bluuebunny/crossref_metadata_2025 huggingface dataset:
The Impact of an Antarctic Circumpolar Current Meander on Air‐Sea Interaction and Water Subduction
Authors: Vilela‐Silva Felipe , Bindoff Nathaniel L. , Phillips Helen E. , Rintoul Stephen R. , Nikurashin Max
Published: July 2024

Standing meanders along the Antarctic Circumpolar Current (ACC) have been shown to be regions of elevated eddy variability, meridional heat transport, and vertical exchange. In this study, we investigate the influence of a standing meander south of Australia on air‐sea heat fluxes, upper ocean structure, and subduction in the 1/10° ACCESS‐OM2 ocean‐sea ice model forced by the JRA55 atmospheric reanalysis. We track the model's Subantarctic and Polar Fronts based on their jet and water mass structure, and produce composites of thermodynamical and dynamical properties of the meander in relaxed and flexed states. The standing meander induces trough‐to‐crest variations in surface heat flux, mixed layer depth (MLD), wind stress curl, vertical velocity, and subduction. At the crests, the ocean loses heat and the mixed layer is deeper; at the troughs, the ocean gains heat and the mixed layer is shallower. Wind stress curl, vertical velocity, and subduction change sign on entering and exiting crests and troughs. Vertical velocity due to the curvature of the meander is an order of magnitude larger than Ekman vertical velocity. The poleward excursion of Polar Front meander crests extends subduction to Antarctic Intermediate Water density classes. Finally, flexing of the meander enhances both air‐sea exchange and vertical velocity. The results show that standing meanders of the ACC influence the distribution and magnitude of air‐sea fluxes of heat and momentum and exchange between the surface and interior ocean.
Implications of Variability and Trends in Coastal Extreme Water Levels
Authors: Sweet William V. , Genz Ayesha S. , Menendez Melisa , Marra John J. , Obeysekera Jayantha
Published: July 2024

Probabilities of coastal extreme water levels (EWLs) are increasing as sea levels rise. Using a time‐dependent statistical model on tide gauge data along U.S. and Pacific Basin coastlines, we show that EWL probability distributions also shift on an annual basis from climate forcing and long‐period tidal cycles. In some regions, combined variability (>15 cm) can be as large or larger than the amount of sea level rise (SLR) experienced over the past 30 years and projected over the next 30 years. Considering SLR and variability by 2050 at a location like La Jolla, California suggests a moderate‐level (damaging) flood today with a 50‐year return level (2% annual chance) would occur about 3–4 times a year during an El Nino nearing the peak of the nodal tide cycle. If interannual variability is overlooked, SLR related impacts could be more severe than anticipated based solely upon decadal‐scale projections.
Investigation of Oil Well Blowouts Triggered by Wastewater Injection in the Permian Basin, USA
Authors: Karanam Vamshi , Lu Zhong , Kim Jin‐Woo
Published: July 2024

Aged hydrocarbon wells, if proper care is not ensured, can crack, get corroded, and leak subsurface fluids. Permian Basin in Texas, home to thousands of such wells, has seen numerous blowouts and wastewater leaks. Our study employs surface deformation derived from satellite observations, and injection well records to investigate these events. The results reveal an over‐pressurized wastewater aquifer producing a surface uplift of 20 cm/yr, likely due to wastewater being injected tens of kilometers away. Focusing on a January 2022 blowout resulting in 3 cm subsidence in 2 weeks, our geophysical model suggests aquifer over‐pressurization as the cause. With an excess pressure of over 3 MPa in the aquifer, several more such blowouts are possible in the near future. This research highlights the urgent need to better understand the impact of subsurface fluid injection and calls for prompt action to mitigate the environmental effects of oil and gas production.
Joint association of sleep quality and physical activity with metabolic dysfunction-associated fatty liver disease: a population-based cross-sectional study in Western China
Authors: Wang Ying , Zhao Qian , Yang Jialu , Wang Yushan , Deng Lei , Xieyire Hamulati , Gulijiehere Tuerxun , Munire Mutalifu , Liu Fen , Li Xiaomei , Xia Min , Liu Yan , Yang Yining
Published: July 2024

Background

Metabolic dysfunction-associated fatty liver disease (MAFLD) is a growing threat leading to substantial disease burden globally. Poor sleep and physical inactivity are common in modern societies and independently associated with MAFLD, however, their joint effects on MAFLD remains unclear.

Methods

This population-based cross-sectional study was conducted in Xinjiang Uygur Autonomous Region, China, between July 2019 and September 2021. Self-reported sleep behaviors and physical activity (PA) were assessed using validated questionnaires. The primary outcome was radiological diagnosis of MAFLD.

Results

Of the 10 089 participants aged 47.0 (9.1) years (51.6% men), 3854 (38.2%) individuals had MAFLD. Poor sleep quality and physical inactivity were independently and jointly associated with an increased prevalence of MAFLD, independent of traditional risk factors (P < 0.05). Compared to subjects with guideline-recommended moderate-to-vigorous PA (MVPA) and good sleep quality, individuals with no recommended MVPA and poor sleep had the highest possibility of MAFLD (odds ratio = 2.36, 95% confidence interval: 1.81 – 3.08). Enhancing sleep quality substantially attenuated MAFLD prevalence regardless of the volume of PA, whereas, engaging in PA well above current guidelines did not adequately counteract the adverse impacts of poor sleep on MAFLD.

Conclusions

Public health awareness and strategies concurrently targeting both sleep quality and PA should be encouraged to curb the climbing prevalence of MAFLD.
Atypical cellular responses mediated by intracellular constitutive active TrkB (NTRK2) kinase domains and a solely intracellular NTRK2-fusion oncogene
Authors: Gupta Rohini , Dittmeier Melanie , Wohlleben Gisela , Nickl Vera , Bischler Thorsten , Luzak Vanessa , Wegat Vanessa , Doll Dennis , Sodmann Annemarie , Bady Elena , Langlhofer Georg , Wachter Britta , Havlicek Steven , Gupta Jahnve , Horn Evi , Lüningschrör Patrick , Villmann Carmen , Polat Bülent , Wischhusen Jörg , Monoranu Camelia M. , Kuper Jochen , Blum Robert
Published: July 2024

Trk (NTRK) receptor and NTRK gene fusions are oncogenic drivers of a wide variety of tumors. Although Trk receptors are typically activated at the cell surface, signaling of constitutive active Trk and diverse intracellular NTRK fusion oncogenes is barely investigated. Here, we show that a high intracellular abundance is sufficient for neurotrophin-independent, constitutive activation of TrkB kinase domains. In HEK293 cells, constitutive active TrkB kinase and an intracellular NTRK2-fusion oncogene (SQSTM1-NTRK2) reduced actin filopodia dynamics, phosphorylated FAK, and altered the cell morphology. Atypical cellular responses could be mimicked with the intracellular kinase domain, which did not activate the Trk-associated MAPK/ERK pathway. In glioblastoma-like U87MG cells, expression of TrkB or SQSTM1-NTRK2 reduced cell motility and caused drastic changes in the transcriptome. Clinically approved Trk inhibitors or mutating Y705 in the kinase domain, blocked the cellular effects and transcriptome changes. Atypical signaling was also seen for TrkA and TrkC. Moreover, hallmarks of atypical pTrk kinase were found in biopsies of Nestin-positive glioblastoma. Therefore, we suggest Western blot-like immunoassay screening of NTRK-related (brain) tumor biopsies to identify patients with atypical panTrk or phosphoTrk signals. Such patients could be candidates for treatment with NTRK inhibitors such as Larotrectinhib or Entrectinhib.
Gene drives: an alternative approach to malaria control?
Authors: Naidoo Kubendran , Oliver Shüné V.
Published: July 2024

Genetic modification for the control of mosquitoes is frequently touted as a solution for a variety of vector-borne diseases. There has been some success using non-insecticidal methods like sterile or incompatible insect techniques to control arbovirus diseases. However, control by genetic modifications to reduce mosquito populations or create mosquitoes that are refractory to infection with pathogens are less developed. The advent of CRISPR-Cas9-mediated gene drives may advance this mechanism of control. In this review, use and progress of gene drives for vector control, particularly for malaria, is discussed. A brief history of population suppression and replacement gene drives in mosquitoes, rapid advancement of the field over the last decade and how genetic modification fits into the current scope of vector control are described. Mechanisms of alternative vector control by genetic modification to modulate mosquitoes’ immune responses and anti-parasite effector molecules as part of a combinational strategy to combat malaria are considered. Finally, the limitations and ethics of using gene drives for mosquito control are discussed.
Thermo-adaptive interfacial solar evaporation enhanced by dynamic water gating
Authors: Wang Yi , Zhao Weinan , Lee Yebin , Li Yuning , Wang Zuankai , Tam Kam Chiu
Published: July 2024

Solar-driven evaporation offers a sustainable solution for water purification, but efficiency losses due to heat dissipation and fouling limit its scalability. Herein, we present a bilayer-structured solar evaporator (SDWE) with dynamic fluidic flow mechanism, designed to ensure a thin water supply and self-cleaning capability. The porous polydopamine (PDA) layer on a nickel skeleton provides photothermal functionality and water microchannels, while the thermo-responsive sporopollenin layer on the bottom acts as a switchable water gate. Using confocal laser microscopy and micro-CT, we demonstrate that this unique structure ensures a steady supply of thin water layers, enhancing evaporation by minimizing latent heat at high temperatures. Additionally, the system initiates a self-cleaning process through bulk water convection when temperature drops due to salt accumulation, thus maintaining increased evaporation efficiency. Therefore, the optimized p-SDWE sample achieved a high evaporation rate of 3.58 kg m−2 h−1 using 93.9% solar energy from 1 sun irradiation, and produces 18–22 liters of purified water per square meter of SDWE per day from brine water. This dynamic water transport mechanism surpasses traditional day-night cycles, offering inherent thermal adaptability for continuous, high-efficiency evaporation.
Expanding N-glycopeptide identifications by modeling fragmentation, elution, and glycome connectivity
Authors: Klein Joshua , Carvalho Luis , Zaia Joseph
Published: July 2024

Accurate glycopeptide identification in mass spectrometry-based glycoproteomics is a challenging problem at scale. Recent innovation has been made in increasing the scope and accuracy of glycopeptide identifications, with more precise uncertainty estimates for each part of the structure. We present a dynamically adapting relative retention time model for detecting and correcting ambiguous glycan assignments that are difficult to detect from fragmentation alone, a layered approach to glycopeptide fragmentation modeling that improves N-glycopeptide identification in samples without compromising identification quality, and a site-specific method to increase the depth of the glycoproteome confidently identifiable even further. We demonstrate our techniques on a set of previously published datasets, showing the performance gains at each stage of optimization. These techniques are provided in the open-source glycomics and glycoproteomics platform GlycReSoft available at https://github.com/mobiusklein/glycresoft.
Elastocaloric, barocaloric and magnetocaloric effects in spin crossover polymer composite films
Authors: Lünser Klara , Kavak Eyüp , Gürpinar Kübra , Emre Baris , Atakol Orhan , Stern-Taulats Enric , Porta Marcel , Planes Antoni , Lloveras Pol , Tamarit Josep-Lluís , Mañosa Lluís
Published: July 2024

Giant barocaloric effects were recently reported for spin-crossover materials. The volume change in these materials suggests that the transition can be influenced by uniaxial stress, and give rise to giant elastocaloric properties. However, no measurements of the elastocaloric properties in these compounds have been reported so far. Here, we demonstrated the existence of elastocaloric effects associated with the spin-crossover transition. We dissolved particles of ([Fe(L)2](BF4)2, [L=2,6di(pyrazol-1-yl)pyridine]) into a polymeric matrix. We showed that the application of tensile uniaxial stress to a composite film resulted in a significant elastocaloric effect. The elastocaloric effect in this compound required lower applied stress than for other prototype elastocaloric materials. Additionally, this phenomenon occurred for low values of strain, leading to coefficient of performance of the material being one order of magnitude larger than that of other elastocaloric materials. We believe that spin-crossover materials are a good alternative to be implemented in eco-friendly refrigerators based on elastocaloric effects.
Interneuron diversity in the human dorsal striatum
Authors: Garma Leonardo D. , Harder Lisbeth , Barba-Reyes Juan M. , Marco Salas Sergio , Díez-Salguero Mónica , Nilsson Mats , Serrano-Pozo Alberto , Hyman Bradley T. , Muñoz-Manchado Ana B.
Published: July 2024

Deciphering the striatal interneuron diversity is key to understanding the basal ganglia circuit and to untangling the complex neurological and psychiatric diseases affecting this brain structure. We performed snRNA-seq and spatial transcriptomics of postmortem human caudate nucleus and putamen samples to elucidate the diversity and abundance of interneuron populations and their inherent transcriptional structure in the human dorsal striatum. We propose a comprehensive taxonomy of striatal interneurons with eight main classes and fourteen subclasses, providing their full transcriptomic identity and spatial expression profile as well as additional quantitative FISH validation for specific populations. We have also delineated the correspondence of our taxonomy with previous standardized classifications and shown the main transcriptomic and class abundance differences between caudate nucleus and putamen. Notably, based on key functional genes such as ion channels and synaptic receptors, we found matching known mouse interneuron populations for the most abundant populations, the recently described PTHLH and TAC3 interneurons. Finally, we were able to integrate other published datasets with ours, supporting the generalizability of this harmonized taxonomy.
C-JUN overexpressing CAR-T cells in acute myeloid leukemia: preclinical characterization and phase I trial
Authors: Zuo Shiyu , Li Chuo , Sun Xiaolei , Deng Biping , Zhang Yibing , Han Yajing , Ling Zhuojun , Xu Jinlong , Duan Jiajia , Wang Zelin , Yu Xinjian , Zheng Qinlong , Xu Xiuwen , Zong Jiao , Tian Zhenglong , Shan Lingling , Tang Kaiting , Huang Huifang , Song Yanzhi , Niu Qing , Zhou Dongming , Feng Sizhou , Han Zhongchao , Wang Guoling , Wu Tong , Pan Jing , Feng Xiaoming
Published: July 2024

Chimeric antigen receptor (CAR) T cells show suboptimal efficacy in acute myeloid leukemia (AML). We find that CAR T cells exposed to myeloid leukemia show impaired activation and cytolytic function, accompanied by impaired antigen receptor downstream calcium, ZAP70, ERK, and C-JUN signaling, compared to those exposed to B-cell leukemia. These defects are caused in part by the high expression of CD155 by AML. Overexpressing C-JUN, but not other antigen receptor downstream components, maximally restores anti-tumor function. C-JUN overexpression increases costimulatory molecules and cytokines through reinvigoration of ERK or transcriptional activation, independent of anti-exhaustion. We conduct an open-label, non-randomized, single-arm, phase I trial of C-JUN-overexpressing CAR-T in AML (NCT04835519) with safety and efficacy as primary and secondary endpoints, respectively. Of the four patients treated, one has grade 4 (dose-limiting toxicity) and three have grade 1–2 cytokine release syndrome. Two patients have no detectable bone marrow blasts and one patient has blast reduction after treatment. Thus, overexpressing C-JUN endows CAR-T efficacy in AML.
Engineering interfacial sulfur migration in transition-metal sulfide enables low overpotential for durable hydrogen evolution in seawater
Authors: Li Min , Li Hong , Fan Hefei , Liu Qianfeng , Yan Zhao , Wang Aiqin , Yang Bing , Wang Erdong
Published: July 2024

Hydrogen production from seawater remains challenging due to the deactivation of the hydrogen evolution reaction (HER) electrode under high current density. To overcome the activity-stability trade-offs in transition-metal sulfides, we propose a strategy to engineer sulfur migration by constructing a nickel-cobalt sulfides heterostructure with nitrogen-doped carbon shell encapsulation (CN@NiCoS) electrocatalyst. State-of-the-art ex situ/in situ characterizations and density functional theory calculations reveal the restructuring of the CN@NiCoS interface, clearly identifying dynamic sulfur migration. The NiCoS heterostructure stimulates sulfur migration by creating sulfur vacancies at the Ni3S2-Co9S8 heterointerface, while the migrated sulfur atoms are subsequently captured by the CN shell via strong C-S bond, preventing sulfide dissolution into alkaline electrolyte. Remarkably, the dynamically formed sulfur-doped CN shell and sulfur vacancies pairing sites significantly enhances HER activity by altering the d-band center near Fermi level, resulting in a low overpotential of 4.6 and 8 mV at 10 mA cm−2 in alkaline freshwater and seawater media, and long-term stability up to 1000 h. This work thus provides a guidance for the design of high-performance HER electrocatalyst by engineering interfacial atomic migration.
Dopamine-mediated interactions between short- and long-term memory dynamics
Authors: Huang Cheng , Luo Junjie , Woo Seung Je , Roitman Lucas A. , Li Jizhou , Pieribone Vincent A. , Kannan Madhuvanthi , Vasan Ganesh , Schnitzer Mark J.
Published: July 2024

In dynamic environments, animals make behavioural decisions on the basis of the innate valences of sensory cues and information learnt about these cues across multiple timescales1–3. However, it remains unclear how the innate valence of a sensory stimulus affects the acquisition of learnt valence information and subsequent memory dynamics. Here we show that in the Drosophila brain, interconnected short- and long-term memory units of the mushroom body jointly regulate memory through dopamine signals that encode innate and learnt sensory valences. By performing time-lapse in vivo voltage-imaging studies of neural spiking in more than 500 flies undergoing olfactory associative conditioning, we found that protocerebral posterior lateral 1 dopamine neurons (PPL1-DANs)4 heterogeneously and bidirectionally encode innate and learnt valences of punishment, reward and odour cues. During learning, these valence signals regulate memory storage and extinction in mushroom body output neurons (MBONs)5. During initial conditioning bouts, PPL1-γ1pedc and PPL1-γ2α′1 neurons control short-term memory formation, which weakens inhibitory feedback from MBON-γ1pedc>α/β to PPL1-α′2α2 and PPL1-α3. During further conditioning, this diminished feedback allows these two PPL1-DANs to encode the net innate plus learnt valence of the conditioned odour cue, which gates long-term memory formation. A computational model constrained by the fly connectome6,7 and our spiking data explains how dopamine signals mediate the circuit interactions between short- and long-term memory traces, yielding predictions that our experiments confirmed. Overall, the mushroom body achieves flexible learning through the integration of innate and learnt valences in parallel learning units sharing feedback interconnections. This hybrid physiological–anatomical mechanism may be a general means by which dopamine regulates memory dynamics in other species and brain structures, including the vertebrate basal ganglia.
Mitochondrial DNA mosaicism in normal human somatic cells
Authors: An Jisong , Nam Chang Hyun , Kim Ryul , Lee Yunah , Won Hyein , Park Seongyeol , Lee Won Hee , Park Hansol , Yoon Christopher J. , An Yohan , Kim Jie-Hyun , Jun Jong Kwan , Bae Jeong Mo , Shin Eui-Cheol , Kim Bun , Cha Yong Jun , Kwon Hyun Woo , Oh Ji Won , Park Jee Yoon , Kim Min Jung , Ju Young Seok
Published: July 2024

Somatic cells accumulate genomic alterations with age; however, our understanding of mitochondrial DNA (mtDNA) mosaicism remains limited. Here we investigated the genomes of 2,096 clones derived from three cell types across 31 donors, identifying 6,451 mtDNA variants with heteroplasmy levels of ≳0.3%. While the majority of these variants were unique to individual clones, suggesting stochastic acquisition with age, 409 variants (6%) were shared across multiple embryonic lineages, indicating their origin from heteroplasmy in fertilized eggs. The mutational spectrum exhibited replication-strand bias, implicating mtDNA replication as a major mutational process. We evaluated the mtDNA mutation rate (5.0 × 10−8 per base pair) and a turnover frequency of 10–20 per year, which are fundamental components shaping the landscape of mtDNA mosaicism over a lifetime. The expansion of mtDNA-truncating mutations toward homoplasmy was substantially suppressed. Our findings provide comprehensive insights into the origins, dynamics and functional consequences of mtDNA mosaicism in human somatic cells.
Chromosome-level genome assembly and annotation of xerophyte secretohalophyte Reaumuria soongarica
Authors: Song Miaomiao , Gong Wei , Tian Yunyun , Meng Yue , Huo Tingyu , Liu Yanan , Zhang Yeming , Dang Zhenhua
Published: July 2024

Reaumuria soongarica is a xerophytic shrub belonging to the Tamaricaceae family. The species is widely distributed in the deserts of Central Asia and is characterized by its remarkable adaptability to saline and barren desert environments. Using PacBio long-read sequencing and Hi-C technologies, we assembled a chromosome-level genome of R. soongarica. The genome assembly has a size of 1.28 Gb with a scaffold N50 of 116.15 Mb, and approximately 1.25 Gb sequences were anchored in 11 pseudo-chromosomes. A completeness assessment of the assembled genome revealed a BUSCO score of 97.5% and an LTR Assembly Index of 12.37. R. soongarica genome had approximately 60.07% repeat sequences. In total, 21,791 protein-coding genes were predicted, of which 95.64% were functionally annotated. This high-quality genome will serve as a foundation for studying the genomic evolution and adaptive mechanisms to arid-saline environments in R. soongarica, facilitating the exploration and utilization of its unique genetic resources.
The odour of an unfamiliar stressed or relaxed person affects dogs’ responses to a cognitive bias test
Authors: Parr-Cortes Z. , Müller C. T. , Talas L. , Mendl M. , Guest C. , Rooney N. J.
Published: July 2024

Dogs can discriminate stressed from non-stressed human odour samples, but the effect on their cognition is unstudied. Using a cognitive bias task, we tested how human odours affect dogs’ likelihood of approaching a food bowl placed at three ambiguous locations (“near-positive”, “middle” and “near-negative”) between trained “positive” (rewarded) and “negative” (unrewarded) locations. Using odour samples collected from three unfamiliar volunteers during stressful and relaxing activities, we tested eighteen dogs under three conditions: no odour, stress odour and relaxed odour, with the order of test odours counterbalanced across dogs. When exposed to stress odour during session three, dogs were significantly less likely to approach a bowl placed at one of the three ambiguous locations (near-negative) compared to no odour, indicating possible risk-reduction behaviours in response to the smell of human stress. Dogs’ learning of trained positive and negative locations improved with repeated testing and was significant between sessions two and three only when exposed to stress odour during session three, suggesting odour influenced learning. This is the first study to show that without visual or auditory cues, olfactory cues of human stress may affect dogs’ cognition and learning, which, if true, could have important consequences for dog welfare and working performance.
Biocompatibility, bioactivity, porosity, and sealer/dentin interface of bioceramic ready-to-use sealers using a dentin-tube model
Authors: Inada Rafaela Nanami Handa , Silva Evelin Carine Alves , Lopes Camila Soares , Queiroz Marcela Borsatto , Torres Fernanda Ferrari Esteves , da Silva Guilherme Ferreira , Cerri Paulo Sérgio , Guerreiro–Tanomaru Juliane Maria , Tanomaru-Filho Mário
Published: July 2024

This study evaluated the biocompatibility, bioactivity, porosity, and sealer/dentin interface of Sealer Plus BC (SP), Bio-C Sealer (BIOC), TotalFill BC Sealer (TF), and AH Plus (AHP). Dentin tubes filled with the sealers and empty tubes (control group) were implanted in the subcutaneous tissue of rats for different periods (n = 6 per group/period). Number of inflammatory cells (ICs), capsule thickness, von Kossa reaction, interleukin-6 (IL-6) and osteocalcin (OCN) were evaluated. Porosity and voids in the interface dentin/sealers were assessed by micro-computed tomography. The data were submitted to ANOVA/Tukey’s tests (α = 0.05). Greater capsule thickness, ICs and IL-6 immunolabeling cells were observed in AHP. No significant difference in thickness of capsule, ICs, and IL-6- immunolabeling cells was detected between SP and TF, in all periods, and after 30 and 60 days between all groups. At 60 days all groups had reduction in capsule thickness, ICs and IL-6 immunolabeling cells. Von Kossa-positive and birefringent structures were observed in the capsules around the sealers. BIOC, SP, and TF exhibited OCN-immunolabeling cells. All sealers had porosity values below 5%, besides low and similar interface voids. BIOC, SP and TF are biocompatible, bioactive, and have low porosity and voids. The dentin-tube model used is an alternative for evaluating bioceramic materials.
Impact of MRI radiomic feature normalization for prognostic modelling in uterine endometrial and cervical cancers
Authors: Hodneland Erlend , Andersen Erling , Wagner-Larsen Kari S. , Dybvik Julie A. , Lura Njål , Fasmer Kristine E. , Halle Mari K. , Krakstad Camilla , Haldorsen Ingfrid
Published: July 2024

Widespread clinical use of MRI radiomic tumor profiling for prognostication and treatment planning in cancers faces major obstacles due to limitations in standardization of radiomic features. The purpose of the current work was to assess the impact of different MRI scanning- and normalization protocols for the statistical analyses of tumor radiomic data in two patient cohorts with uterine endometrial-(EC) (n = 136) and cervical (CC) (n = 132) cancer. 1.5 T and 3 T, T1-weighted MRI 2 min post-contrast injection, T2-weighted turbo spin echo imaging, and diffusion-weighted imaging were acquired. Radiomic features were extracted from within manually segmented tumors in 3D and normalized either using z-score normalization or a linear regression model (LRM) accounting for linear dependencies with MRI acquisition parameters. Patients were clustered into two groups based on radiomic profile. Impact of MRI scanning parameters on cluster composition and prognostication were analyzed using Kruskal–Wallis tests, Kaplan–Meier plots, log-rank test, random survival forests and LASSO Cox regression with time-dependent area under curve (tdAUC) (α = 0.05). A large proportion of the radiomic features was statistically associated with MRI scanning protocol in both cohorts (EC: 162/385 [42%]; CC: 180/292 [62%]). A substantial number of EC (49/136 [36%]) and CC (50/132 [38%]) patients changed cluster when clustering was performed after z-score-versus LRM normalization. Prognostic modeling based on cluster groups yielded similar outputs for the two normalization methods in the EC/CC cohorts (log-rank test; z-score: p = 0.02/0.33; LRM: p = 0.01/0.45). Mean tdAUC for prognostic modeling of disease-specific survival (DSS) by the radiomic features in EC/CC was similar for the two normalization methods (random survival forests; z-score: mean tdAUC = 0.77/0.78; LRM: mean tdAUC = 0.80/0.75; LASSO Cox; z-score: mean tdAUC = 0.64/0.76; LRM: mean tdAUC = 0.76/0.75). Severe biases in tumor radiomics data due to MRI scanning parameters exist. Z-score normalization does not eliminate these biases, whereas LRM normalization effectively does. Still, radiomic cluster groups after z-score- and LRM normalization were similarly associated with DSS in EC and CC patients.
Enhanced hydrogen evolution reaction activity through samarium-doped nickel phosphide (Ni2P) electrocatalyst
Authors: Shahroudi Ali , Habibzadeh Sajjad
Published: July 2024

Hydrogen evolution reaction (HER) stands out among conventional hydrogen production processes by featuring excellent advantages. However, the uncompetitive production cost due to the low energy efficiency has hindered its development, necessitating the introduction of cost-effective electrocatalysts. In this study, we introduced samarium doping as a high-potential approach to improve the electrocatalytic properties of nickel phosphide (Ni2P) for efficient HER. Samarium-doped Ni2P was synthesized via a facile two-step vapor–solid reaction technique. Different physical and electrochemical analyses showed that samarium doping significantly improved pure Ni2P characteristics, such as particle size, specific surface area, electrochemical hydrogen adsorption, intrinsic activity, electrochemical active surface area, and charge transfer ability in favor of HER. Namely, Ni2P doped with 3%mol of samarium (Sm0.03Ni2P) with a Tafel slope of 67.8 mV/dec. and overpotential of 130.6 mV at a current density of 10 mA/cm2 in 1.0 M KOH solution exhibited a notable performance, suggesting Sm0.03Ni2P and samarium doping as a remarkable electrocatalyst and promising promoter for efficient HER process, respectively.
Identification of force chains in wet coal dust layer and the effect of porosity on three-body contact stiffness
Authors: Yang Xinwei , Wu Dongxuan , Bai Yangxi , Chen Hongyue , Wang Xin
Published: July 2024

Aiming at the three-body contact problem of mechanical rough surface containing wet coal dust interface, the three-body contact model of rough surface containing wet coal dust interface is constructed by comprehensively considering the contact deformation of rough surface and contact characteristics of wet coal dust, and based on the crushing theory. By analysing the contact force, load-bearing particle size and adjacent contact angle thresholds of the wet coal dust layer, the force chain identification criterion is formulated. Finally, quantitative calculations of the force chain characteristics are performed to reveal the effect of different initial porosities on the three-body contact stiffness, which is verified experimentally. The results of the study show that the average contact force of the wet coal dust layer can be used as the force chain contact force threshold, the average particle size can be used as the force chain particle size threshold, and the force chain angle threshold is determined by the particle coordination number. As the initial porosity decreases, the number, length and stiffness of force chains in the wet coal dust layer increase significantly, and the stiffness reaches a maximum value of 2.007 × 108 pa/m at the moment of downward pressure to stabilisation, while the trend of force chain bending varies in the opposite direction, and its minimum bending degree decreases to 20°. The maximum relative error between the simulation and experimental results of three-body contact stiffness is 9.64%, which proves the accuracy of the force chain identification criterion and the quantitative calculation of three-body contact stiffness by force chain.
MEDT analysis of mechanism and selectivities in non-catalyzed and lewis acid-catalyzed diels–alder reactions between R-carvone and isoprene
Authors: Idrissi Khadija El , Abdoul-Hakim Mohamed , Saleh Na’il , Garmes Hocine , Syed Asad , Ríos-Gutiérrez Mar , Paray Bilal Ahamad , Verma Meenakshi , Zeroual Abdellah , Domingo Luis R.
Published: July 2024

Within the context of Molecular Electronic Density Theory (MEDT), this study investigates the Diels–Alder reaction among isoprene (2) and R-carvone (1R) applying DFT simulations, with and without Lewis acid (LA) catalysis. The results show that carvone (1R) acts as an electrophile and isoprene (2) as a nucleophile in a polar process. LA catalysis increases the electrophilicity of carvone, thereby improving the reactivity and selectivity of the reaction by reducing the activation Gibbs free energy. Parr functions reveal that the C5=C6 double bond is more reactive than the C9=C10 double bond, indicating chemoselectivity. The examination of the Electron Localization Function (ELF) reveals high regio- and stereoselectivity, indicating an asynchronous mechanism for the LA-catalyzed DA reaction. Furthermore, it is suggested that cycloadduct 3 has great anti-HIV potential because it exhibits lower binding energies than azidothymidine (AZT) in the docking studies of cycloadducts 3 and 4 amongst a primary HIV-1protein (1A8O plus 5W4Q).
T4 DNA polymerase prevents deleterious on-target DNA damage and enhances precise CRISPR editing
Authors: Yang Qiaoyan , Abebe Jonathan S , Mai Michelle , Rudy Gabriella , Kim Sang Y , Devinsky Orrin , Long Chengzu
Published: July 2024

Unintended on-target chromosomal alterations induced by CRISPR/Cas9 in mammalian cells are common, particularly large deletions and chromosomal translocations, and present a safety challenge for genome editing. Thus, there is still an unmet need to develop safer and more efficient editing tools. We screened diverse DNA polymerases of distinct origins and identified a T4 DNA polymerase derived from phage T4 that strongly prevents undesired on-target damage while increasing the proportion of precise 1- to 2-base-pair insertions generated during CRISPR/Cas9 editing (termed CasPlus). CasPlus induced substantially fewer on-target large deletions while increasing the efficiency of correcting common frameshift mutations in DMD and restored higher level of dystrophin expression than Cas9-alone in human cardiomyocytes. Moreover, CasPlus greatly reduced the frequency of on-target large deletions during mouse germline editing. In multiplexed guide RNAs mediating gene editing, CasPlus repressed chromosomal translocations while maintaining gene disruption efficiency that was higher or comparable to Cas9 in primary human T cells. Therefore, CasPlus offers a safer and more efficient gene editing strategy to treat pathogenic variants or to introduce genetic modifications in human applications.
CMG helicase disassembly is essential and driven by two pathways in budding yeast
Authors: Polo Rivera Cristian , Deegan Tom D , Labib Karim P M
Published: July 2024

The CMG helicase is the stable core of the eukaryotic replisome and is ubiquitylated and disassembled during DNA replication termination. Fungi and animals use different enzymes to ubiquitylate the Mcm7 subunit of CMG, suggesting that CMG ubiquitylation arose repeatedly during eukaryotic evolution. Until now, it was unclear whether cells also have ubiquitin-independent pathways for helicase disassembly and whether CMG disassembly is essential for cell viability. Using reconstituted assays with budding yeast CMG, we generated the mcm7-10R allele that compromises ubiquitylation by SCFDia2. mcm7-10R delays helicase disassembly in vivo, driving genome instability in the next cell cycle. These data indicate that defective CMG ubiquitylation explains the major phenotypes of cells lacking Dia2. Notably, the viability of mcm7-10R and dia2∆ is dependent upon the related Rrm3 and Pif1 DNA helicases that have orthologues in all eukaryotes. We show that Rrm3 acts during S-phase to disassemble old CMG complexes from the previous cell cycle. These findings indicate that CMG disassembly is essential in yeast cells and suggest that Pif1-family helicases might have mediated CMG disassembly in ancestral eukaryotes.
A common mechanism for recruiting the Rrm3 and RTEL1 accessory helicases to the eukaryotic replisome
Authors: Olson Ottavia , Pelliciari Simone , Heron Emma D , Deegan Tom D
Published: July 2024

The eukaryotic replisome is assembled around the CMG (CDC45-MCM-GINS) replicative helicase, which encircles the leading-strand DNA template at replication forks. When CMG stalls during DNA replication termination, or at barriers such as DNA-protein crosslinks on the leading strand template, a second helicase is deployed on the lagging strand template to support replisome progression. How these ‘accessory’ helicases are targeted to the replisome to mediate barrier bypass and replication termination remains unknown. Here, by combining AlphaFold structural modelling with experimental validation, we show that the budding yeast Rrm3 accessory helicase contains two Short Linear Interaction Motifs (SLIMs) in its disordered N-terminus, which interact with CMG and the leading-strand DNA polymerase Polε on one side of the replisome. This flexible tether positions Rrm3 adjacent to the lagging strand template on which it translocates, and is critical for replication termination in vitro and Rrm3 function in vivo. The primary accessory helicase in metazoa, RTEL1, is evolutionarily unrelated to Rrm3, but binds to CMG and Polε in an analogous manner, revealing a conserved docking mechanism for accessory helicases in the eukaryotic replisome.
Dengue virus preferentially uses human and mosquito non-optimal codons
Authors: Castellano Luciana A , McNamara Ryan J , Pallarés Horacio M , Gamarnik Andrea V , Alvarez Diego E , Bazzini Ariel A
Published: July 2024

Codon optimality refers to the effect that codon composition has on messenger RNA (mRNA) stability and translation level and implies that synonymous codons are not silent from a regulatory point of view. Here, we investigated the adaptation of virus genomes to the host optimality code using mosquito-borne dengue virus (DENV) as a model. We demonstrated that codon optimality exists in mosquito cells and showed that DENV preferentially uses nonoptimal (destabilizing) codons and avoids codons that are defined as optimal (stabilizing) in either human or mosquito cells. Human genes enriched in the codons preferentially and frequently used by DENV are upregulated during infection, and so is the tRNA decoding the nonoptimal and DENV preferentially used codon for arginine. We found that adaptation during single-host passaging in human or mosquito cells results in the selection of synonymous mutations towards DENV’s preferred nonoptimal codons that increase virus fitness. Finally, our analyses revealed that hundreds of viruses preferentially use nonoptimal codons, with those infecting a single host displaying an even stronger bias, suggesting that host–pathogen interaction shapes virus-synonymous codon choice.
Digital light processing (DLP) 3D printing of polymer networks comprising virus-like particles
Authors: Sadaba Naroa , Bayón Jorge Leganés , Nelson Alshakim , Steinmetz Nicole F.
Published: July 2024

In this work, we introduce a 3D-printable virus-like particle (VLP)-enhanced cross-linked biopolymer system.
Theoretical study on the photophysical properties of thiophene-fused-type BODIPY series molecules in fluorescence imaging and photodynamic therapy
Authors: Cao Jianfang , Chen Xinyu , Ma Xue , Zhang Tianci , Sun Wen
Published: July 2024

DFT reveals that the thiophene ring reduces ΔEST, while weak electron-donating substituents at meso-position of thieno-fused BODIPYs and electron-withdrawing groups at para-position of the phenyl ring in thieno-pyrrole-fused BODIPYs favor ISC.
Two-dimensional Cu-doped G/h-BN/G heterostructures for highly sensitive gas detection: an ab initio study
Authors: Shamsi Alireza
Published: July 2024

Two-dimensional materials like graphene and h-BN have drawn significant interest for gas sensing applications due to their high surface-to-volume ratio and exceptional physical properties.
An ensemble variational quantum algorithm for non-Markovian quantum dynamics
Authors: Walters Peter L. , Tsakanikas Joachim , Wang Fei
Published: July 2024

A variational quantum algorithm is developed for non-Markovian quantum dynamics simulations on a NISQ device.
The fundamental vibrational frequencies and spectroscopic constants of the C2O2H2 isomers: molecules known in simulated interstellar ice analogues
Authors: Watrous Alexandria G. , Fortenberry Ryan C.
Published: July 2024

The full set of rovibrational spectral data has been generated for the five lowest-energy isomers of C2O2H2.
Design, synthesis, and applications of plasmonic semiconductor WO3−x photocatalyst
Authors: Dimple  , Priyanka  , Watanabe Ryo , Fukuhara Choji , Yamashita Hiromi , Verma Priyanka
Published: July 2024

Different synthesis and characterization techniques for WO3−x photocatalysts and recent developments in the application of visible-NIR mediated transformation reactions.
Fabrication of bimetallic MOF-74 derived materials for high-efficiency adsorption of iodine
Authors: Li Wen-Ze , Guo Fu-Yu , Li Jing , Zhang Xiao-Sa , Liu Yu , Luan Jian
Published: July 2024

A series of carbon materials derived from bimetallic MOF-74 prepared by the reflux method were obtained by pyrolysis at high temperature. The structure and iodine adsorption properties of the materials were studied in detail.
A highly efficient in situ redox stabilization strategy for Am–Cm separation using AgBiO3
Authors: Verma Parveen K. , Bhattacharyya Arunasis , Samanta Soumen , Mohapatra Prasanta K.
Published: July 2024

AgBiO3 is reported for the exclusive oxidation of Am3+ → AmO2+ at near-neutral pH conditions at 25 °C. Single-contact Am–Eu and Am–Cm separation with a S.F. >104 was achieved, which is unprecedented in aqueous feed solutions.
Multimodal nanoparticle analysis enabled by a polymer electrolyte nanopore combined with nanoimpact electrochemistry
Authors: Gyasi Agyemang Eugene , Confederat Samuel , Mohanan Gayathri , Azimzadeh Sani Mahnaz , Chau Chalmers , Charnock Dylan , Wälti Christoph , Tschulik Kristina , Edwards Martin Andrew , Actis Paolo
Published: July 2024

We demonstrate the multimodal analysis of a nanoparticle sample by coupling a polymer electrolyte nanopore sensor with nanoimpact electrochemistry and validate the experimental results with a numerical model.
Correction: Beyond Newton's law of cooling in evaluating magnetic hyperthermia performance: a device-independent procedure
Authors: Ruta Sergiu , Fernández-Afonso Yilian , Rannala Samuel E. , Morales M. Puerto , Veintemillas-Verdaguer Sabino , Jones Carlton , Gutiérrez Lucía , Chantrell Roy W. , Serantes David
Published: July 2024

Correction for ‘Beyond Newton's law of cooling in evaluating magnetic hyperthermia performance: a device-independent procedure’ by Sergiu Ruta et al., Nanoscale Adv., 2024, https://doi.org/10.1039/d4na00383g.
Platinum-based chemotherapy: trends in organic nanodelivery systems
Authors: Santos João A. V. , Silva Daniela , Marques Maria Paula M. , Batista de Carvalho Luís A. E.
Published: July 2024

This review explores organic nanodelivery systems in the development of platinum-based anticancer treatments, highlighting benefits, challenges, and potential for groundbreaking therapies.
Copper-catalyzed aerobic annulation of hydrazones with dienones: an efficient route to pyrazole-linked hybrid molecules
Authors: Nayak Kalinga H. , Jijin Robert K. , Sreelekha Mariswamy K. , Babu Beneesh P.
Published: July 2024

A two-step method to synthesize functionalized pyrazole–aziridine, pyrazole–pyrazoline and pyrazole–pyridine hybrids is reported under aerobic copper catalysis using abundant and cost-effective hydrazones and dibenzylideneacetones.
Iodine/Oxone® oxidative system for the synthesis of selenylindoles bearing a benzenesulfonamide moiety as carbonic anhydrase I, II, IX, and XII inhibitors
Authors: Palomba Martina , Angeli Andrea , Galdini Riccardo , Hughineata Alexandra Joana , Perin Gelson , Lenardão Eder João , Marini Francesca , Santi Claudio , Supuran Claudiu T. , Bagnoli Luana
Published: July 2024

An eco-friendly approach that uses Oxone as the oxidant and iodine as the catalyst generates 3-selenelylindoles. Novel derivatives containing a benzenesulfonamide moiety were tested as human carbonic anhydrase I, II, IX and XII inhibitors.
Modelling the elusive conformational activation in kynurenine 3-monooxygenase
Authors: Özkılıç Yılmaz , Stein Matthias
Published: July 2024

Non-equilibrium MD simulations with extensive and multi-dimensional umbrella sampling are used to model the conformational activation step in apo-KMO and inhibitor-KMO complexes.
Correction and removal of expression of concern: Palladium supported on mixed-metal–organic framework (Co–Mn-MOF-74) for efficient catalytic oxidation of CO
Authors: Salama Reda S. , Mannaa Mohammed A. , Altass Hatem M. , Ibrahim Amr Awad , El-Rahman S. Khder Abd
Published: July 2024

Correction and removal of expression of concern for ‘Palladium supported on mixed-metal–organic framework (Co–Mn-MOF-74) for efficient catalytic oxidation of CO’ by Reda S. Salama et al., RSC Adv., 2021, 11, 4318–4326, https://doi.org/10.1039/D0RA09970H.
A novel NIR fluorescent probe for copper(ii) imaging in Parkinson's disease mouse brain
Authors: Chen Jianmei , Luo Rongqing , Li Shuang , Shao Jinping , Wang Ting , Xie Shumei , Xu Li , You Qiuyun , Feng Shumin , Feng Guoqiang
Published: July 2024

A NIR fluorescent probe (DDAO-Cu), capable of crossing the blood–brain barrier, revealed that Cu2+ was enriched in the cortex, hippocampus, and striatum during the advanced stages of Parkinson's disease, but suppressed in the substantia nigra region.
Do tunneling nanotubes drive chemoresistance in solid tumors and other malignancies?
Authors: Sarkari Akshat , Lou Emil
Published: July 2024

Intercellular communication within the tumor microenvironment (TME) is essential for establishing, mediating, and synchronizing cancer cell invasion and metastasis. Cancer cells, individually and collectively, react at the cellular and molecular levels to insults from standard-of-care treatments used to treat patients with cancer. One form of cell communication that serves as a prime example of cellular phenotypic stress response is a type of cellular protrusion called tunneling nanotubes (TNTs). TNTs are ultrafine, actin-enriched contact-dependent forms of membrane protrusions that facilitate long distance cell communication through transfer of various cargo, including genetic materials, mitochondria, proteins, ions, and various other molecules. In the past 5–10 years, there has been a growing body of evidence that implicates TNTs as a novel mechanism of cell-cell communication in cancer that facilitates and propagates factors that drive or enhance chemotherapeutic resistance in a variety of cancer cell types. Notably, recent literature has highlighted the potential of TNTs to serve as cellular conduits and mediators of drug and nanoparticle delivery. Given that TNTs have also been shown to form in vivo in a variety of tumor types, disrupting TNT communication within the TME provides a novel strategy for enhancing the cytotoxic effect of existing chemotherapies while suppressing this form of cellular stress response. In this review, we examine current understanding of interplay between cancer cells occurring via TNTs, and even further, the implications of TNT-mediated tumor-stromal cross-talk and the potential to enhance chemoresistance. We then examine tumor microtubes, an analogous cell protrusion heavily implicated in mediating treatment resistance in glioblastoma multiforme, and end with a brief discussion of the effects of radiation and other emerging treatment modalities on TNT formation.