bluuebunny/crossref_metadata_2025 huggingface dataset:
A review on modeling nutrient dynamics and loadings in forest-dominated watersheds under cold climate conditions
Authors: Liu Yongbo , Shrestha Rajesh , Fong Phil , Yerubandi Ram
Published: April 2024

This review summarized the past and current studies on forest nutrient export and existing watershed water quality models that are capable of predicting nutrient loadings from forest-dominated watersheds. Emphasis was given to the watershed models used under cold climate conditions and their capacities and limitations in assessing the impacts of forest best management practices (BMPs) and climate change scenarios on nutrient loadings at a watershed scale. The nutrient export rates in forest-dominated watersheds were found to vary significantly controlled by local climate and landscape conditions. Some watershed water quality models can estimate nutrient loadings from forests either with a simplified forest growth function or without a forest growth component. No existing watershed water quality models have explicit representation forest BMP functions. Combining or coupling with a forest growth model is required for a realistic simulation of nutrient dynamics and assessing the impact of forest BMPs in a forest-dominated watershed. The review also considered the suitability of models for exploring the potential effects of climate change on hydrologic and nutrient processes relevant to forest management. Discussions on the challenges and limitations of forested watershed water quality models and recommendations for future development were made following the review. The findings of this study can provide valuable references for water quality modeling studies in forest-dominated watersheds under cold climate conditions.
Slope instability mechanism with differential rock mass structure along a fault: a mine landslide from Southwest China
Authors: Wei Tao , Chen GuoQing , Zhu Zhou , Tang Peng , Yan Ming
Published: April 2024

Mine slope stability and mining sustainability are related to the local geological structures, which could change the rock mass structure in deep mining. After 20 years mining in a mudstone mine, western China, the slope structure transforms from anti-dipping structure into a bedding structure by a recently discovered fault (F1), further inducing the two landslides (Landslide #I and Landslide #II). Landslide investigation suggested the residual deposits in Landslide #I first slid over 100 m and overburdened the rear of Landslide #II. The bedding rock with weak interlayers at footwall is separated from the anti-dipping rock at the hanging wall by F1. After excavation, a weak interlayer was exposed and softened by rainfall, resulting in the slip of footwall rock mass and further inducing large scale toppling deformation. The fragmented rock mass sliding along a weak interlayer triggers consequent deformation of adjacent slope, reducing safety reserve of the open mine. The discrete element analysis reveals that the bedding rock mass of footwall slid once the weak interlayer was exposed by mining. And retrogressive deformation transmitted to the hanging wall and induced bending and toppling deformation of anti-dipping rock mass. Mine feasibility assessment should recognize the potential deep geological structures as important in the future.
Exploring the different stages of treated wastewater on various cement types
Authors: ElGazzar Moemn , Elnemr Amr
Published: April 2024

Recycled wastewater in construction presents an opportunity to ease freshwater scarcity while advancing sustainability. This study investigated the influences of cement type and treated wastewater source on setting time and mechanical properties of cement paste and mortar. Three cement types, ordinary Portland cement (CEM I), CEM III/A, and CEM IV/A-P, were encountered. Four plants treated wastewater versus potable water as control. Fifteen mixes were encountered; every 5 mixes addressed certain cement types along with specified treated water types. Two phases were designed; Phase I evaluated setting time in pastes and Phase II evaluated the flexural and compressive strengths of mortar specimens at 2 and 28 days of age. The significant impact of both variables was observed. CEM III/A displayed the fastest setting among the other mixes, while CEM I was the slowest. Wastewater accelerated setting versus distilled water. The mechanical performance also varied based on the cement–wastewater combination. CEM IV/A-P provided optimal strength enhancement up to 50% in flexural and 35% in compressive strength with wastewater compared to CEM I control. Results were attributed to cement–water interactions influencing hydration and microstructure. While CEM I achieved low mechanical strength with wastewater; CEM III/A, and CEM IV/A-P benefits, especially at early ages. Considerable variability highlights the complex interplay of factors governing performance. Coupled chemical-microstructural analysis was recommended to elucidate underlying mechanisms. Overall, tailored cement–wastewater selection shows promise for sustainable concrete, pending further optimization and durability testing. The study provides a platform for context-specific development of eco-efficient construction materials utilizing locally available resources.
Multi-decade land cover/land use dynamics and future predictions for Zambia: 2000–2030
Authors: Chisanga Charles Bwalya , Phiri Darius , Mubanga Kabwe Harnadih
Published: April 2024

Human LULCC is the many driver of environmental changes. Accurate and up-to-date current and predicted information on LULCC is important in land use planning and natural resource management; however, in Zambia, detailed information on LULCC is insufficient. Therefore, this study assessed the dynamics of LULC change (2000–2020) and future projections (2020–2030) for Zambia. The ESA CCI land cover maps, which have been developed from Sentinel-2 images were used in this study. This dataset has a grid spatial resolution of 300 m for the 2000, 2010 and 2020. The 31 ESA CCI Classification were reclassified into ten (10) local Classifications using the r.class module in QGIS 2.18.14. The 2000 and 2010 LULC maps were used to simulate the 2020 LULC scenario using Artificial Neural Network (Multi-layer Perception) algorithms in Modules for Land Use Change Evaluation (MOLUSCE) plugin in QGIS 2.18.14. The 2010 and 2020 maps were used to predict the 2030 LULC classes. The reference 2020 and predicted 2020 LULC maps were used to validate the model. Predicted against observed 2020 LULC map, Kappa (loc) statistic was 0.9869. The 2020 LULC patterns was successfully simulated using ANN-MLP with accuracy level of 95%. LULC classes were predicted for 2030 using the 2010–2020 calibration period. The predicted 2030 LULC types shows an increase in built-up (71.44%) and decrease in cropland (0.73%) with reference to 2020 LULC map. Dense forest (0.19%), grassland (0.85%) and bare land (1.37%) will reduce from 2020–2030. However, seasonally flooded, sparse forest, shrub land, wetland and water body will increase marginally. The largest LULC change is from forest into other LULC types. The insights from this study show that ANN-MLP can be used to predict LULCC, and that the generated information can be employed in land use planning and National Adaptation Plans at regional and national scale.
Assessing Radiative Impacts of African Smoke Aerosols Over the Southeastern Atlantic Ocean
Authors: Logan Timothy , Dong Xiquan , Xi Baike , Zheng Xiaojian , Wu Lily , Abramowitz Aidin , Goluszka Amanda , Harper Maeland
Published: April 2024

Biomass burning smoke aerosols are efficient at attenuating incoming solar radiation. The Layered Atlantic Smoke Interactions with Clouds campaign was conducted from June 2016 to October 2017. The U. S. Department of Energy mobile Atmospheric Radiation Measurement site located on Ascension Island (AMF‐ASI) identified several instances of smoke plume intrusions. Increases in surface and column measurements of aerosol loading were directly related to increases in fine mode fraction, number concentrations of aerosols (Na), and cloud condensation nuclei (NCCN). During periods of weak lower tropospheric stability, smoke particles were more likely to be advected downward either by boundary layer turbulence or cloud top entrainment under non‐overcast sky conditions. Backward trajectory analysis illustrated that smoke aerosols reaching the AMF‐ASI site were fine mode, less aged, strongly absorbing, and had shorter boundary layer trajectories while longer boundary layer trajectories denoted mixtures of weakly absorbing smoke and coarse mode marine aerosols. The most polluted smoke cases of August 2016 and 2017 revealed a notable contrast in radiative forcing per unit aerosol optical depth or radiative forcing efficiency (ΔFeff) at the top of the atmosphere (TOA) and near‐surface (BOA). The weakly (strongly) absorbing 2016 cases exhibited weaker (stronger) ΔFeff at the TOA and BOA suggesting a warming (cooling) effect within the boundary layer. The 2017 cases featured the strongest ΔFeff suggesting more of a cooling effect at the TOA and BOA due to mixing of fresh smoke with marine aerosols during transport.
Deglacial Carbon Escape From the Northern Rim of the Southern Ocean
Authors: Umling N. E. , Sikes E. , Rafter P. , Goodkin N. F. , Southon J. R.
Published: April 2024

The Southern Ocean regulates atmospheric CO2 and Earth's climate as a critical region for air‐sea gas exchange, delicately poised between being a CO2 source and sink. Here, we estimate how long a water mass has remained isolated from the atmosphere and utilize 14C/12C ratios (Δ14C) to trace the pathway and escape route of carbon sequestered in the deep ocean through the mixed layer to the atmosphere. The position of our core at the northern margin of the Southern Indian Ocean, tracks latitudinal shifts of the Southern Ocean frontal zones across the deglaciation. Our results suggest an expanded glacial Antarctic region trapped CO2, whereas deglacial expansion of the subantarctic permitted ventilation of the trapped CO2, contributing to a rapid atmospheric CO2 rise. We identify frontal positions as a key factor balancing CO2 outgassing versus sequestration in a region currently responsible for nearly half of global ocean CO2 uptake.
Antarctic Vortex Dehydration in 2023 as a Substantial Removal Pathway for Hunga Tonga‐Hunga Ha'apai Water Vapor
Authors: Zhou Xin , Dhomse Sandip S. , Feng Wuhu , Mann Graham , Heddell Saffron , Pumphrey Hugh , Kerridge Brian J. , Latter Barry , Siddans Richard , Ventress Lucy , Querel Richard , Smale Penny , Asher Elizabeth , Hall Emrys G. , Bekki Slimane , Chipperfield Martyn P.
Published: April 2024

The January 2022 eruption of Hunga Tonga‐Hunga Ha'apai (HTHH) injected a huge amount (∼150 Tg) of water vapor (H2O) into the stratosphere, along with small amount of SO2. An off‐line 3‐D chemical transport model (CTM) successfully reproduces the spread of the injected H2O through October 2023 as observed by the Microwave Limb Sounder. Dehydration in the 2023 Antarctic polar vortex caused the first substantial (∼20 Tg) removal of HTHH H2O from the stratosphere. The CTM indicates that this process will dominate removal of HTHH H2O for the coming years, giving an overall e‐folding timescale of 4 years; around 25 Tg of the injected H2O is predicted to still remain in the stratosphere by 2030. Following relatively low Antarctic column ozone in midwinter 2023 due to transport effects, additional springtime depletion due to H2O‐related chemistry was small and maximized at the vortex edge (10 DU in column).
The Upper Crustal Deformation Field of Greece Inferred From GPS Data and Its Correlation With Earthquake Occurrence
Authors: Chousianitis Konstantinos , Sboras Sotirios , Mouslopoulou Vasiliki , Chouliaras Gerasimos , Hristopulos Dionissios T.
Published: April 2024

We present a new geodetic strain rate and rotation rate model for Greece that has been derived using a highly dense GPS velocity field. The spatial distribution and the resolved rates of the various velocity gradient tensor quantities provided updated constraints on the present‐day upper crustal deformation in the region and revealed new details not reported previously. The spatial distribution of the second invariant demonstrated that the overall magnitude of strain rates is highest across two well‐defined provinces. The first follows the North Anatolian Fault and its two branches within the north Aegean, crosses central Greece and through the Gulf of Corinth it terminates in western Greece, while the second encompasses the extensional province of western Turkey and the eastern Aegean Sea islands. Our estimates revealed that shearing affects some of the fault‐bounded grabens of central Greece that lie to the SW of the North Aegean Basin implying considerable oblique extension. We identified a narrow region of counterclockwise rotation whose location and kinematics have been induced by the net effect across the intersection of the clockwise rotating domains of western and central Greece. The Aegean microplate and the Anatolian plate are separated by a wide transition zone which accommodates the curved stretching of the entire plate system. In both edges of the Hellenic forearc the dominant mode of crustal strain is E‐W extension. We found that earthquakes of M ≥ 5.6 are spatially well‐correlated with high‐strain areas, indicating that strain rate mapping could be used to inform future probabilistic seismic hazard analyses.
Advanced 3D TH and THM Modeling to Shed Light on Thermal Convection in Fault Zones With Varying Thicknesses
Authors: Duwiquet H. , Genter A. , Guillou‐Frottier L. , Donzé F. V. , Ledru P. , Magri F. , Guillon T. , Horne R. N. , Arbaret L. , Souque C.
Published: April 2024

Fault zones exhibit 3D variable thickness, a feature that remains inadequately explored, particularly with regard to the impact on fluid flow. Upon analyzing an analytic solution, we examine 3D thermal‐hydraulic (TH) dynamical models through a benchmark experiment, which incorporates a fault zone with thickness variations corresponding to realistic orders of magnitude. The findings emphasize an area of interest where vigorous convection drives fluid flow, resulting in a temperature increase to 150°C at a shallow depth of 2.7 km in the thickest sections of the fault zone. Moreover, by considering various tectonic regimes (compressional, extensional, and strike‐slip) within 3D thermal‐hydraulic‐mechanical (THM) models and comparing them to the benchmark experiment, we observe variations in fluid pressure induced by poroelastic forces acting on fluid flow within the area of interest. These tectonic‐induced pressure changes influence the thermal distribution of the region and the intensity of temperature anomalies. Outcomes of this study emphasize the impact of poroelasticity‐driven forces on transfer processes and highlight the importance of addressing fault geometry as a crucial parameter in future investigations of fluid flow in fractured systems. Such research has relevant applications in geothermal energy, CO2 storage, and mineral deposits.
Regional Responses of Vegetation Productivity to the Two Phases of ENSO
Authors: Wu Mousong , Jiang Fei , Scholze Marko , Chen Deliang , Ju Weimin , Wang Songhan , Kaminski Thomas , Lu Zhengyao , Vossbeck Michael , Zheng Minjie
Published: April 2024

The two phases of El‐Niño‐Southern Oscillation (ENSO) influence both regional and global terrestrial vegetation productivity on inter‐annual scales. However, the major drivers for the regional vegetation productivity and their controlling strengths during different phases of ENSO remain unclear. We herein disentangled the impacts of two phases of ENSO on regional carbon cycle using multiple data sets. We found that soil moisture predominantly accounts for ∼40% of the variability in regional vegetation productivity during ENSO events. Our results showed that the satellite‐derived vegetation productivity proxies, gross primary productivity from data‐driven models (FLUXCOM) and observation‐constrained ecosystem model (Carbon Cycle Data Assimilation System) generally agree in depicting the contribution of soil moisture and air temperature in modulating regional vegetation productivity. However, the ensemble of weakly constrained ecosystem models exhibits non‐negligible discrepancies in the roles of vapor pressure deficit and radiation over extra‐tropics. This study highlights the significance of water in regulating regional vegetation productivity during ENSO.
First PWV Retrieval Using MERSI‐LL Onboard FY‐3E and Cross Validation With Co‐Platform Occultation and Ground GNSS
Authors: Jiang Nan , Wu Yuhao , Li Song , Xu Yan , Wang Yubo , Xu Tianhe
Published: April 2024

FY‐3E plays a vital role in the meteorological global earth observing system. Precipitable water vapor (PWV) is an essential parameter for the water cycle and global climate change. Here, we carry out the PWV retrieval using the MERSI‐LL sensor onboard the FY‐3E satellite for the first time. The retrieval accuracy under different cloudage conditions is validated by the extra PWV from ground‐based GNSS and spaceborne occultation. For the results against ground‐based GNSS, the total accuracy shows an RMSE of 2.69–3.36 mm as the clouds increase, and correlation coefficients higher than 0.95. The spatial accuracy distribution indicates that inland stations have higher accuracy than the coast and island stations. As for the results against spaceborne occultation, the verification accuracy varies with the spatial pairing distance, showing poor accuracy in the low latitude area. This study can provide an essential reference for the community to understand the current water vapor inversion performance of MERSI‐LL.
Data Drought in the Humid Tropics: How to Overcome the Cloud Barrier in Greenhouse Gas Remote Sensing
Authors: Frankenberg C. , Bar‐On Y. M. , Yin Y. , Wennberg P. O. , Jacob D. J. , Michalak A. M.
Published: April 2024

Diagnosing land‐atmosphere fluxes of carbon‐dioxide (CO2) and methane (CH4) is essential for evaluating carbon‐climate feedbacks. Greenhouse gas satellite missions aim to fill data gaps in regions like the humid tropics but obtain very few valid measurements due to cloud contamination. We examined data yields from the Orbiting Carbon Observatory alongside Sentinel‐2 cloud statistics. We find that the main contribution to low data yields are frequent shallow cumulus clouds. In the Amazon, the success rate in obtaining valid measurements vary from 0.1% to 1.0%. By far the lowest yields occur in the wet season, consistent with Sentinel‐2 cloud patterns. We find that increasing the spatial resolution of observations to ∼200 m would increase yields by 2–3 orders of magnitude and allow regular measurements in the wet season. Thus, the key to effective tropical greenhouse gas observations lies in regularly acquiring high‐spatial resolution data.
Using Satellite and ARM Observations to Evaluate Cold Air Outbreak Cloud Transitions in E3SM Global Storm‐Resolving Simulations
Authors: Zheng X. , Zhang Y. , Klein S. A. , Zhang M. , Zhang Z. , Deng M. , Tian J. , Terai C. R. , Geerts B. , Caldwell P. , Bogenschutz P. A.
Published: April 2024

This study examines marine boundary layer cloud regime transition during a cold air outbreak (CAO) over the Norwegian Sea, simulated by a global storm‐resolving model (GSRM) known as the Simple Cloud‐Resolving Energy Exascale Earth System Model Atmosphere Model (SCREAM). By selecting observational references based on a combination of large‐scale conditions rather than strict time‐matched comparisons, this study finds that SCREAM qualitatively captures the CAO cloud transition, including boundary layer growth, cloud mesoscale structure, and phase partitioning. SCREAM also accurately locates the greatest ice and liquid in the mesoscale updrafts, however, underestimates supercooled liquid water in cumulus clouds. The model evaluation approach adopted by this study takes advantages of the existing computational‐expensive global simulations of GSRM and the available observations to understand model performance and can be applied to assessments of other cloud regimes in different regions. Such practice provides valuable guidance on the future effort to correct and improve biased model behaviors.
Advances in body composition: a 100-year journey
Authors: Heymsfield Steven B.
Published: April 2024

Knowledge of human body composition at the dawn of the twentieth century was based largely on cadaver studies and chemical analyses of isolated organs and tissues. Matters soon changed by the nineteen twenties when the Czech anthropologist Jindřich Matiegka introduced an influential new anthropometric method of fractionating body mass into subcutaneous adipose tissue and other major body components. Today, one century later, investigators can not only quantify every major body component in vivo at the atomic, molecular, cellular, tissue-organ, and whole-body organizational levels, but go far beyond to organ and tissue-specific composition and metabolite estimates. These advances are leading to an improved understanding of adiposity structure-function relations, discovery of new obesity phenotypes, and a mechanistic basis of some weight-related pathophysiological processes and adverse clinical outcomes. What factors over the past one hundred years combined to generate these profound new body composition measurement capabilities in living humans? This perspective tracks the origins of these scientific innovations with the aim of providing insights on current methodology gaps and future research needs.
Tumour-associated myeloid cells expressing IL-10R2/IL-22R1 as a potential biomarker for diagnosis and recurrence of pancreatic ductal adenocarcinoma
Authors: Lee Hyung Keun , Kim So Young , Chung Soo-Hyun , Choi Bongkun , Kim Ji-Eun , Yoon Dohee , Jang Sung Ill , Yeo Areum , Kang Hyun Goo , Lee Jusung , Choi Yoon Ha , Park Joon Seong , Sung Yoolim , Kim Jong Kyoung , Chang Eun-Ju , Lee Dong Ki
Published: April 2024

Background

Pancreatic ductal adenocarcinoma (PDAC) is an aggressive malignancy with a poor survival rate, largely due to the lack of early diagnosis. Although myeloid cells are crucial in the tumour microenvironment, whether their specific subset can be a biomarker of PDAC progression is unclear.

Methods

We analysed IL-22 receptor expression in PDAC and peripheral blood. Additionally, we analysed gene expression profiles of IL-10R2+/IL-22R1+ myeloid cells and the presence of these cells using single-cell RNA sequencing and murine orthotropic PDAC models, respectively, followed by examining the immunosuppressive function of IL-10R2+/IL-22R1+ myeloid cells. Finally, the correlation between IL-10R2 expression and PDAC progression was evaluated.

Results

IL-10R2+/IL-22R1+ myeloid cells were present in PDAC and peripheral blood. Blood IL-10R2+ myeloid cells displayed a gene expression signature associated with tumour-educated circulating monocytes. IL-10R2+/IL-22R1+ myeloid cells from human myeloid cell culture inhibited T cell proliferation. By mouse models for PDAC, we found a positive correlation between pancreatic tumour growth and increased blood IL-10R2+/IL-22R1+ myeloid cells. IL-10R2+/IL-22R1+ myeloid cells from an early phase of the PDAC model suppressed T cell proliferation and cytotoxicity. IL-10R2+ myeloid cells indicated tumour recurrence 130 days sooner than CA19-9 in post-pancreatectomy patients.

Conclusions

IL-10R2+/IL-22R1+ myeloid cells in the peripheral blood might be an early marker of PDAC prognosis.
FBXO32-mediated degradation of PTEN promotes lung adenocarcinoma progression
Authors: Wu Jie , Wen Ting , Marzio Antonio , Song Dingli , Chen Sisi , Yang Chengcheng , Zhao Fengyu , Zhang Boxiang , Zhao Guang , Ferri Alessandra , Cheng Hao , Ma Jiao , Ren Hong , Chen Qiao Yi , Yang Yiping , Qin Sida
Published: April 2024

FBXO32, a member of the F-box protein family, is known to play both oncogenic and tumor-suppressive roles in different cancers. However, the functions and the molecular mechanisms regulated by FBXO32 in lung adenocarcinoma (LUAD) remain unclear. Here, we report that FBXO32 is overexpressed in LUAD compared with normal lung tissues, and high expression of FBXO32 correlates with poor prognosis in LUAD patients. Firstly, we observed with a series of functional experiments that FBXO32 alters the cell cycle and promotes the invasion and metastasis of LUAD cells. We further corroborate our findings using in vivo mouse models of metastasis and confirmed that FBXO32 positively regulates LUAD tumor metastasis. Using a proteomic-based approach combined with computational analyses, we found a positive correlation between FBXO32 and the PI3K/AKT/mTOR pathway, and identified PTEN as a FBXO32 interactor. More important, FBXO32 binds PTEN via its C-terminal substrate binding domain and we also validated PTEN as a bona fide FBXO32 substrate. Finally, we demonstrated that FBXO32 promotes EMT and regulates the cell cycle by targeting PTEN for proteasomal-dependent degradation. In summary, our study highlights the role of FBXO32 in promoting the PI3K/AKT/mTOR pathway via PTEN degradation, thereby fostering lung adenocarcinoma progression.
Replicative senescence and high glucose induce the accrual of self-derived cytosolic nucleic acids in human endothelial cells
Authors: Ramini Deborah , Giuliani Angelica , Kwiatkowska Katarzyna Malgorzata , Guescini Michele , Storci Gianluca , Mensà Emanuela , Recchioni Rina , Xumerle Luciano , Zago Elisa , Sabbatinelli Jacopo , Santi Spartaco , Garagnani Paolo , Bonafè Massimiliano , Olivieri Fabiola
Published: April 2024

Recent literature shows that loss of replicative ability and acquisition of a proinflammatory secretory phenotype in senescent cells is coupled with the build-in of nucleic acids in the cytoplasm. Its implication in human age-related diseases is under scrutiny. In human endothelial cells (ECs), we assessed the accumulation of intracellular nucleic acids during in vitro replicative senescence and after exposure to high glucose concentrations, which mimic an in vivo condition of hyperglycemia. We showed that exposure to high glucose induces senescent-like features in ECs, including telomere shortening and proinflammatory cytokine release, coupled with the accrual in the cytoplasm of telomeres, double-stranded DNA and RNA (dsDNA, dsRNA), as well as RNA:DNA hybrid molecules. Senescent ECs showed an activation of the dsRNA sensors RIG-I and MDA5 and of the DNA sensor TLR9, which was not paralleled by the involvement of the canonical (cGAS) and non-canonical (IFI16) activation of the STING pathway. Under high glucose conditions, only a sustained activation of TLR9 was observed. Notably, senescent cells exhibit increased proinflammatory cytokine (IL-1β, IL-6, IL-8) production without a detectable secretion of type I interferon (IFN), a phenomenon that can be explained, at least in part, by the accumulation of methyl-adenosine containing RNAs. At variance, exposure to exogenous nucleic acids enhances both IL-6 and IFN-β1 expression in senescent cells. This study highlights the accrual of cytoplasmic nucleic acids as a marker of senescence-related endothelial dysfunction, that may play a role in dysmetabolic age-related diseases.
GENESIS CGDYN: large-scale coarse-grained MD simulation with dynamic load balancing for heterogeneous biomolecular systems
Authors: Jung Jaewoon , Tan Cheng , Sugita Yuji
Published: April 2024

Residue-level coarse-grained (CG) molecular dynamics (MD) simulation is widely used to investigate slow biological processes that involve multiple proteins, nucleic acids, and their complexes. Biomolecules in a large simulation system are distributed non-uniformly, limiting computational efficiency with conventional methods. Here, we develop a hierarchical domain decomposition scheme with dynamic load balancing for heterogeneous biomolecular systems to keep computational efficiency even after drastic changes in particle distribution. These schemes are applied to the dynamics of intrinsically disordered protein (IDP) droplets. During the fusion of two droplets, we find that the changes in droplet shape correlate with the mixing of IDP chains. Additionally, we simulate large systems with multiple IDP droplets, achieving simulation sizes comparable to those observed in microscopy. In our MD simulations, we directly observe Ostwald ripening, a phenomenon where small droplets dissolve and their molecules redeposit into larger droplets. These methods have been implemented in CGDYN of the GENESIS software, offering a tool for investigating mesoscopic biological processes using the residue-level CG models.
Deviations in RSV epidemiological patterns and population structures in the United States following the COVID-19 pandemic
Authors: Rios-Guzman Estefany , Simons Lacy M. , Dean Taylor J. , Agnes Francesca , Pawlowski Anna , Alisoltanidehkordi Arghavan , Nam Hannah H. , Ison Michael G. , Ozer Egon A. , Lorenzo-Redondo Ramon , Hultquist Judd F.
Published: April 2024

Respiratory Syncytial Virus (RSV) is a leading cause of acute respiratory tract infection, with the greatest impact on infants, immunocompromised individuals, and older adults. RSV prevalence decreased substantially in the United States (US) following the implementation of COVID-19-related non-pharmaceutical interventions but later rebounded with abnormal seasonality. The biological and epidemiological factors underlying this altered behavior remain poorly defined. In this retrospective cohort study from 2009 to 2023 in Chicago, Illinois, US, we examined RSV epidemiology, clinical severity, and genetic diversity. We found that changes in RSV diagnostic platforms drove increased detections in outpatient settings post-2020 and that hospitalized adults infected with RSV-A were at higher risk of intensive care admission than those with RSV-B. While population structures of RSV-A remained unchanged, RSV-B exhibited a genetic shift into geographically distinct clusters. Mutations in the antigenic regions of the fusion protein suggest convergent evolution with potential implications for vaccine and therapeutic development.
Bispecific CAR T cell therapy targeting BCMA and CD19 in relapsed/refractory multiple myeloma: a phase I/II trial
Authors: Shi Ming , Wang Jiaojiao , Huang Hongming , Liu Dan , Cheng Hai , Wang Xu , Chen Wei , Yan Zhiling , Sang Wei , Qi Kunming , Li Depeng , Zhu Feng , Li Zhenyu , Qiao Jianlin , Wu Qingyun , Zeng Lingyu , Fei Xiaoming , Gu Weiying , Miao Yuqing , Xu Kailin , Zheng Junnian , Cao Jiang
Published: April 2024

Despite the high therapeutic response achieved with B-cell maturation antigen (BCMA)-specific chimeric antigen receptor (CAR) T-cell therapy in relapsed and refractory multiple myeloma (R/R MM), primary resistance and relapse exist with single-target immunotherapy. Here, we design bispecific BC19 CAR T cells targeting BCMA/CD19 and evaluate antimyeloma activity in vitro and in vivo. Preclinical results indicate that BC19 CAR specifically recognize target antigens, and BC19 CAR T cells mediate selective killing of BCMA or CD19-positive cancer cells. BC19 CAR T cells also exhibit potent antigen-specific anti-tumor activity in xenograft mouse models. We conduct an open-label, single-arm, phase I/II study of BC19 CAR T cells in 50 patients with R/R MM (ChiCTR2000033567). The primary endpoint was safety. BC19 CAR T cells are well tolerated with grade 3 or higher cytokine release syndrome in 8% of patients and grade 1 neurotoxic events in 4% of patients, which meet the pre-specified primary endpoint. Secondary endpoints include overall response rate (92%), median progression-free survival (19.7 months), median overall survival (19.7 months) and median duration of response (not reached). Our study demonstrates that bispecific BC19 CAR T cells are feasible, safe and effective in treating patients with R/R MM.
FastMRI Prostate: A public, biparametric MRI dataset to advance machine learning for prostate cancer imaging
Authors: Tibrewala Radhika , Dutt Tarun , Tong Angela , Ginocchio Luke , Lattanzi Riccardo , Keerthivasan Mahesh B. , Baete Steven H. , Chopra Sumit , Lui Yvonne W. , Sodickson Daniel K. , Chandarana Hersh , Johnson Patricia M.
Published: April 2024

Magnetic resonance imaging (MRI) has experienced remarkable advancements in the integration of artificial intelligence (AI) for image acquisition and reconstruction. The availability of raw k-space data is crucial for training AI models in such tasks, but public MRI datasets are mostly restricted to DICOM images only. To address this limitation, the fastMRI initiative released brain and knee k-space datasets, which have since seen vigorous use. In May 2023, fastMRI was expanded to include biparametric (T2- and diffusion-weighted) prostate MRI data from a clinical population. Biparametric MRI plays a vital role in the diagnosis and management of prostate cancer. Advances in imaging methods, such as reconstructing under-sampled data from accelerated acquisitions, can improve cost-effectiveness and accessibility of prostate MRI. Raw k-space data, reconstructed images and slice, volume and exam level annotations for likelihood of prostate cancer are provided in this dataset for 47468 slices corresponding to 1560 volumes from 312 patients. This dataset facilitates AI and algorithm development for prostate image reconstruction, with the ultimate goal of enhancing prostate cancer diagnosis.
RAS Dataset: A 3D Cardiac LGE-MRI Dataset for Segmentation of Right Atrial Cavity
Authors: Zhu Jinwen , Bai Jieyun , Zhou Zihao , Liang Yaqi , Chen Zhiting , Chen Xiaoming , Zhang Xiaoshen
Published: April 2024

The current challenge in effectively treating atrial fibrillation (AF) stems from a limited understanding of the intricate structure of the human atria. The objective and quantitative interpretation of the right atrium (RA) in late gadolinium-enhanced magnetic resonance imaging (LGE-MRI) scans relies heavily on its precise segmentation. Leveraging the potential of artificial intelligence (AI) for RA segmentation presents a promising solution. However, the successful implementation of AI in this context necessitates access to a substantial volume of annotated LGE-MRI images for model training. In this paper, we present a comprehensive 3D cardiac dataset comprising 50 high-resolution LGE-MRI scans, each meticulously annotated at the pixel level. The annotation process underwent rigorous standardization through crowdsourcing among a panel of medical experts, ensuring the accuracy and consistency of the annotations. Our dataset represents a significant contribution to the field, providing a valuable resource for advancing RA segmentation methods.
Self-compassion and grit mediated the relation between mindfulness and mind wandering based on cross-sectional survey data
Authors: Cheung Rebecca Y. M. , Djekou Lemuela
Published: April 2024

Previous research suggests that mindfulness and mind wandering are opposing constructs. However, little is known about why and how they are negatively related. Through a process-oriented approach, this cross-sectional study tested self-compassion and grit as mediators for the relation between mindfulness and mind wandering. A total of 487 self-identified meditators were recruited from the UK (241 female, 49.49%). Participants reported a mean age of 38.98 years (SD = 10.03), with an average of 2.26 h of meditation practice per week (SD = 4.47). Upon informed consent, the participants completed a self-report questionnaire that assessed the core variables under study. Path analysis indicated that mindfulness was related to self-compassion. Greater self-compassion was, in turn, related to greater grit, which was then related to lower mind wandering. Bootstrapping analysis further indicated that self-compassion and grit as mediators between mindfulness and mind wandering, above and beyond age, gender, hours of meditation, income, and education as covariates. The cross-sectional findings provided initial evidence of mediation by showing that mindfulness and mind wandering were related through self-compassion and grit.
An all phosphorene lattice nanometric spin valve
Authors: Kumari P. , Majumder S. , Kar S. , Rani S. , Nair A. K. , Kumari K. , Kamalakar M. Venkata , Ray S. J.
Published: April 2024

Phosphorene is a unique semiconducting two-dimensional platform for enabling spintronic devices integrated with phosphorene nanoelectronics. Here, we have designed an all phosphorene lattice lateral spin valve device, conceived via patterned magnetic substituted atoms of 3d-block elements at both ends of a phosphorene nanoribbon acting as ferromagnetic electrodes in the spin valve. Through First-principles based calculations, we have extensively studied the spin-dependent transport characteristics of the new spin valve structures. Systematic exploration of the magnetoresistance (MR) of the spin valve for various substitutional atoms and bias voltage resulted in a phase diagram offering a colossal MR for V and Cr-substitutional atoms. Such MR can be directly attributed to their specific electronic structure, which can be further tuned by a gate voltage, for electric field controlled spin valves. The spin-dependent transport characteristics here reveal new features such as negative conductance oscillation and switching of the sign of MR due to change in the majority spin carrier type. Our study creates possibilities for the design of nanometric spin valves, which could enable integration of memory and logic elements for all phosphorene 2D processors.
Nonequal-length image encryption based on bitplane chaotic mapping
Authors: Zhang Ruqing , Zhou Rigui , Luo Jia
Published: April 2024

In recent years, extensive research has focused on encryption algorithms for square images, with relatively little attention given to nonsquare images. This paper introduces a novel encryption algorithm tailored for nonequal length images, integrating bit-plane chaotic mapping and Arnold transformation. To effectively implement the algorithm, the plain image is initially transformed into two equal-sized binary sequences. A new diffusion strategy is then introduced to mutually diffuse these sequences, followed by the use of a chaotic map to control the swapping of binary elements between them, enabling permutation of bits across different bitplanes. Finally, the positional information of the image is scrambled using the Arnold transform, resulting in the generation of the encrypted image. By utilizing nonequal Arnold transformation parameters and the initial value of the Lorenz chaotic map as keys, the transmission of keys is simplified, and the cryptosystem gains infinite key space to resist brute force attacks. Experimental results and security analysis confirm the effectiveness of the proposed quantum image encryption algorithm in encrypting nonsquare images, demonstrating good performance in terms of nonstatistical properties, key sensitivity, and robustness. Furthermore, simulation experiments based on Qiskit successfully validate the correctness and feasibility of the quantum image encryption algorithm.
Recombinant mycobacterial DNA-binding protein 1 with post-translational modifications boosts IFN-gamma production from BCG-vaccinated individuals’ blood cells in combination with CpG-DNA
Authors: Ozeki Yuriko , Yokoyama Akira , Nishiyama Akihito , Yoshida Yutaka , Ohara Yukiko , Mashima Tsukasa , Tomiyama Chikako , Shaban Amina K. , Takeishi Atsuki , Osada-Oka Mayuko , Yamaguchi Takehiro , Tateishi Yoshitaka , Maeyama Jun-ichi , Hakamata Mariko , Moro Hiroshi , Kikuchi Toshiaki , Hayashi Daisuke , Suzuki Fumiko , Yamamoto Toshiko , Iho Sumiko , Katahira Masato , Yamamoto Saburo , Matsumoto Sohkichi
Published: April 2024

Tuberculosis remains a large health threat, despite the availability of the tuberculosis vaccine, BCG. As BCG efficacy gradually decreases from adolescence, BCG-Prime and antigen-booster may be an efficient strategy to confer vaccine efficacy. Mycobacterial DNA-binding protein 1 (MDP1, namely Rv2986c, hupB or HU) is a major Mycobacterium tuberculosis protein that induces vaccine-efficacy by co-administration with CpG DNA. To produce MDP1 for booster-vaccine use, we have created recombinant MDP1 produced in both Escherichia coli (eMDP1) and Mycolicibacterium smegmatis (mMDP1), an avirulent rapid-growing mycobacteria. We tested their immunogenicity by checking interferon (IFN)-gamma production by stimulated peripheral blood cells derived from BCG-vaccinated individuals. Similar to native M. tuberculosis MDP1, we observed that most lysin resides in the C-terminal half of mMDP1 are highly methylated. In contrast, eMDP1 had less post-translational modifications and IFN-gamma stimulation. mMDP1 stimulated the highest amount of IFN-gamma production among the examined native M. tuberculosis proteins including immunodominant MPT32 and Antigen 85 complex. MDP1-mediated IFN-gamma production was more strongly enhanced when combined with a new type of CpG DNA G9.1 than any other tested CpG DNAs. Taken together, these results suggest that the combination of mMDP1 and G9.1 possess high potential use for human booster vaccine against tuberculosis.
Ultrasound imaging of core muscles activity in multiparous women with vaginal laxity: a cross-sectional study
Authors: Hady Doaa A. Abdel , Mabrouk Omar M. , Osman Doaa A.
Published: April 2024

Vaginal laxity (VL) is a common condition among multiparous women, especially those who have delivered vaginally. Since pelvic floor muscles (PFMs) work synergistically with other core muscles, physical therapy protocols that aim to treat VL should train the PFMs in combination with other core muscles. To investigate the activity of core muscles in multiparous women with and without VL, and its relation to sexual function. An observational, cross-sectional study. The study included 100 multiparous women, who were divided into two groups according to their scores on the vaginal laxity questionnaire (VLQ). Women who scored between 1 and 3 on the VLQ were categorized as having VL (n = 48), while those who scored between 5 and 7 were placed in the control group (n = 52). The primary outcomes were PFM displacement, diaphragmatic excursion, transversus abdominis activation ratio, and lumbar multifidus thickness measured by ultrasound imaging. The secondary outcome was sexual functioning, evaluated using the Arabic female sexual function index (ArFSFI). The VL group had significantly lower PFM displacement (mean difference (MD) − 0.42; 95% confidence interval (CI) − 0.49 to − 0.33; p = 0.001), diaphragmatic excursion (MD − 2.75; 95% CI − 2.95 to − 2.55; p = 0.001), lumbar multifidus thickness (MD − 10.08; 95% CI − 14.32 to − 5.82; p = 0.02), and ArFSFI scores (MD − 9.2; 95% CI − 10.59 to − 7.81; p = 0.001) in comparison to the control group (p < 0.05). Nevertheless, the transversus abdominis activation ratio demonstrated no significant difference between the two groups (MD 0.06; 95% CI − 0.05 to 0.17; p = 0.33). Multiparous women with VL had significantly lower PFM displacement, diaphragmatic excursion, lumbar multifidus thickness, and sexual function index scores than women in the control group. The only exception was transversus abdominis activation, which did not differ significantly between the VL and control groups.
Remnant cholesterol trajectory and subclinical arteriosclerosis: a 10-year longitudinal study of Chinese adults
Authors: Yang Ping-ting , Tang Li , Yang Sai-qi , Shi Qiu-ling , Wang Ya-qin , Qin Yue-xiang , Wang Jian-gang , Li Ying
Published: April 2024

We aimed to identify different trajectories of remnant cholesterol (RC) and investigate the association of RC trajectories with vascular endothelial function and atherosclerosis progression in a longitudinal cohort of the Chinese population. A total of 521 participants were included in the flow-mediated vasodilation (FMD) subcohort study, and 7775 participants were included in the brachial-ankle pulse wave velocity (baPWV) subcohort study. All participants had ≥ 3 medical examinations during the 10-year follow-up period. In the FMD subcohort study, three distinct RC trajectories were identified according to the RC range and changing pattern over time: “low” (57.58%), “moderate” (30.90%) and “high” (11.52%). The proportion of the three groups with vascular endothelial dysfunction (FMD < 7.0%) was 20.00%, 39.75% and 60.00% respectively. Taking the low group as a reference, participants in the moderate and high groups had over 1.88 and 2.94 times the odds of vascular endothelial dysfunction (P = 0.048). In the baPWV subcohort study, three distinct RC trajectories were also identified: “low” (54.29%), “moderate” (38.97%) and “high” (6.74%). The proportion of the three groups with atherosclerosis (baPWV > 1400 cm/s) was 38.79%, 51.26% and 59.01% respectively. Taking the low group as a reference, participants in the moderate and high groups had over 1.46 and 2.16 times the odds of atherosclerosis (P < 0.001). The findings indicated that distinct RC trajectories are significantly associated with vascular endothelial function and atherosclerosis. Regular monitoring to identify persistent increases in RC may be more helpful in identifying individuals with a high risk of cardiovascular disease.
Spallation and particles infusion into the extracorporeal circuit during CRRT: a preventable phenomenon
Authors: Ruffa Maria Cristina , Bignante Giacomo , Bocciero Vittorio , Fabbri Sergio , Degl’Innocenti Dario , Cauda Valentina , Villa Gianluca
Published: April 2024

Patients in intensive care are exposed to the risk of microparticle infusion via extracorporeal lines and the resulting complications. A possible source of microparticle release could be the extracorporeal circuit used in blood purification techniques, such as continuous renal replacement therapy (CRRT). Disposable components of CRRT circuits, such as replacement bags and circuit tubing, might release microparticles such as salt crystals produced by precipitation in replacement bags and plastic microparticles produced by spallation. In-line filtration has proven effective in retaining microparticles both in in-vitro and in-vivo studies. In our study, we performed an in-vitro model of CRRT-treatment with the aim of detecting the microparticles produced and released into the circuit by means of a qualitative and quantitative analysis, after sampling the replacement and patient lines straddling a series of in-line filters. Working pressures and flows were monitored during the experiment. This study showed that microparticles are indeed produced and released into the CRRT circuit. The inclusion of in-line filters in the replacement lines allows to reduce the burden of microparticles infused into the bloodstream during extracorporeal treatments, reducing the concentration of microparticles from 14 mg/mL pre in-line filter to 11 mg/mL post in-line filter. Particle infusion and related damage must be counted among the pathophysiological mechanisms supporting iatrogenic damage due to artificial cross-talk between organs during CRRT applied to critically ill patients. This damage can be reduced by using in-line filters in the extracorporeal circuit.
A novel method to eliminate the symmetry dependence of fiber coils for shupe mitigation
Authors: Andac Senol Tugba , Akcaalan Onder , Yertutanol Aylin , Ozbay Ekmel
Published: April 2024

It is a well-known fact that interferometric fiber optic gyroscopes (IFOGs) are easily distorted by thermal effects and distortion results in the degradation of the performance of these sensors. Changing the fiber coil geometry, increasing the winding symmetry, adding fiber buffer layers around the fiber coil, using different modulation methods for multifunctional integrated optic chips, and using special types of fibers, such as photonic crystal fibers, are some alternative solutions for preventing this degradation. This paper, theoretically and experimentally, investigates not only how different types of fiber coil winding methods behave under different rates of temperature change but also presents a novel method, to the best of our knowledge, to eliminate the Shupe effect, without violating the simplest IFOG scheme. This method rules out the importance of the winding symmetry epochally and the need of any extra treatment for the fiber coil to increase the thermal performance of the system. Regardless of the symmetry of the fiber coil winding, the rate error due to the Shupe effect can be reduced to about $$\pm 0.05^\circ /$$

±
0
.

05
∘

/

h for any rate of temperature change with this new method according to the experimental results.