bluuebunny/crossref_metadata_2025 huggingface dataset:
Mitigation of acute lung injury by human bronchial epithelial cell-derived extracellular vesicles via ANXA1-mediated FPR signaling
Authors: Fujita Yu , Kadota Tsukasa , Kaneko Reika , Hirano Yuta , Fujimoto Shota , Watanabe Naoaki , Kizawa Ryusuke , Ohtsuka Takashi , Kuwano Kazuyoshi , Ochiya Takahiro , Araya Jun
Published: May 2024

Acute lung injury (ALI) is characterized by respiratory failure resulting from the disruption of the epithelial and endothelial barriers as well as immune system. In this study, we evaluated the therapeutic potential of airway epithelial cell-derived extracellular vesicles (EVs) in maintaining lung homeostasis. We isolated human bronchial epithelial cell-derived EVs (HBEC-EVs), which endogenously express various immune-related surface markers and investigated their immunomodulatory potential in ALI. In ALI cellular models, HBEC-EVs demonstrated immunosuppressive effects by reducing the secretion of proinflammatory cytokines in both THP-1 macrophages and HBECs. Mechanistically, these effects were partially ascribed to nine of the top 10 miRNAs enriched in HBEC-EVs, governing toll-like receptor-NF-κB signaling pathways. Proteomic analysis revealed the presence of proteins in HBEC-EVs involved in WNT and NF-κB signaling pathways, pivotal in inflammation regulation. ANXA1, a constituent of HBEC-EVs, interacts with formyl peptide receptor (FPR)2, eliciting anti-inflammatory responses by suppressing NF-κB signaling in inflamed epithelium, including type II alveolar epithelial cells. In a mouse model of ALI, intratracheal administration of HBEC-EVs reduced lung injury, inflammatory cell infiltration, and cytokine levels. Collectively, these findings suggest the therapeutic potential of HBEC-EVs, through their miRNAs and ANXA1 cargo, in mitigating lung injury and inflammation in ALI patients.
N(alpha)-acetyltransferase 40-mediated histone acetylation plays an important role in ecdysone regulation of metamorphosis in the red flour beetle, Tribolium castaneum
Authors: Gaddelapati Sharath Chandra , George Smitha , Moola Anilkumar , Sengodan Karthi , Palli Subba Reddy
Published: May 2024

Histone acetylation, a crucial epigenetic modification, is governed by histone acetyltransferases (HATs), that regulate many biological processes. Functions of HATs in insects are not well understood. We identified 27 HATs and determined their functions using RNA interference (RNAi) in the model insect, Tribolium castaneum. Among HATs studied, N-alpha-acetyltransferase 40 (NAA40) knockdown caused a severe phenotype of arrested larval development. The steroid hormone, ecdysone induced NAA40 expression through its receptor, EcR (ecdysone receptor). Interestingly, ecdysone-induced NAA40 regulates EcR expression. NAA40 acetylates histone H4 protein, associated with the promoters of ecdysone response genes: EcR, E74, E75, and HR3, and causes an increase in their expression. In the absence of ecdysone and NAA40, histone H4 methylation by arginine methyltransferase 1 (ART1) suppressed the above genes. However, elevated ecdysone levels at the end of the larval period induced NAA40, promoting histone H4 acetylation and increasing the expression of ecdysone response genes. NAA40 is also required for EcR, and steroid-receptor co-activator (SRC) mediated induction of E74, E75, and HR3. These findings highlight the key role of ecdysone-induced NAA40-mediated histone acetylation in the regulation of metamorphosis.
Severe cardiac and skeletal manifestations in DMD-edited microminipigs: an advanced surrogate for Duchenne muscular dystrophy
Authors: Otake Masayoshi , Imamura Michihiro , Enya Satoko , Kangawa Akihisa , Shibata Masatoshi , Ozaki Kinuyo , Kimura Koichi , Ono Etsuro , Aoki Yoshitsugu
Published: May 2024

Duchenne muscular dystrophy (DMD) is an intractable X-linked muscular dystrophy caused by mutations in the DMD gene. While many animal models have been used to study the disease, translating findings to humans has been challenging. Microminipigs, with their pronounced physiological similarity to humans and notably compact size amongst pig models, could offer a more representative model for human diseases. Here, we accomplished precise DMD modification in microminipigs by co-injecting embryos with Cas9 protein and a single-guide RNA targeting exon 23 of DMD. The DMD-edited microminipigs exhibited pronounced clinical phenotypes, including perturbed locomotion and body-wide skeletal muscle weakness and atrophy, alongside augmented serum creatine kinase levels. Muscle weakness was observed as of one month of age, respiratory and cardiac dysfunctions emerged by the sixth month, and the maximum lifespan was 29.9 months. Histopathological evaluations confirmed dystrophin deficiency and pronounced dystrophic pathology in the skeletal and myocardial tissues, demonstrating that these animals are an unprecedented model for studying human DMD. The model stands as a distinct and crucial tool in biomedical research, offering deep understanding of disease progression and enhancing therapeutic assessments, with potential to influence forthcoming treatment approaches.
Synthetic phage-based approach for sensitive and specific detection of Escherichia coli O157
Authors: Tamura Azumi , Azam Aa Haeruman , Nakamura Tomohiro , Lee Kenichi , Iyoda Sunao , Kondo Kohei , Ojima Shinjiro , Chihara Kotaro , Yamashita Wakana , Cui Longzhu , Akeda Yukihiro , Watashi Koichi , Takahashi Yoshimasa , Yotsuyanagi Hiroshi , Kiga Kotaro
Published: May 2024

Escherichia coli O157 can cause foodborne outbreaks, with infection leading to severe disease such as hemolytic-uremic syndrome. Although phage-based detection methods for E. coli O157 are being explored, research on their specificity with clinical isolates is lacking. Here, we describe an in vitro assembly-based synthesis of vB_Eco4M-7, an O157 antigen-specific phage with a 68-kb genome, and its use as a proof of concept for E. coli O157 detection. Linking the detection tag to the C-terminus of the tail fiber protein, gp27 produces the greatest detection sensitivity of the 20 insertions sites tested. The constructed phage detects all 53 diverse clinical isolates of E. coli O157, clearly distinguishing them from 35 clinical isolates of non-O157 Shiga toxin-producing E. coli. Our efficient phage synthesis methods can be applied to other pathogenic bacteria for a variety of applications, including phage-based detection and phage therapy.
Quantum sensing of microRNAs with nitrogen-vacancy centers in diamond
Authors: Zalieckas Justas , Greve Martin M. , Bellucci Luca , Sacco Giuseppe , Håkonsen Verner , Tozzini Valentina , Nifosì Riccardo
Published: May 2024

Label-free detection of nucleic acids such as microRNAs holds great potential for early diagnostics of various types of cancers. Measuring intrinsic biomolecular charge using methods based on field effect has been a promising way to accomplish label-free detection. However, the charges of biomolecules are screened by counter ions in solutions over a short distance (Debye length), thereby limiting the sensitivity of these methods. Here, we measure the intrinsic magnetic noise of paramagnetic counter ions, such as Mn2+, interacting with microRNAs using nitrogen-vacancy (NV) centers in diamond. All-atom molecular dynamics simulations show that microRNA interacts with the diamond surface resulting in excess accumulation of Mn ions and stronger magnetic noise. We confirm this prediction by observing an increase in spin relaxation contrast of the NV centers, indicating higher Mn2+ local concentration. This opens new possibilities for next-generation quantum sensing of charged biomolecules, overcoming limitations due to the Debye screening.
Vaccine effectiveness against emerging COVID-19 variants using digital health data
Authors: Varrelman Tanner J. , Rader Benjamin , Remmel Christopher , Tuli Gaurav , Han Aimee R. , Astley Christina M. , Brownstein John S.
Published: May 2024

Background

Participatory surveillance of self-reported symptoms and vaccination status can be used to supplement traditional public health surveillance and provide insights into vaccine effectiveness and changes in the symptoms produced by an infectious disease. The University of Maryland COVID Trends and Impact Survey provides an example of participatory surveillance that leveraged Facebook’s active user base to provide self-reported symptom and vaccination data in near real-time.

Methods

Here, we develop a methodology for identifying changes in vaccine effectiveness and COVID-19 symptomatology using the University of Maryland COVID Trends and Impact Survey data from three middle-income countries (Guatemala, Mexico, and South Africa). We implement conditional logistic regression to develop estimates of vaccine effectiveness conditioned on the prevalence of various definitions of self-reported COVID-like illness in lieu of confirmed diagnostic test results.

Results

We highlight a reduction in vaccine effectiveness during Omicron-dominated waves of infections when compared to periods dominated by the Delta variant (median change across COVID-like illness definitions: −0.40, IQR[−0.45, −0.35]. Further, we identify a shift in COVID-19 symptomatology towards upper respiratory type symptoms (i.e., cough and sore throat) during Omicron periods of infections. Stratifying COVID-like illness by the National Institutes of Health’s (NIH) description of mild and severe COVID-19 symptoms reveals a similar level of vaccine protection across different levels of COVID-19 severity during the Omicron period.

Conclusions

Participatory surveillance data alongside methodologies described in this study are particularly useful for resource-constrained settings where diagnostic testing results may be delayed or limited.
Density functional theory study of the electronic and optical properties of pentagraphyne nanotubes
Authors: Deb Jyotirmoy , Singh N. Bedamani , Sarkar Utpal
Published: May 2024

Pentagraphyne nanotubes (PG-yneNTs), a novel one-dimensional (1D) carbon allotrope with fascinating electronic and optical properties, paving the way for diverse applications.
Synthesis and growth mechanism of vertically aligned graphene sheets with precise control over the number of layers for lithium–oxygen batteries
Authors: Kumar Atul , Dager Akansha , Kumar Mukesh , Shamra Sudhanshu , Baliyan Ankur , Kumar Vinit
Published: May 2024

Engineering carbon nanowall (CNW) nanostructures is a daunting task. Machine learning powered analysis can assist the synthesis of vertical few-layer graphene (FLGs) nanostructures with precise control over the layers.
Efficient mapping of CO adsorption on Cu1−xMx bimetallic alloys via machine learning
Authors: Salomone Mattia , Re Fiorentin Michele , Risplendi Francesca , Raffone Federico , Sommer Timo , García-Melchor Max , Cicero Giancarlo
Published: May 2024

A two-step machine learning model to predict CO binding energies on CuM(111)/(100) bimetallic surfaces and enhance the CO2RR selectivity towards C2 products.
Effects of the multiscale porosity of decellularized platelet-rich fibrin-loaded zinc-doped magnesium phosphate scaffolds in bone regeneration
Authors: Rath Pritish , Mandal Santanu , Das Pratik , Sahoo Satyabrata Nigamananda , Mandal Samiran , Ghosh Debaki , Nandi Samit Kumar , Roy Mangal
Published: May 2024

In recent years, metallic ion-doped magnesium phosphate (MgP)-based degradable bioceramics have emerged as alternative bone substitute materials owing to their excellent biocompatibility, bone-forming ability, and controlled degradability.
A novel N-CNDs/PAni modified molecular imprinted polymer for ultraselective and sensitive detection of ciprofloxacin in lentic ecosystems: a dual responsive optical sensor
Authors: Murugan Komal , Natarajan Abirami
Published: May 2024

The research study describes the development of a hybrid nanocomposite called nitro-doped carbon nanodots/polyaniline/molecularly imprinted polymer (N-CNDs/PAni/MIP).
Dual modifications of sensitizers and lanthanide ions on a two-dimensional zirconium-based metal–organic framework for photoluminescent detection
Authors: Chang Jhe-Wei , Lin Tzu-Chi , Chen You-Liang , Han Po-Chun , Yang Shang-Cheng , Tsai Meng-Dian , Wu Kevin C.-W. , Kung Chung-Wei
Published: May 2024

Luminescent 2D Zr-based MOFs for sensing Fe(iii) ions were synthesized by dual post-synthetic modifications of photosensitizing ligands and terbium ions.
Exploration of 4-substituted thiophene-based azo dyes for dye-sensitized solar cells and non-linear optical materials: synthesis and an in silico approach
Authors: Sharma Suryapratap J. , Sekar Nagaiyan
Published: May 2024

Effect of secondary donor on DSSC performance.
An isotope dilution mass spectrometry overview: tips and applications for the measurement of radionuclides
Authors: Quemet Alexandre , Hubert Amélie , Gourgiotis Alkiviadis , Sánchez Hernández Ana María , Crozet Marielle , Bailly Guillaume , Dobney Andrew , Duhamel Georges , Hiess Joe , Repinc Urska , Mialle Sébastien , Boulet Béatrice , Escoube Raphaëlle , Bouvier-Capely Céline , Pointurier Fabien , Picart Sébastien
Published: May 2024

A useful guide and a critical review of the applications of ID-MS to radionuclide measurement is provided.
Switching to external flows: perturbations of developing vasculature within chicken chorioallantoic membrane
Authors: Padmanaban Prasanna , van Galen Danny , Salehi-Nik Nasim , Zakharova Mariia , Segerink Loes , Rouwkema Jeroen
Published: May 2024

Not only the flow of liquid through vasculature, but also external fluid flows can affect the organization and maturation of vessels.
Unveiling the potent activity of a synthetic ion transporter against multidrug-resistant Gram-positive bacteria and biofilms
Authors: Mukherjee Sudip , Shinde Sopan Valiba , Talukdar Pinaki , Haldar Jayanta
Published: May 2024

Synthetic ion-transporter kills multidrug-resistant Gram-positive bacteria and disrupts their biofilms.
Photodynamic treatment of Staphylococcus aureus with non-iron hemin analogs in the presence of hydrogen peroxide
Authors: Sivasubramaniam Badhu Prashanthika , Washer Benjamin M. , Watanabe Yuichiro , Ragheb Kathryn E. , Robinson J. Paul , Wei Alexander
Published: May 2024

The susceptibility of S. aureus to photodynamic inactivation can be greatly impacted by treatment with H2O2, depending on the timing of its exposure.
Templated gold nanocaps for surface-enhanced Raman scattering (SERS) sensors based on monolayer polystyrene colloidal arrays
Authors: Xia Yunjie , Sun Mengnan , Huang Rongjian , Qi Shuyan , Zhang Li , Jia Yaru , Li Zihou , Xu Huilin , Wang Mingkun , Huang Wei , Zhang Jiantao , Wu Aiguo , Chen Bo
Published: May 2024

Gold nanocaps modified with Ag nanoparticles exhibit superior SERS signals when compared to gold nanocaps and a silicon substrate, for the detection of rhodamine 6G molecules.
Engineering Co3O4@3DOM LaCoO3 multistage-pore nanoreactor with superior SO2 resistance for toluene catalytic combustion
Authors: Shi Zhan , Dong Fang , Han Weiliang , Dong Xiuyan , Tang Zhicheng
Published: May 2024

The Co3O4@LaCoO3 catalyst was prepared using Building-Bottle-Around-Ship strategies and demonstrated outstanding catalytic activity for the catalytic combustion of toluene and excellent resistance to sulfur due to the multilevel pore structure.
Strain-based design, direct macrocyclization, and metal complexation of thiazole-containing calix[3]pyrrole analogues
Authors: Watanabe Keita , Shibata Kotaro , Ichino Tomoya , Ide Yuki , Yoneda Tomoki , Maeda Satoshi , Inokuma Yasuhide
Published: May 2024

AFIR- and StrainViz-based evaluation of macrocyclic ring strain allowed rational design and high-yield synthesis of calix[3]pyrrole analogues. Among them, calix[1]pyrrole[2]thiazole afforded various metal complexes including water-stable organozinc.
Influence of alkali metal ions (K+ and Na+) on the preparation of magnesium hydroxide hexagonal flakes
Authors: Weng Cunjian , Song Xuewen , Zhu Haibin , Luo Xianping
Published: May 2024

Magnesium hydroxide (Mg(OH)2), as a green halogen-free flame retardant, has attracted significant attention in the field of flame retardant composite materials.
Photogalvanics of copper and brass working electrodes in the NaOH-Allura Red-d-galactose-DDAC electrolyte for solar power generation
Authors: Koli Pooran , Saren Jyoti
Published: May 2024

Experimental setup for the photogalvanics of copper and brass working electrodes (here,Ais a digital multimeter used as an ammeter;Vis another digital multimeter used as voltmeter;Ris a potentiometer/rheostat;Kis a key).
Enhanced photocatalytic efficiency of porous ZnO coral-like nanoplates for organic dye degradation
Authors: Hanh Nguyen Hong , Thi Minh Nguyet Quan , Van Chinh Tran , Duong La Duc , Xuan Tien Tran , Van Duy Lai , Hoa Nguyen Duc
Published: May 2024

ZnO nanomaterials have been extensively used as photocatalysts for the removal of pollutants in aqueous environments.
Probing capping mechanisms and polymer matrix loading of biogenic vaterite CaCO3–Ag hybrid through X-ray photoelectron spectroscopy (XPS)
Authors: Azarian Mohammad Hossein , Nijpanich Supinya , Chanlek Narong , Sutapun Wimonlak
Published: May 2024

XPS revealed Ag+ and Ag0 in biogenic vaterite CaCO3–Ag microspheres. CMC and PSS capping agents influenced Ag species distribution. Polymorph transformations and vaterite's stability were highlighted.
Alloying Pd with Ru enables electroreduction of nitrate to ammonia with ∼100% faradaic efficiency over a wide potential window
Authors: Hu Yue , Liu Jiawei , Luo Wenyu , Dong Jinfeng , Lee Carmen , Zhang Nan , Chen Mengxin , Xu Yifan , Wu Dongshuang , Zhang Mingsheng , Zhu Qiang , Hu Erhai , Geng Dongsheng , Zhong Lixiang , Yan Qingyu
Published: May 2024

A designed Pd74Ru26 achieved a high-level dynamic equilibrium of adsorption and coupling between *H and various nitrogen intermediates during eNO3−RR.
Clinically used drug arsenic trioxide targets XIAP and overcomes apoptosis resistance in an organoid-based preclinical cancer model
Authors: Shi Liwa , Lu Jing , Xia Xin , Liu Xue , Li Hongyan , Li Xinghua , Zhu Jun , Li Xiaofeng , Sun Hongzhe , Yang Xinming
Published: May 2024

Drug resistance in tumor cells remains a persistent clinical challenge in the pursuit of effective anticancer therapy. Herein, we repurpose clinically used drug arsenic trioxide to target XIAP and overcome cisplatin drug resistance in tumors.
Nanoscale and chiral metal–organic frameworks for asymmetric reactions in water: bridging Lewis acid catalysis and biological systems
Authors: Srimontree Watchara , Kitanosono Taku , Yamashita Yasuhiro , Kobayashi Shū
Published: May 2024

A new chiral UiO-type MOF with scandium tris(dodecyl sulfate) showed superior catalytic performance to the usual micellar catalysis in the presence of proteins, demonstrating the ability to prevent active Lewis acid sites from mortiferous deactivation.
Crucial gating residues govern the enhancement of peroxygenase activity in an engineered cytochrome P450 O-demethylase
Authors: Zhao Panxia , Jiang Yiping , Wang Qian , Chen Jie , Yao Fuquan , Cong Zhiqi
Published: May 2024

The structurally crucial gating effect is elucidated for regulating the inflow of H2O2 to enhance the peroxygenase activity of engineered CYP199A4 variants, which showed O-demethylation activity toward a variety of methoxy-substituted benzoic acids.
Upcycling of plastic waste to atomic nickel site-decorated carbon for efficient electrochemical CO2 conversion
Authors: Feng Lan-Hui , Lv Zhi-Hui , Kong Yi-Jie , Hu Xin-Ming
Published: May 2024

We recycle solid plastic waste to valorize gaseous CO2 waste, demonstrating a sustainable strategy to address the environmental problems of plastic pollution and climate change simultaneously.
An aqueous Zn-polyoxometalate battery for decoupled hydrogen production from alkaline water electrolysis
Authors: Wang Xin-Qing , Liu Meng-Jiao , Wu Xiao-Yuan , Wang Sa-Sa , Wu Weiming , Lu Can-Zhong
Published: May 2024

An aqueous Zn-polyoxometalate battery was designed for decoupled H2 production from water electrolysis with highly dispersed ultrafine Pt nanoparticles on nickel–cobalt hydroxide nanosheets at a low Pt loading as a free-standing HER electrode.
A redox-active porous polymer based on poly(imide-triazine) as a high-performance cathode for lithium-ion batteries
Authors: El Oueslati Refka , Jismy Badr , Flamme Benjamin , Leclerc Nicolas , Ghamouss Fouad , Abarbri Mohamed
Published: May 2024

A dual redox-active porous polymer cathode provides very high discharge capacity (422 mA h g−1 at 0.5 A g−1), excellent rate capability (268 mA h g−1 at 10 A g−1) and long-term cycling stability (80% retention after 500 cycles and 65% retention after 4000 cycles).
In situ construction of Ohmic/Schottky-type MoS2/Sv-ZnIn2S4/Cu(OH)2 dual-junction photocatalysts with enhanced water splitting into hydrogen generation activity
Authors: Yan Aihua , Zhang Tongyang , Huang Fei , Lu Shijian , Wang Quande , Yuan Huaqi , Gao Ye , Zhao Wenxue , Zhang Jixu , Su Zigao
Published: May 2024

Multichannel-optimized MoS2/Sv-ZnIn2S4/Cu(OH)2 composites, integrating sulfur vacancy, Ohmic junction and Schottky junction, were synthesized by an in situ technique. Benefiting from the synergistic effect, the staggered composites exhibited enhanced photocatalytic hydrogen production activity.
High proton conduction by full hydration in highly oxygen deficient perovskite
Authors: Saito Kei , Umeda Kensei , Fujii Kotaro , Mori Kazuhiro , Yashima Masatomo
Published: May 2024

We report high proton conductivity (10 mS cm−1 at 235 °C) of stable BaSc0.8W0.2O2.8, which is attributed to (1) high proton concentration due to full hydration and large amount of oxygen vacancies and (2) high proton mobility due to reduced proton trapping.
Dual delivery of carbon monoxide and doxorubicin using haemoglobin–albumin cluster: proof of concept for well-tolerated cancer therapy
Authors: Ito Chihiro , Taguchi Kazuaki , Yamada Taiga , Hanaya Kengo , Enoki Yuki , Sugai Takeshi , Komatsu Teruyuki , Matsumoto Kazuaki
Published: May 2024

The dual delivery of CO and DOX using HemoAct is a promising strategy as an anti-tumour agent to realise well-tolerated cancer therapy with minimal cardiotoxicity.
Lignin–cellulose complexes derived from agricultural wastes for combined antibacterial and tissue engineering scaffolds for cutaneous leishmaniasis wounds
Authors: Huët Marie Andrea Laetitia , Phul Itisha Chummun , Goonoo Nowsheen , Li Zhikai , Li Xiaopeng , Bhaw-Luximon Archana
Published: May 2024

Conversion of agricultural waste into tissue engineering scaffold for treatment of infected cutaneous leishmaniasis wounds.
A lightweight porous shear stiffening composite foam with excellent mechanical–thermal coupling protection performance
Authors: Xuan Tingting , Wang Sheng , Liu Shuai , Wang Wenhui , Li Zimu , Hu Yuan , Gong Xinglong
Published: May 2024

Lightweight SSE-EVA foam (SEF) with excellent compression resilience and mechanical-thermal protection was prepared by foaming. It owned application potential in thermal camouflage and thermal storage materials.
Assessing the design rules of electrides
Authors: Yao Zhikun , Zhao Yanzhen , Zhang Wenjun , Burton Lee A.
Published: May 2024

There are three heuristic criteria commonly used to identify electrides: an apparent valence of plus one, empty space in the crystal structure and the presence of a strongly electron-donating cation.
Cross‐talk reduction in metamaterial and non‐uniform transmission lines
Authors: Abbasi Hamid Reza , Rashed‐Mohassel Jalil A. , Moghadasi Mohammad Naser
Published: May 2024

The electromagnetic compatibility analysis of RF circuitry is essential due to the adverse effects on sensitive components. Two metamaterial unit cells with slow‐wave properties are presented for cross‐talk reduction in transmission lines. The analytical expressions for computing equivalent lumped elements of the lines are then provided. The dispersion diagram is obtained from the parameters extracted from the measurement. A microstrip as the generator line and five identical CRLH unit cells as the receptor line are then used and a significant reduction in cross‐talk is observed in comparison to conventional lines. A non‐uniform transmission line with two different CRLH unit cells as the receptor line is then employed and found effective in further cross‐talk reduction between the lines. The lengths of the lines and numbers of cells are kept the same in all lines for comparison. The simulated results are validated by measurements.
Abell 0399–Abell 0401 radio bridge spectral index: First multi-frequency detection
Authors: Pignataro G. V. , Bonafede A. , Bernardi G. , de Gasperin F. , Brunetti G. , Pasini T. , Vazza F. , Biava N. , de Jong J. M. G. H. J. , Cassano R. , Botteon A. , Brüggen M. , Röttgering H. J. A. , van Weeren R. J. , Shimwell T. W.
Published: May 2024

Aims. Recent low-frequency radio observations at 140 MHz discovered a bridge of diffuse emission with a length of 3 Mpc that connects the galaxy clusters Abell 0399 and Abell 0401. We present follow-up observations at 60 MHz to constrain the spectral index of the bridge, which has only been detected at 140 and 144 MHz so far.

Methods. We analysed deep (∼18 h) LOw Frequency ARray (LOFAR) Low Band Antenna (LBA) data at 60 MHz to detect the bridge at very low frequencies. We then conducted a multi-frequency study with LOFAR HBA data at 144 MHz and uGMRT data at 400 MHz. Assuming second-order Fermi mechanisms for the re-acceleration of relativistic electrons driven by turbulence in the radio bridge regions, we compared the observed radio spectrum with theoretical synchrotron models.

Results. The bridge is detected in the 75″ resolution LOFAR image at 60 MHz, and its emission fully connects the region between the two galaxy clusters. Between 60 MHz and 144 MHz, we found an integrated spectral index value of α60144 = −1.44 ± 0.16 for the bridge emission. For the first time, we produced spectral index and related uncertainties maps for a radio bridge. We produce a radio spectrum that shows a significant steepening between 144 and 400 MHz.

Conclusions. This detection at low frequencies provides important information for models of particle acceleration and magnetic field structure on very extended scales. The spectral index gives important clues about the origin of inter-cluster diffuse emission. The steepening of the spectrum above 144 MHz can be explained in a turbulent re-acceleration framework, assuming that the acceleration timescales are longer than ∼200 Myr.
Response of the nitrification sludge to oxytetracycline and operating the nitrifying reactor for oxytetracycline wastewater treatment
Authors: Lv Wei , Chen Yongzhi
Published: May 2024

The nitrify-based technology has already been regarded as an economical and efficient strategy to remove nitrogen. This study investigated different oxytetracycline (OTC) concentrations inhibited the nitrifying process of an aerobic wastewater treatment system in short-term shocks. The stability of ammonia nitrogen removal had declined trend and demonstrated nitrite accumulation when the concentration of oxytetracycline was 0,1,2,5,10,20mg/L, respectively. And the ammonia oxidation reaction time decreased from 240 min to 120 min. Mixed liquid suspended solids (MLSS) decreased by 50.69%, 48.53%, 74.28%, 65.03%, and 72.97%, respectively. Compared to control OTC (0 mg/L), S-PN decreased from 2.256 mg·gVSS-1 to 0.016 mg·gVSS-1, 0.294 mg·gVSS-1, 0.094 mg·gVSS-1, 0.649 mg·gVSS-1, 0.349 mg·gVSS-1. Total EPS decreased from 7.795 mg·gVSS-1 by 17.00%, 32.91%, 45.09%, 43.04%, and 29.57%, respectively. High-throughput sequencing analyses showed that Proteobacteria and Bacteroidetes were the most phylum. The relative abundance of Nitrospira decreased as the OTC concentration increased, while that of Comamonas increased.
Biogas Production from the Co- and Tri-digestion of Pineapple Wastes with Food Wastes and Pig Manure
Authors: Avena Louise Grace , Almendrala Michelle , Marron Eloi John , Obille Joseph Aldrich
Published: May 2024

Anaerobic digestion (AD) of pineapple wastes (PW) was determined to observe its effects on biogas production when co- and tri-digested with pig manure (PM) and food waste (FW). The highest cumulative biogas yield was seen in R3 (245 mL/g VS), followed by R4 (179 mL/g VS) and R1 (168 mL/g VS), while the lowest was recorded in R2 (150 mL/g VS). Co-digestion of PW with FW showed an increase of 45.8%, while tri-digestion of PW with PM and FW had an increase of 6.55% compared to the biogas yield of mono-digestion. However, co-digestion of PW with PM decreased by 10.7%, indicating an inhibitory effect.
Biogas Production from Napier Grass (Pennisetum purpureum) and Distillery Wastewater: Kinetic Study
Authors: Avena Louise Grace , Almendrala Michelle , Mojica Kristine Gayle , Rodriguez Rumina
Published: May 2024

Kinetic study was conducted for the biogas production from Napier grass and distillery wastewater. The experimental outcomes of batch reactors were fitted into modified Gompertz (MGM), modified Richards (MRM), and Logistics function (LF) kinetic models. Based on the results, MGM and MRM were found to be the best fit for biogas production from the anaerobic mono- and co-digestion of DWW and NG under specific conditions. Reactors R4 and R5, indicated a negative lag phase (λ), suggesting that biogas production commenced immediately on the first day and the respective systems are conducive to the survival of microorganisms. The maximum biogas potential (A) of the batches followed the order R2 < R1 < R3 < R4 < R5 while the maximum biogas production rate (Rm) of the batches in ascending order is R2 < R1 < R3 < R4 < R5.
A RESTful approach to tape management in StoRM
Authors: Vianello Enrico , Agostini Federica , Cappelli Laura , Diotalevi Tommaso , Galavotti Angelo , Gasparetto Jacopo , Giacomini Francesco , Lanzi Samuele , Miccoli Roberta , Shtimmerman Aksieniia , Vilaça Pinheiro Soares Marcelo
Published: May 2024

The STOrage Resource Manager (StoRM) service implements the SRM specification to recall files from tape. Although the SRM protocol has been successfully used for many years, its complexity has pushed the WLCG community to adopt a simpler approach, more coherent with current web te- chnologies. The WLCG tape REST API offers a common HTTP interface which allows clients to manage disk residency of tape-stored files and observe the progress of file transfers to disk. In the context of the StoRM project devel- oped at INFN-CNAF, the StoRM Tape service implements this HTTP interface. It is deployed as a standalone component and uses an NGINX reverse proxy as authentication engine and an Open Policy Agent (OPA) service as authorization policy decision point. This new service will be distributed at the INFN Tier-1 in order to coexist with the current StoRM deployments, in particular with the Grid-Enabled Mass Storage System (GEMSS).
EOS software evolution enabling LHC Run 3
Authors: Caffy Cedric , Amadio Guilherme , Guenther Jaroslav , Lekshmanan Abhishek , Mascetti Luca , Peters Andreas , Reis Manuel , Simon Michal Kamil , Sindrilaru Elvin , Smith David
Published: May 2024

EOS has been the main storage system at CERN for more than a decade, continuously improving in order to meet the ever evolving requirements of the LHC experiments and the whole physics user community. In order to satisfy the demands of LHC Run-3, in terms of storage performance and tradeoff between cost and capacity, EOS was enhanced with a set of new functionalities and features that we will detail in this paper.

First of all, we describe the use of erasure coded layouts in a large-scale deployment which enables an efficient use of available storage capacity, while at the same time providing end-users with better throughput when accessing their data. This new operating model implies more coupling between the machines in a cluster, which in turn leads to the next set of EOS improvements that we discuss, targeting I/O traffic shaping, better I/O scheduling policies and tagged traffic prioritization. Increasing the size of the EOS clusters to cope with experiment demands, means stringent constraints on the data integrity and durability that we addressed by a re-designed consistency check engine. Another focus area of EOS development was to minimize the operational load by making the internal operational procedures (draining, balancing or conversions) more robust and efficient, to allow managing easily multiple clusters and avoid possible scaling issues.

All these improvements available in the EOS 5 release series, are coupled with the new XRootD 5 framework which brings additional security features like TLS support and optimizations for large data transfers like page read and page write functionalities. Last but not least, the area of authentication/authorization methods has seen important developments by adding support for different types of bearer tokens that we will describe along with EOS specific token extensions. We conclude by highlighting potential areas of the EOS architecture that might require further developments or re-design in order to cope with the ever-increasing demands of our end-users.
Multidatabase The Future of the data storage in Particle Physics and Astronomy
Authors: Hřivnáč Julius , Peloton Julien
Published: May 2024

Particle Physics experiments and Astronomy telescopes store alarge amount of data, most of those data are usually stored in simple files in various formats. Databases are used only to a limited extend, while database technology has made a tremendous progress in recent years, offering a large spectrum of applications in all possible domains. Those possibilities are still largely underused.

The article demonstrates the data architecture transparently using multiple database types, namely SQL database, NoSQL database and Graph database. Each database is used for the domain where it is the most appropriate and the cross-technology access is offered to users. The strong and weak points of all three technologies are discussed. Several possible ways of organizing interactionbetweendatabases aredescribed.

The architecture is illustrated on the concrete implementation of the data storage oftheFinkproject, usingJanusGraph andHBasetechnologiesto store alerts from theRubinObservatory. HBaseis used to store thebulkdata and the structuralinformationis storedinGraphs, allowing transparent access to alldata and deep analyses of relationbetween alerts and other objects. Ways for implementing heterogeneous database architecture in general HEP applications are outlined.
Operation of the CERN disk storage infrastructure during LHC Run-3
Authors: Caffy Cedric , Amadio Guilherme , Arsuaga Rios Maria , Batalha Reis Manuel , Capitoni Niccolo , Contescu Cristian , Guenther Jaroslav , Mascetti Luca , Peters Andreas , Sindrilaru Elvin , Vrachnaki Ioanna , Lekshmanan Abhishek
Published: May 2024

The CERN IT Storage group operates multiple distributed storage systems to support all CERN data storage requirements. The storage and distribution of physics data generated by LHC and non-LHC experiments is one of the biggest challenges the group has to take on during LHC Run-3.

EOS [1], the CERN distributed disk storage system is playing a key role in LHC data-taking. During the first ten months of 2022, more than 440PB have been written by the experiments and 2.9EB have been read out. The data storage requirements of LHC Run-3 are higher than what was previously delivered. The storage operations team has started investigating multiple areas to upgrade and optimize the current storage resources. A new, dedicated and redundant EOS infrastructure based on 100Gbit servers was installed, commissioned and deployed for the ALICE Online and Offline (O2) project. This cluster can sustain high-throughput data transfer between the ALICE Event Processing Nodes (EPN) and the CERN’s data center.

This paper will present the architecture, techniques and workflows in place allowing EOS to deliver fast, reliable and scalable data storage to meet experiment needs during LHC Run-3 and beyond.
TileCalibWeb Robot tool for ATLAS Calorimeter conditions and calibrations data handling in Run 3
Authors: Smirnov Yuri , Chakraborty Dhiman , Parrish Elliot , Solodkov Alexander , Strizenec Pavol
Published: May 2024

Every sub-detector in the ATLAS experiment at the LHC, including Liquid Argon and TileCal, writes conditions and calibration data into an ORACLE Database (DB). In order to provide an interface for reliable interactions both with the Conditions Online and Offline DBs a unique semiautomatic web based application, TileCalibWeb Robot, has been developed. TileCalibWeb is being used in LHC Run 3 by ATLAS Calorimeter data preparation, data quality and calibration experts as well as by shifters on duty. The architecture and functionality of the tool is discussed. Use cases for updating the conditions data of various types and formats are presented. The interface provides the user with the option to choose the strategy of the DB update. Options include a short text input typed directly into the browser as well as more complicated methods using data files prepared in advance. TileCalibWeb significantly simplifies the procedure of the preparation and writing of conditions and calibration data both into Online and Offline DBs in parallel, verifies user input and automatically publishes bookkeeping records.
Using MQTT and Node-RED to monitor the ATLAS Meta-data Interface (AMI) stack and define metadata aggregation tasks in a pipelined way
Authors: Odier Jérôme , Lambert Fabian , Fulachier Jérôme , Jaume Maxime , Delsart Pierre-Antoine
Published: May 2024

ATLAS Metadata Interface (AMI) is a generic ecosystem for metadata aggregation, transformation and cataloging. Each sub-system of the stack has recently been improved in order to acquire messaging/telemetry capabilities. This paper describes the whole stack monitoring with the Message Queuing Telemetry Transport (MQTT) protocol and Node-RED, a tool for wiring together hardware/software devices. Finally, this paper shows how Node-RED is used to graphically define metadata aggregation tasks, in a pipelined way, without introducing any single point of failure.
XRootD S3 Gateway for WLCG Storage
Authors: Hanushevsky Andrew , Yang Wei
Published: May 2024

The S3 Gateway is a server based application that provides a bridge between protocols and security used in the HEP community to S3 protocols and its associated security model. This allows the use of common copy tools based on the HEP security models to store or download data from S3 based storage. This storage can reside in a public or private cloud. This paper details the motivation for implementing such a service and how it can address certain problem when dealing with storage only accessible via S3 protocol.
A High-Speed Asynchronous Data I/O Method for HEPS
Authors: Fu Shiyuan , Wang Lu , Cheng Yaodong , Hu Yu , Liu Rui , Wang Lei , Wang Shuang , Liu Jianli , Sun Haokai , Qi Fazhi
Published: May 2024

The High Energy Photon Source (HEPS) is expected to produce a substantial volume of data, lead to immense data I/O pressure during computing. Inefficient data I/O can significantly impact computing performance.

To address this challenge, firstly, we have developed a data I/O framework for HEPS. This framework consists of three layers: data channel layer, distributed memory management layer, and I/O interface layer. It mask the underlying data differences in formats and sources, while implementing efficient I/O methods. Additionally, it supports both stream computing and batch computing.

Secondly, we have designed a data processing pipeline scheme aimed at reducing I/O latency and optimizing I/O bandwidth utilization during the processing of high-throughput data. This involves breaking down the computing task into several stages, including data loading, data pre-processing, data processing, and data writing, which are executed asynchronously and in parallel.

Finally, we introduce the design of stream data I/O process. The primary objective of stream data I/O is to enable real-time online processing of raw data, avoiding I/O bottlenecks caused by disk storage. This approach ensures the stability of data transmission and integrates distributed memory management to guarantee data integrity in memory.
A vendor-unlocked ITS GPU reconstruction in ALICE
Authors: Concas Matteo
Published: May 2024

In LHC Run 3, ALICE experiment’s upgrades enable recording Pb-Pb collisions at a 50 kHz rate using trigger-less continuous readout, managing a peak data rate of 1 TB/s primarily through GPU utilization. Two main phases of data processing exist: the synchronous phase, focused on TPC reconstruction consuming most computing resources, and the asynchronous phase with more GPU resources available. The Inner Tracking System (ITS) has been successfully ported to GPUs for primary vertex finding and track reconstruction, leveraging automatic code generation to support multiple GPU brands with a single code base. This work not only enhances ALICE’s computational capability but also sets a precedent for offloading reconstruction tasks to GPUs in other detectors.
First year of experience with the new operational monitoring tool for data taking in CMS during Run 3
Authors: Amoiridis Vassileios , Behrens Ulf , Bocci Andrea , Branson James , Brummer Philipp , Cano Eric , Cittolin Sergio , Da Silva Almeida Da Quintanilha Joao , Darlea Georgiana-Lavinia , Deldicque Christian , Dobson Marc , Dvorak Antonin , Gigi Dominique , Glege Frank , Gomez-Ceballos Guillelmo , Gorniak Patrycja , Gutić Neven , Hegeman Jeroen , Izquierdo Moreno Guillermo , James Thomas Owen , Karimeh Wassef , Kartalas Miltiadis , Krawczyk Rafał Dominik , Li Wei , Long Kenneth , Meijers Frans , Meschi Emilio , Morović Srećko , Orsini Luciano , Paus Christoph , Petrucci Andrea , Pieri Marco , Rabady Dinyar Sebastian , Racz Attila , Rizopoulos Theodoros , Sakulin Hannes , Schwick Christoph , Šimelevičius Dainius , Tzanis Polyneikis , Vazquez Velez Cristina , Žejdl Petr , Zhang Yousen , Zogatova Dominika
Published: May 2024

The Online Monitoring System (OMS) at the Compact Muon Solenoid experiment (CMS) at CERN aggregates and integrates different sources of information into a central place and allows users to view, compare and correlate information. It displays real-time and historical information. The tool is heavily used by run coordinators, trigger experts and shift crews, to ensure the quality and efficiency of data taking. It provides aggregated information for many use cases including data certification. OMS is the successor of Web Based Monitoring (WBM), which was in use during Run 1 and Run 2 of the LHC. WBM started as a small tool and grew substantially over the years so that maintenance became challenging. OMS was developed from scratch following several design ideas: to strictly separate the presentation layer from the data aggregation layer, to use a well-defined standard for the communication between presentation layer and aggregation layer, and to employ widely used frameworks from outside the HEP community. A report on the experience from the operation of OMS for the first year of data taking of Run 3 in 2022 is presented.
Upgrade of Online Storage and Express-Reconstruction System for the Belle II experiment
Authors: Park Seokhee , Itoh Ryosuke , Suzuki Soh Yamagata , Jacobi Daniel , Yamada Satoru , Kunigo Takuto , Levit Dmytro
Published: May 2024

The backend of the Belle II data acquisition system consists of a high-level trigger system, online storage, and an express-reconstruction system for online data processing. The high-level trigger system was updated to use the ZeroMQ networking library from the old ring buffer and TCP/IP socket, and the new system is successfully operated. However, the online storage and express-reconstruction system use the old type of data transportation. For future maintainability, we expand the same ZeroMQ library-based system to the online storage and express-reconstruction system. At the same time, we introduce two more updates in the backend system. First, online side raw data output becomes compressed ROOT format which is the official format of the Belle II data. The update helps to reduce the bandwidth of the online to offline data transfer and offline-side computing resource usage for data format conversion and compression. Second, high-level trigger output-based event selection is included in the online storage. The event selection allows more statistics of data quality monitoring from the express-reconstruction system. In the presentation, we show the description and test result of the upgrade before applying it to the beam operation and data taking.
Geant4 electromagnetic physics for Run3 and Phase2 LHC
Authors: Hahnfeld Jonas , Ivanchenko Vladimir , Novak Mihaly , Pandola Luciano , Sawkey Daren
Published: May 2024

For the new Geant4 series 11.X, the electromagnetic (EM) physics sub-libraries were revised and reorganized in view of requirements for simulation of Phase-2 LHC experiments. EM physics simulation takes a significant fraction of the available CPU during massive production of Monte Carlo events for LHC experiments. We present the recent evolution of Geant4 EM sublibraries for the simulation of gamma, electron, and positron transport. Updates of other components of EM physics are also discussed. These developments are included in the new Geant4 version 11.1 (December 2022). The most important modifications concern the reorganization of the initialization of EM physics and the introduction of alternative tracking software. These modifications affect the CPU efficiency of any simulation, and CPU savings depend on geometry and physics configuration for the concrete experimental setup. We will discuss several methods: gamma general process, Woodcock tracking, transportation with multiple scattering process, alternative tracking manager, and the new G4HepEm library. These developments provide a basis for the implementation of EM particle transport on co-processors and GPU. We also will present very recent updates in physics processes and in configuration of EM physics.
PARSIFAL: Parametrized simulation of triple-GEM and micro-RWELL response to a charged particle
Authors: Farinelli R.
Published: May 2024

PARSIFAL (PARametrized SImulation) is a software tool that can reproduce the complete response of both triple-GEM and micro-RWELL-based trackers. It takes into account the involved physical processes by their simple parametrization and thus in a very fast way. Existing software such as GARFIELD++ is robust and reliable, but CPU time-consuming. The implementation of PARSIFAL was driven by the necessity to reduce the processing time, without losing the precision of a complete simulation. A series of parameters, that can be extracted from the GARFIELD++ simulation, are set as input to PARSIFAL, which then runs independently from GARFIELD++. PARSIFAL can simulate samples with high statistics much faster, taking into account the various steps (ionization, diffusion, multiplication, signal induction, and electronics) from the simple sampling from parameterized distributions. In the case of the micro-RWELL MPGD, the effect of the high resistivity layer on the charge spread on the anode was introduced, following M.S. Dixit and A. Rankin’s treatment. PARSIFAL was used to simulate triple-GEM chambers and the results were tuned to match experimental data from testbeams. In this case, the adopted electronics was APV-25 readout by SRS system, which has been simulated in the code. The same procedure was later applied to micro-RWELL chambers, readout by the TIGER ASIC and the GEMROC system. These new electronics were added to PARSIFAL code, and the simulated-to-real data was tuned. A presentation of the full code will be given in this contribution, setting the focus on the latest implementations and a first comparison with experimental data from micro-RWELL.