bluuebunny/crossref_metadata_2025 huggingface dataset:
Gravity‐Driven Jointing in Layered Rocks: Mechanical Analysis and Numerical Modeling
Authors: Chemenda A. I.
Published: May 2024

The origin of open‐mode fractures or joints, common in sedimentary basins (reservoirs), remains incompletely understood. These fractures require effective tensile stress for their formation, yet they usually develop at depths where effective compressive stresses dominate. Through 2‐D finite‐difference elastoplastic modeling, we demonstrate that effective tensile stresses and fracturing can be internally generated in stiff competent layers separated by compliant incompetent layers. Two primary factors drive this phenomenon: the layered structure of sedimentary units with varying mechanical properties of the layers and the lithostatic compression of the unit, leading to its gravity‐driven horizontal widening or stretching. This stretching occurs when the average horizontal stress over the unit’s thickness is compressive. Various mechanisms can accommodate the stretching, including preexisting faults or weak zones, free borders like canyons, and horizontal extension of tectonic or gravitational origin. Tensile horizontal effective stresses σxx occur within the competent layers, while the incompetent layers generally remain under effective compression. The magnitude of σxx increases with the lithostatic stress or burial depth, as does the tensile strength σt of incompletely lithified sediments. Jointing occurs within depth intervals where |σxx| > σt. In our modeling approach, effective tensile stresses σxx are generated due to lithostatic compression σv. In the previous numerical modeling studies, these stresses resulted from extension directly applied to the lateral boundaries of the layers and did not depend on σv. We provide an analysis of the distinctions between these two approaches.
Why Does Extreme Precipitation Occur in Borneo During Both El Niño and La Niña Winters?
Authors: Zhang Wen‐Jun , Wu Renguang , Dai Panxi , Yeh Sang‐Wook
Published: May 2024

Extreme precipitation over the Maritime Continent (MC) is not only vital for local livelihoods, but also influences atmospheric circulation in tropical and extra‐tropical regions. The warm (cold) phase of El Niño‐Southern Oscillation usually leads to dry (wet) condition around the MC in boreal winter. This study unravels that extreme precipitation occurs in Borneo during both El Niño and La Niña winters. Extreme precipitation in Borneo is associated with tripole and dipole anomalous vertical motion pattern, respectively, over the MC‐tropical Pacific in El Niño and La Niña years. A parallel analysis reveals that weak precipitation in Borneo in El Niño and La Niña years occurs with dipole and tripole anomalous vertical motion pattern, respectively, over the MC‐tropical Pacific. The amplitude of the equatorial central‐eastern Pacific sea surface temperature (SST) anomalies may be a factor in the change of anomalous vertical motion pattern over the MC‐tropical Pacific. Further analysis identifies a tendency of extreme precipitation in late December to early−mid January and weak precipitation in February in Borneo. This suggests a critical role of seasonal change in the eastern equatorial Pacific SST in the occurrence of extreme precipitation in Borneo.
4D Electrical Resistivity Imaging of Stress Perturbations Induced During High‐Pressure Shear Stimulation Tests
Authors: Johnson T. C. , Burghardt J. , Strickland C. , Sirota D. , Vermeul V. , Knox H. , Schwering P. , Blankenship D. , Kneafsey T. ,   the EGS Collab Team
Published: May 2024

Fluid flow through fractured media is typically governed by the distribution of fracture apertures, which are in turn governed by stress. Consequently, understanding subsurface stress is critical for understanding and predicting subsurface fluid flow. Although laboratory‐scale studies have established a sensitive relationship between effective stress and bulk electrical conductivity in crystalline rock, that relationship has not been extensively leveraged to monitor stress evolution at the field scale using electrical or electromagnetic geophysical monitoring approaches. In this paper we demonstrate the use time‐lapse 3‐dimensional (4D) electrical resistivity tomography to image perturbations in the stress field generated by pressurized borehole packers deployed during shear‐stimulation attempts in a 1.25 km deep metamorphic crystalline rock formation.
CMIP6 Models Rarely Simulate Antarctic Winter Sea‐Ice Anomalies as Large as Observed in 2023
Authors: Diamond Rachel , Sime Louise C. , Holmes Caroline R. , Schroeder David
Published: May 2024

In 2023, Antarctic sea‐ice extent (SIE) reached record lows, with winter SIE falling to 2.5Mkm2 below the satellite era average. With this multi‐model study, we investigate the occurrence of anomalies of this magnitude in latest‐generation global climate models. When these anomalies occur, SIE takes decades to recover: this indicates that SIE may transition to a new, lower, state over the next few decades. Under internal variability alone, models are extremely unlikely to simulate these anomalies, with return period >1000 years for most models. The only models with return period <1000 years for these anomalies have likely unrealistically large interannual variability. Based on extreme value theory, the return period is reduced from 2650 years under internal variability to 580 years under a strong climate change forcing scenario.
Thank You to Our 2023 Peer Reviewers
Authors: Griffies Stephen M. , Fan Jiwen , Huang Yuanyuan , MacBean Natasha , Schneider Tapio
Published: May 2024

Plain Language Summary

The editors of Journal of Advances in Modeling Earth Systems thank the 919 reviewers who provided 1,413 reviews during 2023. Their hard work, done anonymously, benefits authors, and readers.
Reg4 deficiency aggravates pancreatitis by increasing mitochondrial cell death and fibrosis
Authors: Yan Weihui , Wang Ying , Lu Ying , Peng Shicheng , Wu Bo , Cai Wei , Xiao Yongtao
Published: May 2024

Regenerating gene family member 4 (Reg4) has been implicated in acute pancreatitis, but its precise functions and involved mechanisms have remained unclear. Herein, we sought to investigate the contribution of Reg4 to the pathogenesis of pancreatitis and evaluate its therapeutic effects in experimental pancreatitis. In acute pancreatitis, Reg4 deletion increases inflammatory infiltrates and mitochondrial cell death and decreases autophagy recovery, which are rescued by the administration of recombinant Reg4 (rReg4) protein. In chronic pancreatitis, Reg4 deficiency aggravates inflammation and fibrosis and inhibits compensatory cell proliferation. Moreover, C-X-C motif ligand 12 (CXCL12)/C-X-C motif receptor 4 (CXCR4) axis is sustained and activated in Reg4-deficient pancreas. The detrimental effects of Reg4 deletion are attenuated by the administration of the approved CXCR4 antagonist plerixafor (AMD3100). Mechanistically, Reg4 mediates its function in pancreatitis potentially via binding its receptor exostosin-like glycosyltransferase 3 (Extl3). In conclusion, our findings suggest that Reg4 exerts a therapeutic effect during pancreatitis by limiting inflammation and fibrosis and improving cellular regeneration.
The role of USP7-YY1 interaction in promoting colorectal cancer growth and metastasis
Authors: Shao Zhi-Ying , Yang Wen-Dong , Qiu Hui , He Zhi-Hong , Lu Meng-Ru , Shen Qi , Ding Jin , Zheng Jun-Nian , Bai Jin
Published: May 2024

Colorectal cancer (CRC) remains a significant global health issue with high incidence and mortality. Yin Yang 1 (YY1) is a powerful transcription factor that acts dual roles in gene activation and repression. High expression level of YY1 has been reported in CRC, indicating the existence of stable factors of YY1 in CRC cells. We aimed to identify the key molecules and underlying mechanisms responsible for stabilizing YY1 expression in CRC. Mass spectrometry analysis was utilized to identify USP7 as a potential molecule that interacted with YY1. Mechanically, USP7 stabilizes YY1 expression at the protein level by interfering its K63 linkage ubiquitination. YY1 exerts its oncogenic function through transcriptionally activating TRIAP1 but suppressing LC3B. In addition, at the pathological level, there is a positive correlation between the expression of YY1 and the budding of CRC. This study has revealed the intricate interplay between YY1 and USP7 in CRC, suggesting that they could serve as novel therapeutic targets or predictive biomarkers for CRC patients.
Simultaneous rift-scale inflation of a deep crustal sill network in Afar, East Africa
Authors: La Rosa A. , Pagli C. , Wang H. , Sigmundsson F. , Pinel V. , Keir D.
Published: May 2024

Decades of studies at divergent plate margins have revealed networks of magmatic sills at the crust-mantle boundary. However, a lack of direct observations of deep magma motion limits our understanding of magma inflow from the mantle into the lower crust and the mechanism of sill formation. Here, satellite geodesy reveals rift-scale deformation caused by magma inflow in the deep crust in the Afar rift (East Africa). Simultaneous inflation of four sills, laterally separated by 10s of km and at depths ranging 9–28 km, caused uplift across a ~ 100-km-wide zone, suggesting the sills are linked to a common mantle source. Our results show the supply of magma into the lower crust is temporally episodic, occurring across a network of sills. This process reflects inherent instability of melt migration through porous mantle flow and may be the fundamental process that builds the thick igneous crust beneath magmatic rifts and rifted margins globally.
Mitoribosome structure with cofactors and modifications reveals mechanism of ligand binding and interactions with L1 stalk
Authors: Singh Vivek , Itoh Yuzuru , Del’Olio Samuel , Hassan Asem , Naschberger Andreas , Flygaard Rasmus Kock , Nobe Yuko , Izumikawa Keiichi , Aibara Shintaro , Andréll Juni , Whitford Paul C. , Barrientos Antoni , Taoka Masato , Amunts Alexey
Published: May 2024

The mitoribosome translates mitochondrial mRNAs and regulates energy conversion that is a signature of aerobic life forms. We present a 2.2 Å resolution structure of human mitoribosome together with validated mitoribosomal RNA (rRNA) modifications, including aminoacylated CP-tRNAVal. The structure shows how mitoribosomal proteins stabilise binding of mRNA and tRNA helping to align it in the decoding center, whereas the GDP-bound mS29 stabilizes intersubunit communication. Comparison between different states, with respect to tRNA position, allowed us to characterize a non-canonical L1 stalk, and molecular dynamics simulations revealed how it facilitates tRNA transitions in a way that does not require interactions with rRNA. We also report functionally important polyamines that are depleted when cells are subjected to an antibiotic treatment. The structural, biochemical, and computational data illuminate the principal functional components of the translation mechanism in mitochondria and provide a description of the structure and function of the human mitoribosome.
Functionality of chimeric TssA proteins in the type VI secretion system reveals sheath docking specificity within their N-terminal domains
Authors: Fecht Selina , Paracuellos Patricia , Subramoni Sujatha , Tan Casandra Ai Zhu , Ilangovan Aravindan , Costa Tiago R. D. , Filloux Alain
Published: May 2024

The genome of Pseudomonas aeruginosa encodes three type VI secretion systems, each comprising a dozen distinct proteins, which deliver toxins upon T6SS sheath contraction. The least conserved T6SS component, TssA, has variations in size which influence domain organisation and structure. Here we show that the TssA Nt1 domain interacts directly with the sheath in a specific manner, while the C-terminus is essential for oligomerisation. We built chimeric TssA proteins by swapping C-termini and showed that these can be functional even when made of domains from different TssA sub-groups. Functional specificity requires the Nt1 domain, while the origin of the C-terminal domain is more permissive for T6SS function. We identify two regions in short TssA proteins, loop and hairpin, that contribute to sheath binding. We propose a docking mechanism of TssA proteins with the sheath, and a model for how sheath assembly is coordinated by TssA proteins from this position.
Cytomegalovirus drives Vδ1+ γδ T cell expansion and clonality in common variable immunodeficiency
Authors: Chan Samantha , Morgan Benjamin , Yong Michelle K. , Margetts Mai , Farchione Anthony J. , Lucas Erin C. , Godsell Jack , Giang Nhi Ai , Slade Charlotte A. , von Borstel Anouk , Bryant Vanessa L. , Howson Lauren J.
Published: May 2024

The function and phenotype of γδ T cells in the context of common variable immunodeficiency (CVID) has not been explored. CVID is a primary immunodeficiency disorder characterized by impaired antibody responses resulting in increased susceptibility to infections. γδ T cells are a subset of unconventional T cells that play crucial roles in host defence against infections. In this study, we aim to determine the roles and functions of γδ T cells in CVID. We observe a higher frequency of Vδ1+ γδ T cells compared to healthy controls, particularly in older patients. We also find a higher proportion of effector-memory Vδ1+ γδ T cells and a more clonal T cell receptor (TCR) repertoire in CVID. The most significant driver of the Vδ1+ γδ T cell expansion and phenotype in CVID patients is persistent cytomegalovirus (CMV) viremia. These findings provide valuable insights into γδ T cell biology and their contribution to immune defence in CVID.
Efficacy of empirical Ciprofloxacin or Cefixime plus Metronidazole therapy for the treatment of liver abscess: a randomized control clinical trial
Authors: Priya G Lakshmi , Dhibar Deba Prasad , Saroch Atul , Sharma Navneet , Sharma Vishal , Verma Nipun , Chaluvashetty Sreedhara Bettadahally , Prakash Ajay , Kaur Harsimran
Published: May 2024

Liver abscess is a potentially life-threatening medical emergency. Prompt empirical antimicrobial with or without percutaneous aspiration or drainage is therapeutic. The rational for using empirical intravenous broad-spectrum antimicrobials upfront instead of oral Fluoroquinolone or Cephalosporin is contentious. In this double blind randomized control clinical trial 69 participants received Ciprofloxacin (500 mg q 12 hourly) and 71 participants received Cefixime (200 mg q 12 hourly) orally for 2 weeks. Both the group received oral Metronidazole (800 mg q 8 hourly) for 2 weeks and percutaneous drainage or aspiration of the abscess was done as per indication and followed-up for 8 weeks. Out of 140 participants, 89.3% (N = 125) achieved clinical cure, 59 (85.5%) in Ciprofloxacin group and 66 (93%) in Cefixime group (p = 0.154). Mean duration of antimicrobial therapy was 16.2 ± 4.3 days, 15.1 ± 4.5 days in Ciprofloxacin group and 16.0 ± 4.2 days in Cefixime group (p = 0.223). Total 15 (10.7%) participants had treatment failure, 10 (14.5%) in Ciprofloxacin group and 5 (7.0%) in Cefixime group (p = 0.154). The most common reason for treatment failure was need of prolong (> 4 weeks) antimicrobial therapy due to persistent hepatic collection requiring drainage, which was significantly (p = 0.036) higher in Ciprofloxacin (14.5%, N = 10) group, compared to the Cefixime (4.2%, N = 3) group. In conclusion, both, the Ciprofloxacin or Cefixime plus Metronidazole for duration of 2–3 weeks were efficacious as empirical oral antimicrobial regimen along with prompt percutaneous drainage or aspiration for the treatment of uncomplicated liver abscess with similar efficacy. Oral Cefixime was better than Ciprofloxacin in term of lesser chance of treatment failure due to persistent collection which is required to be investigated further in larger clinical trial.

Trial registration: clinicaltrials.gov PRS ID: NCT03969758, 31/05/2019.
On-chip flow cytometer using integrated photonics for the detection of human leukocytes
Authors: Jooken Stijn , Zinoviev Kirill , Yurtsever Günay , De Proft Anabel , de Wijs Koen , Jafari Zeinab , Lebanov Ana , Jeevanandam Gaudhaman , Kotyrba Mateusz , Gorjup Erwin , Fondu Jelle , Lagae Liesbet , Libbrecht Sarah , Van Dorpe Pol , Verellen Niels
Published: May 2024

Differentiation between leukocyte subtypes like monocytes and lymphocytes is essential for cell therapy and research applications. To guarantee the cost-effective delivery of functional cells in cell therapies, billions of cells must be processed in a limited time. Yet, the sorting rates of commercial cell sorters are not high enough to reach the required yield. Process parallelization by using multiple instruments increases variability and production cost. A compact solution with higher throughput can be provided by multichannel flow cytometers combining fluidics and optics on-chip. In this work, we present a micro-flow cytometer with monolithically integrated photonics and fluidics and demonstrate that both the illumination of cells, as well as the collection of scattered light, can be realized using photonic integrated circuits. Our device is the first with sufficient resolution for the discrimination of lymphocytes and monocytes. Innovations in microfabrication have enabled complete integration of miniaturized photonic components and fluidics in a CMOS-compatible wafer stack. In combination with external optics, the device is ready for the collection of fluorescence using the on-chip excitation.
A qualitative survey on factors affecting depression and anxiety in patients with rheumatoid arthritis: a cross-sectional study in Syria
Authors: Khadour Fater A. , Khadour Younes A. , Ebrahem Bashar M.
Published: May 2024

Depression and anxiety often coexist with rheumatoid arthritis (RA) and affect the course of the disease. These mental health conditions can be overlooked or underdiagnosed in people with RA. There is conflicting evidence in previous studies regarding this topic, indicating that further research is necessary to provide a thorough understanding of the relationship between anxiety, depression, and RA. This study aims to determine the factors correlated with depression and anxiety symptoms in RA patients by evaluating disease activity at the same time. This cross-sectional study was conducted at four outpatient rehabilitation centers in four Syrian provinces: Damascus, Homs, Hama, and Latakia. The study included RA patients who attended the RA department of rehabilitation centers from January 1 to June 31, 2023. RA patients who presented at a rheumatology clinic were selected consecutively. RA patients were included in the study in accordance with the ACR/EULAR classification criteria, disease activity was assessed by disease activity score based on the 28-joint count (DAS28), and patients with DAS28 > 2.6 were considered to have active RA. The demographic data, as well as disease duration, educational status, Disease Activity Score with 28-joint counts (DAS28), health assessment questionnaire (HAQ) score, and the hospital anxiety and depression scale (HADS), were the parameters used in the analysis. Two hundred and twelve patients (female, 75%) with a mean age of 49.3 ± 13.1 years and a mean disease duration of 8.3 ± 6.9 years were studied. Depression was diagnosed in 79 (37.3%) patients and anxiety in 36 (16.9%) patients. Patients with depression and/or anxiety had higher HAQ and DAS28 scores compared to other RA patients. Blue-collar workers exhibited a higher prevalence of anxiety, whereas females, housewives, and individuals with lower educational attainment demonstrated a higher prevalence of depression. The current study found high rates of anxiety and depression in RA patients, highlighting the significant burden of these mental health conditions compared to the general population. It is essential for healthcare providers not to overlook the importance of psychiatric evaluations, mental health assessments, and physical examinations of RA patients.
Liming potential and characteristics of biochar produced from woody and non-woody biomass at different pyrolysis temperatures
Authors: Murtaza Ghulam , Usman Muhammad , Iqbal Javed , Hyder Sajjad , Solangi Farheen , Iqbal Rashid , Okla Mohammad K. , Al-Ghamdi Abdullah Ahmed , Elsalahy Heba H. , Tariq Waseem , Al-Elwany Omar A. A. I.
Published: May 2024

Large amount of wastes are burnt or left to decompose on site or at landfills where they cause air pollution and nutrient leaching to groundwater. Waste management strategies that return these food wastes to agricultural soils recover the carbon and nutrients that would otherwise have been lost, enrich soils and improve crop productivity. The incorporation of liming materials can neutralize the protons released, hence reducing soil acidity and its adverse impacts to the soil environment, food security, and human health. Biochar derived from organic residues is becoming a source of carbon input to soil and provides multifunctional values. Biochar can be alkaline in nature, with the level of alkalinity dependent upon the feedstock and processing conditions. This study conducted a characterization of biochar derived from the pyrolysis process of eggplant and Acacia nilotica bark at temperatures of 300 °C and 600 °C. An analysis was conducted on the biochar kinds to determine their pH, phosphorus (P), as well as other elemental composition. The proximate analysis was conducted by the ASTM standard 1762-84, while the surface morphological features were measured using a scanning electron microscope. The biochar derived from Acacia nilotica bark exhibited a greater yield and higher level of fixed carbon while possessing a lower content of ash and volatile components compared to biochar derived from eggplant. The eggplant biochar exhibits a higher liming ability at 600 °C compared to the acacia nilotica bark-derived biochar. The calcium carbonate equivalent, pH, potassium (K), and phosphorus (P) levels in eggplant biochars increased as the pyrolysis temperature increased. The results suggest that biochar derived from eggplant could be a beneficial resource for storing carbon in the soil, as well as for addressing soil acidity and enhancing nutrients availability, particularly potassium and phosphorus in acidic soils.
Comparative study of photocatalysis with bulk and nanosheet graphitic carbon nitrides enhanced with silver
Authors: Michalska Monika , Pavlovsky Jiri , Simha Martynkova Grazyna , Kratosova Gabriela , Hornok Viktoria , Nagy Peter B. , Novak Vlastimil , Szabo Tamas
Published: May 2024

The main goal of this research is to investigate the effectiveness of graphitic carbon nitride (g-C3N4, g-CN) in both bulk and nanosheet forms, which have been surface-modified with silver nanoparticles (Ag NPs), as photocatalysts for the degradation of acid orange 7 (AO7), a model dye. The photodegradation of AO7 dye molecules in water was used to test the potential photocatalytic properties of these powder materials under two different lamps with wavelengths of 368 nm (UV light) and 420 nm (VIS light). To produce Ag NPs (Ag content 0.5, 1.5, and 3 wt%) on the g-CN materials, a new synthesis route based on a wet and low-temperature method was proposed, eliminating the need for reducing agents. The photodegradation activity of the samples increased with increasing silver content, with the best photocatalytic performances achieved for bulk g-CN samples and nanosheet silver-modified samples (with the highest content of 3 wt% Ag) under UV light, i.e., more than 75% and 78%, respectively. The VIS-induced photocatalytic activity of both examined series was higher than that of UV. The highest activities of 92% and 98% were achieved for the 1.5% Ag-modified g-CN bulk and nanosheet materials. This research presents an innovative, affordable, and environmentally friendly chemical approach to synthesizing photocatalysts that can be used for degrading organic pollutants in wastewater treatment.
Evaluating nomogram models for predicting survival outcomes in gastric gastrointestinal stromal tumors with SEER database analysis
Authors: Yong Liuliang , Li Lanjun , Wu Jun , Liang Pan , Gao Jianbo
Published: May 2024

Gastrointestinal stromal tumors (GISTs) predominantly develop in the stomach. While nomogram offer tremendous therapeutic promise, there is yet no ideal nomogram comparison customized specifically for handling categorical data and model selection related gastric GISTs. (1) We selected 5463 patients with gastric GISTs from the SEER Research Plus database spanning from 2000 to 2020; (2) We proposed an advanced missing data imputation algorithm specifically designed for categorical variables; (3) We constructed five Cox nomogram models, each employing distinct methods for the selection and modeling of categorical variables, including Cox (Two-Stage), Lasso-Cox, Ridge-Cox, Elastic Net-Cox, and Cox With Lasso; (4) We conducted a comprehensive comparison of both overall survival (OS) and cancer-specific survival (CSS) tasks at six different time points; (5) To ensure robustness, we performed 50 randomized splits for each task, maintaining a 7:3 ratio between the training and test cohorts with no discernible statistical differences. Among the five models, the Cox (Two-Stage) nomogram contains the fewest features. Notably, at Near-term, Mid-term, and Long-term intervals, the Cox (Two-Stage) model attains the highest Area Under the Curve (AUC), top-1 ratio, and top-3 ratio in both OS and CSS tasks. For the prediction of survival in patients with gastric GISTs, the Cox (Two-Stage) nomogram stands as a simple, stable, and accurate predictive model with substantial promise for clinical application. To enhance the clinical utility and accessibility of our findings, we have deployed the nomogram model online, allowing healthcare professionals and researchers worldwide to access and utilize this predictive tool.
Aspartame carcinogenic potential revealed through network toxicology and molecular docking insights
Authors: Chen Dandan , Hou Xianbing
Published: May 2024

The research employed network toxicology and molecular docking techniques to systematically examine the potential carcinogenic effects and mechanisms of aspartame (l-α-aspartyl-l-phenylalanine methyl ester). Aspartame, a commonly used synthetic sweetener, is widely applied in foods and beverages globally. In recent years, its safety issues, particularly the potential carcinogenic risk, have garnered widespread attention. The study first constructed an interaction network map of aspartame with gastric cancer targets using network toxicology methods and identified key targets and pathways. Preliminary validation was conducted through microarray data analysis and survival analysis, and molecular docking techniques were employed to further examine the binding affinity and modes of action of aspartame with key proteins. The findings suggest that aspartame has the potential to impact various cancer-related proteins, potentially raising the likelihood of cellular carcinogenesis by interfering with biomolecular function. Furthermore, the study found that the action patterns and pathways of aspartame-related targets are like the mechanisms of known carcinogenic pathways, further supporting the scientific hypothesis of its potential carcinogenicity. However, given the complexity of the in vivo environment, we also emphasize the necessity of validating these molecular-level findings in actual biological systems. The study introduces a fresh scientific method for evaluating the safety of food enhancers and provides a theoretical foundation for shaping public health regulations.
Gene expression supports a single origin of horns and antlers in hoofed mammals
Authors: Calamari Zachary T. , Flynn John J.
Published: May 2024

Horns, antlers, and other bony cranial appendages of even-toed hoofed mammals (ruminant artiodactyls) challenge traditional morphological homology assessments. Cranial appendages all share a permanent bone portion with family-specific integument coverings, but homology determination depends on whether the integument covering is an essential component or a secondary elaboration of each structure. To enhance morphological homology assessments, we tested whether juvenile cattle horn bud transcriptomes share homologous gene expression patterns with deer antlers relative to pig outgroup tissues, treating the integument covering as a secondary elaboration. We uncovered differentially expressed genes that support horn and antler homology, potentially distinguish them from non-cranial-appendage bone and other tissues, and highlight the importance of phylogenetic outgroups in homology assessments. Furthermore, we found differentially expressed genes that could support a shared cranial neural crest origin for horns and antlers and expression patterns that refine our understanding of the timing of horn and antler differentiation.
Targeting glutamine metabolism improves sarcoma response to radiation therapy in vivo
Authors: Patel Rutulkumar , Cooper Daniel E. , Kadakia Kushal T. , Allen Annamarie , Duan Likun , Luo Lixia , Williams Nerissa T. , Liu Xiaojing , Locasale Jason W. , Kirsch David G.
Published: May 2024

Diverse tumor metabolic phenotypes are influenced by the environment and genetic lesions. Whether these phenotypes extend to rhabdomyosarcoma (RMS) and how they might be leveraged to design new therapeutic approaches remains an open question. Thus, we utilized a Pax7Cre-ER-T2/+; NrasLSL-G12D/+; p53fl/fl (P7NP) murine model of sarcoma with mutations that most frequently occur in human embryonal RMS. To study metabolism, we infuse 13C-labeled glucose or glutamine into mice with sarcomas and show that sarcomas consume more glucose and glutamine than healthy muscle tissue. However, we reveal a marked shift from glucose consumption to glutamine metabolism after radiation therapy (RT). In addition, we show that inhibiting glutamine, either through genetic deletion of glutaminase (Gls1) or through pharmacological inhibition of glutaminase, leads to significant radiosensitization in vivo. This causes a significant increase in overall survival for mice with Gls1-deficient compared to Gls1-proficient sarcomas. Finally, Gls1-deficient sarcomas post-RT elevate levels of proteins involved in natural killer cell and interferon alpha/gamma responses, suggesting a possible role of innate immunity in the radiosensitization of Gls1-deficient sarcomas. Thus, our results indicate that glutamine contributes to radiation response in a mouse model of RMS.
Recurring seasonality exposes dominant species and niche partitioning strategies of open ocean picoeukaryotic algae
Authors: Eckmann Charlotte A. , Bachy Charles , Wittmers Fabian , Strauss Jan , Blanco-Bercial Leocadio , Vergin Kevin L. , Parsons Rachel J. , Kudela Raphael M. , Johnson Rod , Bolaños Luis M. , Giovannoni Stephen J. , Carlson Craig A. , Worden Alexandra Z.
Published: May 2024

Ocean spring phytoplankton blooms are dynamic periods important to global primary production. We document vertical patterns of a diverse suite of eukaryotic algae, the prasinophytes, in the North Atlantic Subtropical Gyre with monthly sampling over four years at the Bermuda Atlantic Time-series Study site. Water column structure was used to delineate seasonal stability periods more ecologically relevant than seasons defined by calendar dates. During winter mixing, tiny prasinophytes dominated by Class II comprise 46  ±  24% of eukaryotic algal (plastid-derived) 16S rRNA V1-V2 amplicons, specifically Ostreococcus Clade OII, Micromonas commoda, and Bathycoccus calidus. In contrast, Class VII are rare and Classes I and VI peak during warm stratified periods when surface eukaryotic phytoplankton abundances are low. Seasonality underpins a reservoir of genetic diversity from multiple prasinophyte classes during warm periods that harbor ephemeral taxa. Persistent Class II sub-species dominating the winter/spring bloom period retreat to the deep chlorophyll maximum in summer, poised to seed the mixed layer upon winter convection, exposing a mechanism for initiating high abundances at bloom onset. Comparisons to tropical oceans reveal broad distributions of the dominant sub-species herein. This unparalleled window into temporal and spatial niche partitioning of picoeukaryotic primary producers demonstrates how key prasinophytes prevail in warm oceans.
Energetic particle precipitation influences global secondary ozone distribution
Authors: Jia Jia , Murberg Lise E. , Løvset Tiril , Orsolini Yvan J. , Espy Patrick J. , Zeller Lilou C. G. , Salinas Cornelius Csar Jude H. , Lee Jae N. , Wu Dong , Zhang Jiarong
Published: May 2024

The secondary ozone layer is a global peak in ozone abundance in the upper mesosphere-lower thermosphere (UMLT) around 90-95 km. The effect of energetic particle precipitation (EPP) from geomagnetic processes on this UMLT ozone remains largely unexplored. In this research we investigated how the secondary ozone responds to EPP using satellite observations. In addition, the residual Mean Meridional Circulation (MMC) derived from model simulations and the atomic oxygen [O], atomic hydrogen [H], temperature measurements from satellite observations were used to characterise the residual circulation changes during EPP events. We report regions of secondary ozone enhancement or deficit across low, mid and high latitudes as a result of global circulation and transport changes induced by EPP. The results are supported by a sensitivity test using an empirical model.
Vertical and horizontal transmission of plant viruses: two extremes of a continuum?
Authors: García-Ordóñez Lucía , Pagán Israel
Published: May 2024

Parasites have a variety of mechanisms to be transmitted to new susceptible hosts, which can be largely grouped in two main modes: vertical (i.e., from parents to the offspring) and horizontal (i.e., between hosts regardless of descent). Because between-host dispersal is a key trait for parasite fitness, scientists studying host-parasite interactions have been long interested in understanding the evolution of their transmission mode(s). Most work in this regard has been theoretical, which resulted in the development of the so-called Continuum hypothesis. This theory states that because vertically transmitted parasites require the host to reproduce, the evolution of this mode of transmission will involve reduced virulence (i.e., the effect of infection on host fecundity) in order to allow maximal host viable progeny production. Conversely, the evolution of horizontal transmission does not have this limitation and parasites with this mode of transmission will evolve higher virulence. Therefore, a trade-off between both modes of transmission across a continuum of virulence values is predicted, with each transmission mode located at the extremes of the continuum. Using plant viruses as a focal parasite, here we review existing theory surrounding the Continuum hypothesis and the experimental work testing the predictions of the theory. Finally, we briefly discuss molecular mechanisms that may explain the existence of vertical-to-horizontal transmission trade-offs and potential implications for the management of virus epidemics.
Energy stress promotes P-bodies formation via lysine-63-linked polyubiquitination of HAX1
Authors: Zhan Wanqi , Li Zhiyang , Zhang Jie , Liu Yongfeng , Liu Guanglong , Li Bingsong , Shen Rong , Jiang Yi , Shang Wanjing , Gao Shenjia , Wu Han , Wang Ya’nan , Chen Wankun , Wang Zhizhang
Published: May 2024

Energy stress, characterized by the reduction of intracellular ATP, has been implicated in various diseases, including cancer. Here, we show that energy stress promotes the formation of P-bodies in a ubiquitin-dependent manner. Upon ATP depletion, the E3 ubiquitin ligase TRIM23 catalyzes lysine-63 (K63)-linked polyubiquitination of HCLS1-associated protein X-1 (HAX1). HAX1 ubiquitination triggers its liquid‒liquid phase separation (LLPS) and contributes to P-bodies assembly induced by energy stress. Ubiquitinated HAX1 also interacts with the essential P-body proteins, DDX6 and LSM14A, promoting their condensation. Moreover, we find that this TRIM23/HAX1 pathway is critical for the inhibition of global protein synthesis under energy stress conditions. Furthermore, high HAX1 ubiquitination, and increased cytoplasmic localization of TRIM23 along with elevated HAX1 levels, promotes colorectal cancer (CRC)-cell proliferation and correlates with poor prognosis in CRC patients. Our data not only elucidate a ubiquitination-dependent LLPS mechanism in RNP granules induced by energy stress but also propose a promising target for CRC therapy.
Functional canonical RNAi in mice expressing a truncated Dicer isoform and long dsRNA
Authors: Buccheri Valeria , Pasulka Josef , Malik Radek , Loubalova Zuzana , Taborska Eliska , Horvat Filip , Roos Kulmann Marcos Iuri , Jenickova Irena , Prochazka Jan , Sedlacek Radislav , Svoboda Petr
Published: May 2024

Canonical RNA interference (RNAi) is sequence-specific mRNA degradation guided by small interfering RNAs (siRNAs) made by RNase III Dicer from long double-stranded RNA (dsRNA). RNAi roles include gene regulation, antiviral immunity or defense against transposable elements. In mammals, RNAi is constrained by Dicer’s adaptation to produce another small RNA class—microRNAs. However, a truncated Dicer isoform (ΔHEL1) supporting RNAi exists in mouse oocytes. A homozygous mutation to express only the truncated ΔHEL1 variant causes dysregulation of microRNAs and perinatal lethality in mice. Here, we report the phenotype and canonical RNAi activity in DicerΔHEL1/wt mice, which are viable, show minimal miRNome changes, but their endogenous siRNA levels are an order of magnitude higher. We show that siRNA production in vivo is limited by available dsRNA, but not by Protein kinase R, a dsRNA sensor of innate immunity. dsRNA expression from a transgene yields sufficient siRNA levels to induce efficient RNAi in heart and muscle. DicerΔHEL1/wt mice with enhanced canonical RNAi offer a platform for examining potential and limits of mammalian RNAi in vivo.
Adipocyte HSL is required for maintaining circulating vitamin A and RBP4 levels during fasting
Authors: Steinhoff Julia S , Wagner Carina , Dähnhardt Henriette E , Košić Kristina , Meng Yueming , Taschler Ulrike , Pajed Laura , Yang Na , Wulff Sascha , Kiefer Marie F , Petricek Konstantin M , Flores Roberto E , Li Chen , Dittrich Sarah , Sommerfeld Manuela , Guillou Hervé , Henze Andrea , Raila Jens , Wowro Sylvia J , Schoiswohl Gabriele , Lass Achim , Schupp Michael
Published: May 2024

Vitamin A (retinol) is distributed via the blood bound to its specific carrier protein, retinol-binding protein 4 (RBP4). Retinol-loaded RBP4 is secreted into the circulation exclusively from hepatocytes, thereby mobilizing hepatic retinoid stores that represent the major vitamin A reserves in the body. The relevance of extrahepatic retinoid stores for circulating retinol and RBP4 levels that are usually kept within narrow physiological limits is unknown. Here, we show that fasting affects retinoid mobilization in a tissue-specific manner, and that hormone-sensitive lipase (HSL) in adipose tissue is required to maintain serum concentrations of retinol and RBP4 during fasting in mice. We found that extracellular retinol-free apo-RBP4 induces retinol release by adipocytes in an HSL-dependent manner. Consistently, global or adipocyte-specific HSL deficiency leads to an accumulation of retinoids in adipose tissue and a drop of serum retinol and RBP4 during fasting, which affects retinoid-responsive gene expression in eye and kidney and lowers renal retinoid content. These findings establish a novel crosstalk between liver and adipose tissue retinoid stores for the maintenance of systemic vitamin A homeostasis during fasting.
Sensitive photoelectric sensing for 5-HMF detection
Authors: He Xin , Jiang Caiyun , Yang Jie , Sheng Shuangchao , Wang Yuping
Published: May 2024

A photoelectric sensing method was developed for the highly sensitive detection of 5-HMF using hollow TiO2 nanospheres. The detection limit was as low as 0.001 nM, and the stability was good (RSD = 2.4%).
Dynamics of carbene formation in the reaction of methane with the tantalum cation in the gas phase
Authors: Meta Marcel , Huber Maximilian E. , Birk Maurice , Wedele Martin , Ončák Milan , Meyer Jennifer
Published: May 2024

The dynamics of carbene formation in the reaction of methane with the tantalum cation is explored by combining experimentally measured differential cross sections with ab initio calculations.
Online monitoring of epithelial barrier kinetics and cell detachment during cisplatin-induced toxicity of renal proximal tubule cells
Authors: Takata Yuji , Banan Sadeghian Ramin , Fujimoto Kazuya , Yokokawa Ryuji
Published: May 2024

Real-time and non-invasive assessment of tissue health is crucial for maximizing the potential of microphysiological systems (MPS) for drug-induced nephrotoxicity screening.
NFC-enabled photothermal-based microfluidic paper analytical device for glucose detection
Authors: Khachornsakkul Kawin , Del-Rio-Ruiz Ruben , Asci Cihan , Sonkusale Sameer
Published: May 2024

Near-field communication technology and gold nanomaterials were integrated with photothermal paper microfluidic devices for enzyme-free glucose quantification.
Development of in vitro microfluidic models to study endothelial responses to pulsatility with different mechanical circulatory support devices
Authors: Wang Xueying , Liang Lixue , Giridharan Guruprasad A. , Sethu Palaniappan , Wang Yanxia , Qin Kai-rong , Qu Peng , Wang Yu
Published: May 2024

CPD can replace CFVAD with pulsatile working modes to a certain extent to treat non-severe HF. The proposed in vitro microfluidic models provided scientific basis for selecting different mechanical circulatory support devices.
First organic fluorescence immunoassay for the detection of Enterobacter cloacae in food matrixes
Authors: Shenbagavalli Kathiravan , Suganya Kannan , Sundaram Ellairaja , Murugan Marudhamuthu , Sivasamy Vasantha Vairathevar
Published: May 2024

For the first time, a novel fluorescent moiety, 2-amino-4-(7-formyl-1,8-dihydropyren-2-yl)-7-hydroxy-4H-chromene-3-carbonitrile (ACC), was synthesized by an ultrasonication method.
The chemical memory of smoking tobacco
Authors: Gallart-Mateu D. , Dualde P. , Coscollà C. , Soriano J. M. , de la Guardia M.
Published: May 2024

The concentration in urine of N-acetyl-hydroxy-propyl-cisteine (3HPMA), acrolein metabolite, can be used as a marker of the illness risk of smokers and the relative concentration to creatinine employed to verify the effect of moving from burned tobacco practice to nicotine vaping.
Construction of a novel aminofluorene-based ratiometric near-infrared fluorescence probe for detecting carboxylesterase activity in living cells
Authors: Li Jun-Mei , Liu Yan-Zhao , Lv Xiao-Fang , Zhou Ding-Heng , Zhang Hong , Chen Yu-Jin , Li Kun
Published: May 2024

Herein, we constructed a novel aminofluorene-based fluorescence probe (FEN-CE) for the detection of carboxylesterase (CE) in living cells by a ratiometric near-infrared (NIR) fluorescence signal.
Complete amide cis–trans switching synchronized with disulfide bond formation and cleavage in a proline-mimicking system
Authors: Cheng Yuhe , Hyodo Tadashi , Yamaguchi Kentaro , Ohwada Tomohiko , Otani Yuko
Published: May 2024

A typical naturally occurring disulfide structure in proteins is an 8-membered disulfide ring formed between two adjacent cysteine (Cys–Cys) residues.
Impact of optimised quasi-block structures on the properties of polymer electrolytes
Authors: Rollo-Walker Greg , Hasanpoor Meisam , Malic Nino , Azad Faezeh Makhlooghi , O’Dell Luke , White Jacinta , Chiefari John , Forsyth Maria
Published: May 2024

Quasi-block copolymer electrolytes offer an ideal block morphology for ion transport in next-generation solid-state electrolytes.
Two-dimensional Janus X2STe (X = B, Al) monolayers: the effect of surface selectivity and adsorption of small gas molecules on electronic and optical properties
Authors: Zengin Y. , Mogulkoc Y.
Published: May 2024

This investigation delves into the adsorption characteristics of CO, NO, NO2, NH3, and O2 on two-dimensional (2D) Janus group-III materials, specifically Al2XY and B2XY.
Data-driven stabilization of NimPdn–m nanoalloys: a study using density functional theory and data mining approaches
Authors: Souza Tiago M. , Pena Lucas B. , Da Silva Juarez L. F. , Galvão Breno R. L.
Published: May 2024

Data mining algorithms and Spearman correlation analysis are coupled to DFT calculations in the search for descriptors that drive the stability of NiPd clusters. A unique kind of core–shell segregation is revealed.
Application of established computational techniques to identify potential SARS-CoV-2 Nsp14-MTase inhibitors in low data regimes
Authors: Nigam AkshatKumar , Hurley Matthew F. D. , Li Fengling , Konkoľová Eva , Klíma Martin , Trylčová Jana , Pollice Robert , Çinaroǧlu Süleyman Selim , Levin-Konigsberg Roni , Handjaya Jasemine , Schapira Matthieu , Chau Irene , Perveen Sumera , Ng Ho-Leung , Kaniskan H. Ümit , Han Yulin , Singh Sukrit , Gorgulla Christoph , Kundaje Anshul , Jin Jian , Voelz Vincent A. , Weber Jan , Nencka Radim , Boura Evzen , Vedadi Masoud , Aspuru-Guzik Alán
Published: May 2024

Workflow used for identifying inhibitors of the SARS-CoV-2 non-structural protein 14 (nsp14), a key player in viral RNA methylation.
Regulating the thermal expansion of a [FePt(CN)4] layer by axial coordination and dimensional reduction
Authors: Ma Rui , Chen Liang , Liu Zhanning , Lin Kun , Li Qiang , Ji Weihua , Xu Hankun , Chen Xin , Deng Jinxia , Xing Xianran
Published: May 2024

This work describes three compounds composed of a two-dimensional [FePt(CN)4] layer and its negative thermal expansion behaviour.
Urea and ammonium fluoride di-nitrogen and Cu & Fe bi-metal co-doped carbon felt as cathode for electro-Fenton degradation of norfloxacin: 1O2-dominated oxidation pathway
Authors: Li Jing , Gao Lili , Chen Yue , Meng Xinyi , Li Xuelian , Qi Kai , Zhang Jiandong
Published: May 2024

Dual nitrogen source co-doped carbon with copper and iron induces 1O2 degradation of norfloxacin.
Correction: Retrosynthesis from transforms to predictive sustainable chemistry and nanotechnology: a brief tutorial review
Authors: Mikolajczyk Alicja , Zhdan Uladzislau , Antoniotti Sylvain , Smolinski Adam , Jagiello Karolina , Skurski Piotr , Harb Moussab , Puzyn Tomasz , Polanski Jaroslaw
Published: May 2024

Correction for ‘Retrosynthesis from transforms to predictive sustainable chemistry and nanotechnology: a brief tutorial review’ by Alicja Mikolajczyk et al., Green Chem., 2023, 25, 2971–2991, https://doi.org/10.1039/D2GC04750K.
Correction: Characterization of polymer properties and identification of additives in commercially available research plastics
Authors: Cuthbertson Amy A. , Lincoln Clarissa , Miscall Joel , Stanley Lisa M. , Maurya Anjani K. , Asundi Arun S. , Tassone Christopher J. , Rorrer Nicholas A. , Beckham Gregg T.
Published: May 2024

Correction for ‘Characterization of polymer properties and identification of additives in commercially available research plastics’ by Amy A. Cuthbertson et al., Green Chem., 2024, https://doi.org/10.1039/d4gc00659c.
Differential impact of biogenic and chemically synthesized zinc oxide nanoparticles on anti-aging, anti-oxidant and anti-cancerous activities: a mechanism based study
Authors: Inam Mubashra , Haider Zahra , Anjum Sumaira , Soliman Mohamed Mohamed , Ahmad Bushra , Hussain Muhammad Iftikhar , Hano Christophe
Published: May 2024

Zinc oxide nanoparticles (ZnONPs), characterized by their nanoscale dimensions and unique properties, have emerged as promising materials in various applications.
Self-supporting catalysts beat powder electrodes for the electrocatalytic oxygen evolution reaction: a cobalt-based catalyst as an example
Authors: Zhao Huipeng , Du Xiaoqiang , Zhang Xiaoshuang
Published: May 2024

In view of large-scale applications, binder-free supported catalysts should be given more attention for catalyst preparation using the hydrothermal fabrication approach.
Imaging of ultrafast photoexcited electron dynamics in pentacene nanocrystals on a graphite substrate
Authors: Shibuta Masahiro , Nakajima Atsushi
Published: May 2024

Photoexcited electron transfer from p-type organic nanocrystals to a two-dimensional substrate is directly visualized in real time.