bluuebunny/crossref_metadata_2025_split huggingface dataset:
Uptake of COVID-19 vaccinations amongst 3,433,483 children and young people: meta-analysis of UK prospective cohorts
Authors: Aldridge Sarah J. , Agrawal Utkarsh , Murphy Siobhán , Millington Tristan , Akbari Ashley , Almaghrabi Fatima , Anand Sneha N. , Bedston Stuart , Goudie Rosalind , Griffiths Rowena , Joy Mark , Lowthian Emily , de Lusignan Simon , Patterson Lynsey , Robertson Chris , Rudan Igor , Bradley Declan T. , Lyons Ronan A. , Sheikh Aziz , Owen Rhiannon K. 
Published: March 2024

AbstractSARS-CoV-2 infection in children and young people (CYP) can lead to life-threatening COVID-19, transmission within households and schools, and the development of long COVID. Using linked health and administrative data, we investigated vaccine uptake among 3,433,483 CYP aged 5–17 years across all UK nations between 4th August 2021 and 31st May 2022. We constructed national cohorts and undertook multi-state modelling and meta-analysis to identify associations between demographic variables and vaccine uptake. We found that uptake of the first COVID-19 vaccine among CYP was low across all four nations compared to other age groups and diminished with subsequent doses. Age and vaccination status of adults living in the same household were identified as important risk factors associated with vaccine uptake in CYP. For example, 5–11 year-olds were less likely to receive their first vaccine compared to 16–17 year-olds (adjusted Hazard Ratio [aHR]: 0.10 (95%CI: 0.06–0.19)), and CYP in unvaccinated households were less likely to receive their first vaccine compared to CYP in partially vaccinated households (aHR: 0.19, 95%CI 0.13–0.29).
Quantum spin liquid signatures in monolayer 1T-NbSe2
Authors: Zhang Quanzhen , He Wen-Yu , Zhang Yu , Chen Yaoyao , Jia Liangguang , Hou Yanhui , Ji Hongyan , Yang Huixia , Zhang Teng , Liu Liwei , Gao Hong-Jun , Jung Thomas A. , Wang Yeliang 
Published: March 2024

AbstractQuantum spin liquids (QSLs) are in a quantum disordered state that is highly entangled and has fractional excitations. As a highly sought-after state of matter, QSLs were predicted to host spinon excitations and to arise in frustrated spin systems with large quantum fluctuations. Here we report on the experimental observation and theoretical modeling of QSL signatures in monolayer 1T-NbSe2, which is a newly emerging two-dimensional material that exhibits both charge-density-wave (CDW) and correlated insulating behaviors. By using scanning tunneling microscopy and spectroscopy (STM/STS), we confirm the presence of spin fluctuations in monolayer 1T-NbSe2 by observing the Kondo resonance as monolayer 1T-NbSe2 interacts with metallic monolayer 1H-NbSe2. Subsequent STM/STS imaging of monolayer 1T-NbSe2 at the Hubbard band energy further reveals a long-wavelength charge modulation, in agreement with the spinon modulation expected for QSLs. By depositing manganese-phthalocyanine (MnPc) molecules with spin S = 3/2 onto monolayer 1T-NbSe2, new STS resonance peaks emerge at the Hubbard band edges of monolayer 1T-NbSe2. This observation is consistent with the spinon Kondo effect induced by a S = 3/2 magnetic impurity embedded in a QSL. Taken together, these experimental observations indicate that monolayer 1T-NbSe2 is a new promising QSL material.
Cavity-coupled telecom atomic source in silicon
Authors: Johnston Adam , Felix-Rendon Ulises , Wong Yu-En , Chen Songtao 
Published: March 2024

AbstractNovel T centers in silicon hold great promise for quantum networking applications due to their telecom band optical transitions and the long-lived ground state electronic spins. An open challenge for advancing the T center platform is to enhance its weak and slow zero phonon line (ZPL) emission. In this work, by integrating single T centers with a low-loss, small mode-volume silicon photonic crystal cavity, we demonstrate an enhancement of the fluorescence decay rate by a factor of F = 6.89. Efficient photon extraction enables the system to achieve an average ZPL photon outcoupling rate of 73.3 kHz under saturation, which is about two orders of magnitude larger than the previously reported value. The dynamics of the coupled system is well modeled by solving the Lindblad master equation. These results represent a significant step towards building efficient T center spin-photon interfaces for quantum information processing and networking applications.
TANGO6 regulates cell proliferation via COPI vesicle-mediated RPB2 nuclear entry
Authors: Feng Zhi , Liu Shengnan , Su Ming , Song Chunyu , Lin Chenyu , Zhao Fangying , Li Yang , Zeng Xianyan , Zhu Yong , Hou Yu , Ren Chunguang , Zhang Huan , Yi Ping , Ji Yong , Wang Chao , Li Hongtao , Ma Ming , Luo Lingfei , Li Li 
Published: March 2024

AbstractCoat protein complex I (COPI) vesicles mediate the retrograde transfer of cargo between Golgi cisternae and from the Golgi to the endoplasmic reticulum (ER). However, their roles in the cell cycle and proliferation are unclear. This study shows that TANGO6 associates with COPI vesicles via two transmembrane domains. The TANGO6 N- and C-terminal cytoplasmic fragments capture RNA polymerase II subunit B (RPB) 2 in the cis-Golgi during the G1 phase. COPI-docked TANGO6 carries RPB2 to the ER and then to the nucleus. Functional disruption of TANGO6 hinders the nuclear entry of RPB2, which accumulates in the cytoplasm, causing cell cycle arrest in the G1 phase. The conditional depletion or overexpression of TANGO6 in mouse hematopoietic stem cells results in compromised or expanded hematopoiesis. Our study results demonstrate that COPI vesicle-associated TANGO6 plays a role in the regulation of cell cycle progression by directing the nuclear transfer of RPB2, making it a potential target for promoting or arresting cell expansion.
Enhanced assembly of bacteriophage T7 produced in cell-free reactions under simulated microgravity
Authors: Lehr François-Xavier , Pavletić Bruno , Glatter Timo , Heimerl Thomas , Moeller Ralf , Niederholtmeyer Henrike 
Published: March 2024

AbstractOn-demand biomanufacturing has the potential to improve healthcare and self-sufficiency during space missions. Cell-free transcription and translation reactions combined with DNA blueprints can produce promising therapeutics like bacteriophages and virus-like particles. However, how space conditions affect the synthesis and self-assembly of such complex multi-protein structures is unknown. Here, we characterize the cell-free production of infectious bacteriophage T7 virions under simulated microgravity. Rotation in a 2D-clinostat increased the number of infectious particles compared to static controls. Quantitative analyses by mass spectrometry, immuno-dot-blot and real-time PCR showed no significant differences in protein and DNA contents, suggesting enhanced self-assembly of T7 phages in simulated microgravity. While the effects of genuine space conditions on the cell-free synthesis and assembly of bacteriophages remain to be investigated, our findings support the vision of a cell-free synthesis-enabled “astropharmacy”.
Mechanisms and energetics of calcium aluminosilicate glass dissolution through ab initio molecular dynamics-metadynamics simulations
Authors: Liu Meili , Ruiz Pestana Luis 
Published: March 2024

AbstractThe dissolution of silicate glasses has implications in diverse fields ranging from the immobilization of radioactive waste to the development of sustainable alternatives to Portland cement. Here, we used ab initio molecular dynamics simulations biased with well-tempered metadynamics to study Si-O-T bridge dissociation in calcium aluminosilicate glasses, crucial for understanding their dissolution. In a departure from the conventional Michalske-Freiman model, our findings reveal a nucleophilic substitution reaction mechanism characterized by a short-lived, 5-fold coordinated Si intermediate or transition state, depending on the Si bridge coordination, with a near-trigonal bipyramidal geometry. We find that the reorganization required for reaching this state causes the activation energy barriers to be dependent on the Si bridge coordination, with Si Q3 species serving as the rate-limiting step in the dissolution reaction. Our findings not only challenge long-standing theoretical models but also pave the way for more accurate and comprehensive frameworks for understanding the dissolution of silicate glasses in various applications.
GO2Sum: generating human-readable functional summary of proteins from GO terms
Authors: Giri Swagarika Jaharlal , Ibtehaz Nabil , Kihara Daisuke 
Published: March 2024

AbstractUnderstanding the biological functions of proteins is of fundamental importance in modern biology. To represent a function of proteins, Gene Ontology (GO), a controlled vocabulary, is frequently used, because it is easy to handle by computer programs avoiding open-ended text interpretation. Particularly, the majority of current protein function prediction methods rely on GO terms. However, the extensive list of GO terms that describe a protein function can pose challenges for biologists when it comes to interpretation. In response to this issue, we developed GO2Sum (Gene Ontology terms Summarizer), a model that takes a set of GO terms as input and generates a human-readable summary using the T5 large language model. GO2Sum was developed by fine-tuning T5 on GO term assignments and free-text function descriptions for UniProt entries, enabling it to recreate function descriptions by concatenating GO term descriptions. Our results demonstrated that GO2Sum significantly outperforms the original T5 model that was trained on the entire web corpus in generating Function, Subunit Structure, and Pathway paragraphs for UniProt entries.
Structural analysis of phosphoribosyltransferase-mediated cell wall precursor synthesis in Mycobacterium tuberculosis
Authors: Gao Shan , Wu Fangyu , Gurcha Sudagar S. , Batt Sarah M. , Besra Gurdyal S. , Rao Zihe , Zhang Lu 
Published: March 2024

AbstractIn Mycobacterium tuberculosis, Rv3806c is a membrane-bound phosphoribosyltransferase (PRTase) involved in cell wall precursor production. It catalyses pentosyl phosphate transfer from phosphoribosyl pyrophosphate to decaprenyl phosphate, to generate 5-phospho-β-ribosyl-1-phosphoryldecaprenol. Despite Rv3806c being an attractive drug target, structural and molecular mechanistic insight into this PRTase is lacking. Here we report cryogenic electron microscopy structures for Rv3806c in the donor- and acceptor-bound states. In a lipidic environment, Rv3806c is trimeric, creating a UbiA-like fold. Each protomer forms two helical bundles, which, alongside the bound lipids, are required for PRTase activity in vitro. Mutational and functional analyses reveal that decaprenyl phosphate and phosphoribosyl pyrophosphate bind the intramembrane and extramembrane cavities of Rv3806c, respectively, in a distinct manner to that of UbiA superfamily enzymes. Our data suggest a model for Rv3806c-catalysed phosphoribose transfer through an inverting mechanism. These findings provide a structural basis for cell wall precursor biosynthesis that could have potential for anti-tuberculosis drug development.
HYADES - A Global Archive of Annual Maxima Daily Precipitation
Authors: Vargas Godoy Mijael Rodrigo , Papalexiou Simon Michael , Markonis Yannis 
Published: March 2024

AbstractTime series of annual maxima daily precipitation are crucial for understanding extreme precipitation behavior and its shifts toward nonstationarity with global warming. Extreme precipitation insight assists hydraulic infrastructure design, water resource management, natural hazard prevention, and climate change adaptation. However, not even a third of the records are of sufficient length, and the number of active stations keeps decreasing. Herein, we present HYADES: archive of yearly maxima of daily precipitation records, a global dataset derived from the Global Historical Climatology Network database of daily records (GHCN-Daily). The HYADES dataset contains records from 39 206 stations (heterogeneously distributed worldwide) with record lengths varying from 16 to 200 years between 1805 and 2023. HYADES was extracted through a methodology designed to accurately capture the true maxima even in the presence of missing values within the records. The method’s thresholds were determined and evaluated through Monte Carlo simulations. Our approach demonstrates a 96.73% success rate in detecting the true maxima while preserving time series statistical properties of interest (L-moments and temporal monotonic trend).
Transcriptomic profiling of Poa pratensis L. under treatment of various phytohormones
Authors: Meng Chen , Peng Xiaomei , Zhang Yu , Pedro García-Caparrós , Li Yumeng , Zhang Yanni , Duan Yuanwen , Sun Xudong 
Published: March 2024

AbstractPoa pratensis L. (Poaceae) is a valuable grass across the north hemisphere, inhabiting diverse environments with wide altitudinal span, where ubiquitous various kinds of stresses. Phytohormones would be helpful to improve tolerance to abiotic and biotic stresses, but the responses of transcriptome regulation of P. pratensis to exogenous phytohormones application remain unclear. In this study, we explored the alteration of plant physiological responses by the application of phytohormones. Aiming to achieve this knowledge, we got full-length transcriptome data 42.76 Gb, of which 74.9% of transcripts were completed. Then used 27 samples representing four treatments conducted at two time points (1 h and 6 h after application) to generate RNA-seq data. 371 and 907 common DEGs were identified in response to four phytohormones application, respectively, these DEGs were involved in “plant hormone signal transduction”, “carbon metabolism” and “plant-pathogen interaction”. Finally, P. pratensis basic research can gain valuable information regarding the responses to exogenous application of phytohormones in physiological indicators and transcriptional regulations in order to facilitate the development of new cultivars.
Theoretical electronic structure with spin–orbit coupling effect of the molecules SrAt and BaAt for laser cooling studies
Authors: Madi Amal , El-Kork Nayla , Zeid Israa , Korek Mahmoud 
Published: March 2024

AbstractAb initio CASSCF/MRCI + Q calculations have been used to investigate the electronic structure and transition properties of the alkaline earth astatine molecules SrAt and BaAt. The adiabatic potential energy curves have been computed and plotted for the low-lying electronic states in the representations 2S+1Λ+/− and Ω(±) (with and without spin–orbit coupling effect). The spectroscopic and vibrational constants have been deduced for the corresponding bound states. An analysis of the Franck–Condon factors, the Einstein Coefficients, and the branching ratios among different vibrational levels has shown that both SrAt and BaAt molecules are suitable candidates for Doppler and Sysphus laser cooling. Experimental laser cooling schemes and conditions for these two molecules have been proposed. These results may pave the way for new spectroscopic and laser cooling experiments of alkaline earth astatine molecules.
Mapping the habitat refugia of Isidella elongata under climate change and trawling impacts to preserve Vulnerable Marine Ecosystems in the Mediterranean
Authors: Georges Vincent , Vaz Sandrine , Carbonara Pierluigi , Fabri Marie-Claire , Fanelli Emanuela , Follesa Maria Cristina , Garofalo Germana , Gerovasileiou Vasilis , Jadaud Angélique , Maiorano Porzia , Marin Pilar , Mytilineou Chryssi , Orejas Covadonga , Del Mar Otero Maria , Smith Chris J. , Thasitis Ioannis , Lauria Valentina 
Published: March 2024

AbstractThe bamboo-coral Isidella elongata is a key habitat-forming species in the deep Mediterranean Sea. This alcyonacean is listed as an indicator of Vulnerable Marine Ecosystems (VMEs) and as Critically Endangered due to bottom trawling impacts. In this work, a modeling approach was used to predict and map the habitat suitability of I. elongata in the Mediterranean Sea under current environmental conditions. Occurrence data were modeled as a function of environmental parameters. Using climate change scenarios and fishing effort data, the risk of climate change and fisheries impacts on habitat suitability were estimated, and climate refugia were identified. A drastic loss of habitat is predicted, and climate change scenarios suggest a loss of 60% of suitable habitats by 2100. In the central Mediterranean, climate refugia overlapped with active fishing grounds. This study represents the first attempt to identify hot spots for the protection of soft bottom Vulnerable Marine Ecosystems for the entire Mediterranean Sea, and highlights areas most at risk from trawling. This work is relevant to the objectives of the EU Marine Strategy Framework and Maritime Spatial Planning Directives, the Biodiversity Strategy for 2030 regarding priority areas for conservation.
Fabrication of green anti-microbial and anti-static cement building bricks
Authors: Reffaee Abeer , Saied Mona , hamieda Shimaa Farag , Amin Sh. K. 
Published: March 2024

AbstractThe design cement mix of grade 350 was created in accordance with Egyptian Standards by partially substituting the fine aggregate with WPVC waste in various weight percentages (10, 20, 30, 40, 50, 75, and 100%). A control mix with 0% replacement was also prepared. The W/C ratio was about 0.5 for all mixes. Compressive, flexure strength, bulk density, and absorption tests were studied. For WPVC replacement, until 30%, compressive strength and flexure strength are acceptable with respect to standerds. Thermal treatment at 200 °C improves the compressive strength, flexure strength and water absorption for 20% WPVC only. The dielectric properties of all cement paste mixes before and after heat treatment, over a frequency range (0.1–106 Hz), were measured as a function of frequency. For dielectric properties and conductivity, an improvement was obtained until 30% WPVC. After this percentage, the dielectric properties and the conductivity got worse. So, cement paste with 30% WPVC as replacement of sand is the optimum ratio with conductivity in range of 10−12 S/cm, which is a good choice for antistatic cement paste applications (10−10–10−12 S/cm). The antimicrobial efficacy of the prepared cement samples of WPVC concentrations (0, 20 and 30) % were studied, the number of grown microbial colonies decreased for all the samples compared to control tap water and decreased by introducing WPVC into the cement paste sample. So, it is recommended to use these samples in places that should be carefully shielded from bacterial infections and static electric charge dangers.
The association between dietary intake of branched-chain amino acids and odds and severity of rheumatoid arthritis
Authors: Soleimani Damaneh Mohadeseh , Aryaeian Naheed , Khajoenia Shole , Azadbakht Leila , Hosseini-Baharanchi Fatemeh Sadat 
Published: March 2024

AbstractThis case–control study investigated the link between dietary branched-chain amino acids (BCAAs) and the risk and severity of rheumatoid arthritis (RA). We assessed dietary BCAA intake in 95 RA patients and 190 matched controls using a food frequency questionnaire. We also assessed the disease severity using the disease activity score 28 (DAS-28), ESR, VAS, morning stiffness, and tender and swollen joints. Higher BCAA intake, expressed as a percentage of total protein, was significantly associated with increased risk of RA for total BCAAs (OR 2.14, 95% CI 1.53–3.00, P < 0.001), leucine (OR 2.40, 95% CI 1.70–3.38, P < 0.001), isoleucine (OR 2.04, 95% CI 1.46–2.85, P < 0.001), and valine (OR 1.87, 95% CI 1.35–2.59, P < 0.001). These associations remained significant even after adjusting for potential confounders (P < 0.001). However, BCAA intake did not show any significant association with RA severity in either crude or multivariate models (P > 0.05). Our findings suggest that higher dietary BCAA intake may contribute to the development of RA, but further research is needed to confirm these observations and explore the underlying mechanisms.
Potential fumigant toxicity of essential oils against Sitotroga cerealella (Olivier) (Lepidoptera: Gelechiidae) and its egg parasitoid Trichogramma evanescens (Hymenoptera: Trichogrammatidae)
Authors: Elbehery Huda H. , Ibrahim Samar S. 
Published: March 2024

AbstractSitotroga cerealella is a serious pest of a wide range of stored cereal grains. An essential element of an integrated pest control approach is the application of plant oils as a substitute for chemical insecticides. This study aimed to investigate the fumigant toxicity of Allium sativum and Mentha piperita essential oils against S. cerealella adult moths and the egg parasitoid Trichogramma evanescens. Gas chromatography–mass spectrometry analyses detected that Diallyl trisulfide (37.97%) and dl-Menthol (47.67%) as main compounds in A. sativum and M. piperita, respectively. The results showed that, A. sativum at 10.0, 5.0, and 2.5 µL/L air resulted in 100% insect mortality after 24 h exposure. The concentrations of 10.0 and 5.0 µL/L air of M. piperita oil resulted in 100 and 96% insect mortality, respectively. The parasitoid adult emergence in the F1 reduced when exposed to LC99 of A. sativum and M. piperita oils by 10.89 and 9.67%, respectively. Also, the parasitism of emerged parasitoid decreased by 9.25 and 5.84% (class I-harmless), respectively. Therefore A. sativum and M. piperita have the potential to be used as bio-fumigant for the management of S. cerealella and can be used alongside the T. evanescens in integrated pest management.
Gα12 and endoplasmic reticulum stress-mediated pyroptosis in a single cycle of dextran sulfate-induced mouse colitis
Authors: Tak Jihoon , An Quanxi , Lee Sang Gil , Lee Chang Hoon , Kim Sang Geon 
Published: March 2024

AbstractInflammatory bowel disease (IBD) pathogenesis involves complex inflammatory events and cell death. Although IBD involves mainly necrosis in the digestive tract, pyroptosis has also been recognized. Nonetheless, the underlying basis is elusive. Gα12/13 overexpression may affect endoplasmic reticulum (ER) stress. This study examined how Gα12/13 and ER stress affect pyroptosis using dextran sulfate sodium (DSS)-induced colitis models. Gα12/13 levels were increased in the distal and proximal colons of mice exposed to a single cycle of DSS, as accompanied by increases of IRE1α, ATF6, and p-PERK. Moreover, Il-6, Il-1β, Ym1, and Arg1 mRNA levels were increased with caspase-1 and IL-1β activation, supportive of pyroptosis. In the distal colon, RIPK1/3 levels were enhanced to a greater degree, confirming necroptosis. By contrast, the mice subjected to three cycles of DSS treatments showed decreases of Gα12/13, as accompanied by IRE1α and ATF6 suppression, but increases of RIPK1/3 and c-Cas3. AZ2 treatment, which inhibited Gα12, has an anti-pyroptotic effect against a single cycle of colitis. These results show that a single cycle of DSS-induced colitis may cause ER stress-induced pyroptosis as mediated by Gα12 overexpression in addition to necroptosis, but three cycles model induces only necroptosis, and that AZ2 may have an anti-pyroptotic effect.