bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractColorectal 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

AbstractDecades 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

AbstractThe 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

AbstractThe 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

AbstractThe 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

AbstractLiver 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

AbstractDifferentiation 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

AbstractDepression 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

AbstractLarge 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

AbstractThe 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

AbstractGastrointestinal 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

AbstractThe 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

AbstractHorns, 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

AbstractDiverse 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.