water levels, waves and bed level dynamics across elevation gradients in mangrove forests facilitate/limit seedling dynamics. For this study, a new seedling establishment and growth model was integrated into a process‐based hydrodynamic and morphodynamic numerical model. This biophysical model was applied to a fringing mangrove forest located in the southern Firth of Thames, Aotearoa, New Zealand. This study quantifies the increasing establishment density and survival probability of mangrove seedlings from the lower‐elevated unvegetated intertidal flat toward the higher‐elevated mature mangrove forest. Three cross‐shore zones with distinctive seedling dynamics were identified: (a) a zone with daily tidal inundation where seedling dynamics are episodic and limited by the dispersal of individual propagules that rapidly anchor to the substrate by root growth, (b) a zone with daily to bi‐weekly tidal inundation where seedling dynamics respond to variations in spring‐neap tidal cycles and, (c) a zone with less than bi‐weekly inundation where seedling dynamics are governed by high propagule supply and seedling survival probability. The seedling establishment density and survival probability are dominated by annual extremes in tidal hydroperiod and bed shear stresses, respectively. The obtained parameterizations can be used to incorporate seedling dynamics in decadal‐timescale mangrove forest development models that are instrumental for mangrove management and restoration.
Analysis of measurable residual disease by IG/TR gene rearrangements: quality assurance and updated EuroMRD guidelines
Authors: van der Velden Vincent H. J. , Dombrink Isabel , Alten Julia , Cazzaniga Giovanni , Clappier Emmanuelle , Drandi Daniela , Eckert Cornelia , Fronkova Eva , Hancock Jeremy , Kotrova Michaela , Kraemer Rebekka , Montonen Mirkka , Pfeifer Heike , Pott Christiane , Raff Thorsten , Trautmann Heiko , Cavé Hélène , Schäfer Beat W. , van Dongen Jacques J. M. , Trka Jan , Brüggemann Monika ,   EuroMRD Consortium, van der Velden Vincent H. J. , Raff Thorsten , van Dongen Jacques J. M. 
Published: May 2024

AbstractMinimal/measurable residual disease (MRD) diagnostics using real-time quantitative PCR analysis of rearranged immunoglobulin and T-cell receptor gene rearrangements are nowadays implemented in most treatment protocols for patients with acute lymphoblastic leukemia (ALL). Within the EuroMRD Consortium, we aim to provide comparable, high-quality MRD diagnostics, allowing appropriate risk-group classification for patients and inter-protocol comparisons. To this end, we set up a quality assessment scheme, that was gradually optimized and updated over the last 20 years, and that now includes participants from around 70 laboratories worldwide. We here describe the design and analysis of our quality assessment scheme. In addition, we here report revised data interpretation guidelines, based on our newly generated data and extensive discussions between experts. The main novelty is the partial re-definition of the “positive below quantitative range” category by two new categories, “MRD low positive, below quantitative range” and “MRD of uncertain significance”. The quality assessment program and revised guidelines will ensure reproducible and accurate MRD data for ALL patients. Within the Consortium, similar programs and guidelines have been introduced for other lymphoid diseases (e.g., B-cell lymphoma), for new technological platforms (e.g., digital droplet PCR or Next-Generation Sequencing), and for other patient-specific MRD PCR-based targets (e.g., fusion genes).
Exploring the prognostic significance of arm-level copy number alterations in triple-negative breast cancer
Authors: Doré Samuel , Ali Mariam , Sorin Mark , McDowell Sheri A. C. , Desharnais Lysanne , Breton Valérie , Yu Miranda W. , Arabzadeh Azadeh , Ryan Malcolm I. , Milette Simon , Quail Daniela F. , Walsh Logan A. 
Published: May 2024

AbstractSomatic copy number alterations (SCNAs) are prevalent in cancer and play a significant role in both tumorigenesis and therapeutic resistance. While focal SCNAs have been extensively studied, the impact of larger arm-level SCNAs remains poorly understood. Here, we investigated the association between arm-level SCNAs and overall survival in triple-negative breast cancer (TNBC), an aggressive subtype of breast cancer lacking targeted therapies. We identified frequent arm-level SCNAs, including 21q gain and 7p gain, which correlated with poor overall survival in TNBC patients. Further, we identified the expression of specific genes within these SCNAs associated with survival. Notably, we found that the expression of RIPK4, a gene located on 21q, exhibited a strong correlation with poor overall survival. In functional assays, we demonstrated that targeting Ripk4 in a murine lung metastatic TNBC model significantly reduced tumor burden, improved survival, and increased CD4+ and CD8+ T cell infiltration. RIPK4 enhanced the survival of triple-negative breast cancer cells at secondary sites, thereby facilitating the formation of metastatic lesions. Our findings highlight the significance of arm-level SCNAs in breast cancer progression and identify RIPK4 as a putative driver of TNBC metastasis and immunosuppression.
Prospects and challenges for the application of tissue engineering technologies in the treatment of bone infections
Authors: Qin Leilei , Yang Shuhao , Zhao Chen , Yang Jianye , Li Feilong , Xu Zhenghao , Yang Yaji , Zhou Haotian , Li Kainan , Xiong Chengdong , Huang Wei , Hu Ning , Hu Xulin 
Published: May 2024

AbstractOsteomyelitis is a devastating disease caused by microbial infection in deep bone tissue. Its high recurrence rate and impaired restoration of bone deficiencies are major challenges in treatment. Microbes have evolved numerous mechanisms to effectively evade host intrinsic and adaptive immune attacks to persistently localize in the host, such as drug-resistant bacteria, biofilms, persister cells, intracellular bacteria, and small colony variants (SCVs). Moreover, microbial-mediated dysregulation of the bone immune microenvironment impedes the bone regeneration process, leading to impaired bone defect repair. Despite advances in surgical strategies and drug applications for the treatment of bone infections within the last decade, challenges remain in clinical management. The development and application of tissue engineering materials have provided new strategies for the treatment of bone infections, but a comprehensive review of their research progress is lacking. This review discusses the critical pathogenic mechanisms of microbes in the skeletal system and their immunomodulatory effects on bone regeneration, and highlights the prospects and challenges for the application of tissue engineering technologies in the treatment of bone infections. It will inform the development and translation of antimicrobial and bone repair tissue engineering materials for the management of bone infections.
Involvement of H2A variants in DNA damage response of zygotes
Authors: Wang Yuan , Tsukioka Dai , Oda Shoji , Suzuki Masataka G. , Suzuki Yutaka , Mitani Hiroshi , Aoki Fugaku 
Published: May 2024

AbstractPhosphorylated H2AX, known as γH2AX, forms in response to genotoxic insults in somatic cells. Despite the high abundance of H2AX in zygotes, the level of irradiation-induced γH2AX is low at this stage. Another H2A variant, TH2A, is present at a high level in zygotes and can also be phosphorylated at its carboxyl end. We constructed H2AX- or TH2A-deleted mice using CRISPR Cas9 and investigated the role of these H2A variants in the DNA damage response (DDR) of zygotes exposed to γ-ray irradiation at the G2 phase. Our results showed that compared to irradiated wild-type zygotes, irradiation significantly reduced the developmental rates to the blastocyst stage in H2AX-deleted zygotes but not in TH2A-deleted ones. Furthermore, live cell imaging revealed that the G2 checkpoint was activated in H2AX-deleted zygotes, but the duration of arrest was significantly shorter than in wild-type and TH2A-deleted zygotes. The number of micronuclei was significantly higher in H2AX-deleted embryos after the first cleavage, possibly due to the shortened cell cycle arrest of damaged embryos and, consequently, the insufficient time for DNA repair. Notably, FRAP analysis suggested the involvement of H2AX in chromatin relaxation. Moreover, phosphorylated CHK2 foci were found in irradiated wild-type zygotes but not in H2AX-deleted ones, suggesting a critical role of these foci in maintaining cell cycle arrest for DNA repair. In conclusion, H2AX, but not TH2A, is involved in the DDR of zygotes, likely by creating a relaxed chromatin structure with enhanced accessibility for DNA repair proteins and by facilitating the formation of pCHK2 foci to prevent premature cleavage.
Deciphering the potential role of PGRN in regulating CD8+ T cell antitumor immunity
Authors: Zhang Wenyu , Qin Huan , Wang Guosheng , Zhang Jing , He Wenjuan , Feng Chunmei , Wan Huimin , Wang Feilong , Guo Zhongliang 
Published: May 2024

AbstractA key factor contributing to resistance in immune checkpoint blockade (ICB) therapies is CD8+ T-cell tolerance in the tumor microenvironment (TME), partly resulting from upregulating coinhibitory receptors. Here, we describe the role of PGRN as a coinhibitory molecule that modulates the antitumor response of CD8+ T cells, thus presenting a novel immunosuppressive target for lung cancer. The in vivo subcutaneous transplanted lung cancer model showed that PGRN expression was elevated on CD8+ T cells that infiltrated transplanted lung cancers. Furthermore, PGRN deficiency was found to specifically encourage the infiltration of CD8+ T cells, enhance their proliferation, migration, and activation, and resist apoptosis, ultimately inhibiting tumor growth. This was achieved by PGRN knockout, increasing the production of T cell chemokine CCL3, which boosts the antitumor immune response induced by CD8+ T cells. Critically, the PD-L1 inhibitor exhibited a synergistic effect in enhancing the antitumor response in PGRN–/– mice. In summary, our findings highlight the significance of PGRN as a novel target for boosting CD8+ T cells antitumor immunity and its potential to overcome the resistance in ICB therapy.
MLKL, a new actor of UVB-induced apoptosis in human diploid dermal fibroblasts
Authors: Gary Anne-Sophie , Amouret Sophie , Montoni Alicia , Rochette Patrick J. 
Published: May 2024

AbstractUltraviolet radiation (UVR) is a major environmental mutagen. In skin, UVR can initiate cancer through the induction of mutagenic DNA damage and promote its progression. An important cancer prevention mechanism is the regulated cell death (RCD), which can safely dispose of damaged cells. Apoptosis, a well-known RCD, is known to be activated by UVR, but part of the mechanism and proteins involved in UVR-induced apoptosis are still to be discovered. Receptor-interacting serine/threonine-protein kinase 3 (RIPK3) and mixed lineage kinase domain-like (MLKL) are two proteins involved in necroptosis, a form of RCD. Here, we have evaluated the implication of RIPK3 and MLKL in UVB-induced cell death in human diploid dermal fibroblasts. Our results show that RIPK3 and MLKL play opposite roles in UVB-induced cell death, in a necroptosis independent pathway. We showed that RIPK3 protects cells from UVB cell death, while MLKL sensitizes cells to UVB-induced apoptosis. Taken together these results are the first to show the implication of RIPK3 and MLKL in survival and apoptosis, respectively, bringing two new actors in UVB-induced cell death pathway.
Efficacy and safety of novel multifunctional M10 CAR-T cells in HIV-1-infected patients: a phase I, multicenter, single-arm, open-label study
Authors: Mao Yunyu , Liao Qibin , Zhu Youwei , Bi Mingyuan , Zou Jun , Zheng Nairong , Zhu Lingyan , Zhao Chen , Liu Qing , Liu Li , Chen Jun , Gu Ling , Liu Zhuoqun , Pan Xinghao , Xue Ying , Feng Meiqi , Ying Tianlei , Zhou Pingyu , Wu Zhanshuai , Xiao Jian , Zhang Renfang , Leng Jing , Sun Yongtao , Zhang Xiaoyan , Xu Jianqing 
Published: May 2024

AbstractChimeric antigen receptor T (CAR-T) cells have been proposed for HIV-1 treatment but have not yet demonstrated desirable therapeutic efficacy. Here, we report newly developed anti-HIV-1 CAR-T cells armed with endogenic broadly neutralizing antibodies (bNAbs) and the follicle-homing receptor CXCR5, termed M10 cells. M10 cells were designed to exercise three-fold biological functions, including broad cytotoxic effects on HIV-infected cells, neutralization of cell-free viruses produced after latency reversal, and B-cell follicle homing. After demonstrating the three-fold biological activities, M10 cells were administered to treat 18 HIV-1 patients via a regimen of two allogenic M10 cell infusions with an interval of 30 days, with each M10 cell infusion followed by two chidamide stimulations for HIV-1 reservoir activation. Consequently, 74.3% of M10 cell infusions resulted in significant suppression of viral rebound, with viral loads declining by an average of 67.1%, and 10 patients showed persistently reduced cell-associated HIV-1 RNA levels (average decrease of 1.15 log10) over the 150-day observation period. M10 cells were also found to impose selective pressure on the latent viral reservoir. No significant treatment-related adverse effects were observed. Overall, our study supported the potential of M10 CAR-T cells as a novel, safe, and effective therapeutic option for the functional cure of HIV-1/AIDS.
Understanding the effect of microstructure and composition on localized corrosion susceptibility of 6xxx aluminum alloys
Authors: Adapala Priyanka , Avey Thomas , Yuan Yudie , Lim Mary Lyn , Bhaskaran Ganesh , Das Sazol , Luo Alan , Frankel Gerald S. 
Published: May 2024

AbstractThe corrosion performance of 6xxx series Al alloys has been found to depend on small changes in composition and microstructure. The corrosion behaviors of three aluminum alloys, AA6111, AA6451, and AA6016, were investigated. AA6111, containing primarily α (Al15 (Fe,Mn)3Si2) intermetallic particles (IMPs), and AA6016, containing primarily β (Al8Fe2Si) IMPs, exhibited the best and the worst overall corrosion performances, respectively, as indicated by the extent of corrosion in exposure tests. However, this ranking was not predicted by the standard interpretation of potentiodynamic polarization curves measured on the alloys. The corrosion susceptibilities of the three alloys were further investigated by evaluating the electrochemical behavior of the component phases separately. Bulk analogs of the component phases were fabricated using standard alloy casting techniques. The fabricated bulk analogs of α and β IMPs, as well as the three alloy matrix phases, were tested using either macrocell or microcell testing. An explanation for the alloy performances was developed by combining the behavior of the component phases.