bluuebunny/crossref_metadata_2025_split huggingface dataset:
Cycle threshold dynamics of non–severe acute respiratory coronavirus virus 2 (SARS-CoV-2) respiratory viruses
Authors: Ehrenzeller Selina , Zaffini Rebecca , Pecora Nicole D. , Kanjilal Sanjat , Rhee Chanu , Klompas Michael 
Published: January 2024

AbstractObjective:Many providers use severe acute respiratory coronavirus virus 2 (SARS-CoV-2) cycle thresholds (Ct values) as approximate measures of viral burden in association with other clinical data to inform decisions about treatment and isolation. We characterized temporal changes in Ct values for non–SARS-CoV-2 respiratory viruses as a first step to determine whether cycle thresholds could play a similar role in the management of non–SARS-CoV-2 respiratory viruses.Design:Retrospective cohort study.Setting:Brigham and Women’s Hospital, Boston.Methods:We retrospectively identified all adult patients with positive nasopharyngeal PCRs for influenza, respiratory syncytial virus (RSV), parainfluenza, human metapneumovirus (HMPV), rhinovirus, or adenovirus between January 2022 and March 2023. We plotted Ct distributions relative to days since symptom onset, and we assessed whether distributions varied by immunosuppression and other comorbidities.Results:We analyzed 1,863 positive samples: 506 influenza, 502 rhinovirus, 430 RSV, 219 HMPV, 180 parainfluenza, 26 adenovirus. Ct values were generally 25–30 on the day of symptom onset, lower over the ensuing 1–3 days, and progressively higher thereafter with Ct values ≥30 after 1 week for most viruses. Ct values were generally higher and more stable over time for rhinovirus. There was no association between immunocompromised status and median intervals from symptom onset until Ct values were ≥30.Conclusions:Ct values relative to symptom onset for influenza, RSV, and other non–SARS-CoV-2 respiratory viruses generally mirror patterns seen with SARS-CoV-2. Further data on associations between Ct values and viral viability, transmissibility, host characteristics, and response to treatment for non-SARS-CoV-2 respiratory viruses are needed to determine how clinicians and infection preventionists might integrate Ct values into treatment and isolation decisions.
Functional response and mutual interference in the parasitoid Coptera haywardi (Oglobin) (Hymenoptera: Diapriidae) attacking Anastrepha ludens (Loew) (Diptera: Tephritidae) pupae
Authors: Clemente Gibran , Toledo Jorge , Pérez-Lachaud Gabriela , Valle-Mora Javier F. , Liedo Pablo , Montoya Pablo 
Published: January 2024

AbstractFunctional response and mutual interference are important attributes of natural enemies that should be analysed in species with the potential to be used as biological control agents in order to increase the predictive power of the possible benefits and/or consequences of their release in the field. Our main objective was to determine the functional response and mutual interference of Coptera haywardi (Oglobin), a pupal parasitoid of economically important fruit flies (Diptera: Tephritidae). The functional response of C. haywardi on A. ludens pupae corresponded to a type II model, with an attack rate of 0.0134 host pupa/h and a handling time of 1.843 h, which reveals a meticulous selection process of pupal hosts. The effect of mutual interference among foraging females was negatively correlated with increased parasitoid density in the experimental arena, showing a gradual decline in attack rate per individual female. The increase in the number of foraging females also had an impact on the number of oviposition scars per pupa and the number of immature parasitoids per dissected pupa, but not on the percentage of adult emergence or the sex ratio. Our results suggest that C. haywardi could act as a complementary parasitoid in the control of fruit fly pupae, since the random distribution of these pupae in the soil would decrease the possibility of aggregation and mutual interference between foraging females.
Fluctuation in redox conditions and the evolution of early Cambrian life constrained by nitrogen isotopes in the middle Yangtze Block, South China
Authors: Wei Kai , Cao Hansheng , Chen Fajin , Wang Zaiyun , An Zhihui , Huang Hanli , Chen Chunqing 
Published: January 2024

AbstractThe Ediacaran–Cambrian (E-C) transition (∼542–517 Ma) witnessed the rapid evolution of Cambrian animals, which was accompanied by carbon cycling anomalies and a significant increase in the concentration of oxygen in Earth’s atmosphere. The mechanisms stimulating the evolution of complex eukaryotes, however, remain problematic, especially concerning the link between biological evolution and contemporaneous changes in the oceanic environment. In this study, integrated δ13Ccarb–δ13Corg–δ15N compositions were analysed from the YD-4 core samples to understand redox fluctuations and nitrogen cycling of the middle Yangtze Block across the E-C transition. Two negative δ13Ccarb excursions (N1 and N2) and a positive δ13Ccarb excursion (P1) are identified from the studied samples and are supposedly of primary origin. Constrained by of the U-Pb age, biolithology and pattern of isotopic variation, N1, P1 and N2 are comparable to the Basal Cambrian Carbon Isotope Excursion (BACE), Zhujiaqing Carbon Isotope Excursion (ZHUCE) and Shiyantou Carbon Isotope Excursion (SHICE). We interpreted the decreased δ15N values in this study as resulting from intensified atmospheric nitrogen fixation driven by enhanced denitrification associated with expanded marine anoxia, as well as partial ammonium assimilation, while increased δ15N values suggest weakened denitrification associated with an amplified oxic water mass. The temporal coincidence of N1 and N2, with two episodes of negative δ15N excursions, and of P1, with a positive δ15N excursion, suggests that variable oceanic redox conditions and nitrogen bioavailability may have influenced the evolution of the Cambrian eukaryote-dominated community.
General Synod of the Church of Ireland
Authors: Turner Cate 
Published: January 2024

The Church of Ireland General Synod had been held online in 2021 and in person in 2022. This year – the third meeting of the triennium – the first two days were held in Clayton White's Hotel, Wexford (Friday 12 May and Saturday 13 May) with day 3 taking place remotely on the evening of Tuesday 16 May. (Another evening, Thursday 18 May, had also been set aside for meeting but this was not required.)
General Synod of the Church of England
Authors: Dobson Edward 
Published: January 2024

The first item of business at the February group of sessions was to revive the General Synod (Remote Meetings) (Temporary Standings Orders) Measure 2020, which enabled Synod to conduct hybrid meetings. Previously in operation during the COVID-19 pandemic, the standing order had lapsed and was brought back into operation until 5 February 2026.
Recurrent and chaotic outbreaks in SIR model
Authors: Gai Chunyi , Kolokolnikov Theodore , Schrader Jan , Sharma Vedant 
Published: January 2024

AbstractWe examine several extensions to the basic Susceptible-Infected-Recovered model, which are able to induce recurrent outbreaks (the basic Susceptible-Infected-Recovered model by itself does not exhibit recurrent outbreaks). We first analyse how slow seasonal variations can destabilise the endemic equilibrium, leading to recurrent outbreaks. In the limit of slow immunity loss, we derive asymptotic thresholds that characterise this transition. In the outbreak regime, we use asymptotic matching to obtain a two-dimensional discrete map which describes outbreak times and strength. We then analyse the resulting map using linear stability and numerics. As the frequency of forcing is increased, the map exhibits a period-doubling route to chaos which alternates with periodic outbreaks of increasing frequency. Other extensions that can lead to recurrent outbreaks include the addition of noise, state-dependent variation and fine-graining of model classes.
Beyond boundaries: exploring radiographers’ experiences and solutions in organ-at-risk delineation for radiotherapy planning
Authors: Attard Antoine , Mercieca Susan 
Published: January 2024

Abstract

Introduction:
This study aimed to assess the perception of radiographers on the difficulties encountered during the delineation of organs at risk (OARs) for radiotherapy planning and the methods that could be used to facilitate this process.

Methodology:
A self-designed questionnaire was distributed to all radiographers (n = 29) employed at the radiotherapy department in Malta. The survey assessed the challenges faced by the radiographers during the delineation of various OARs and inquired about the perceived effectiveness of specific measures that could be used to facilitate the delineation process using a Likert scale ranging from 1 (not difficult/effective) to 5 (very difficult/effective).

Results:
The response rate was 79%. Overall, the delineation of OARs was rated as slightly difficult (mean score 1.95 ± 0.33). Nevertheless, some OARs, such as the parotid, stomach and brain stem, were deemed more difficult to contour with a mean score of 3 or higher. The implementation of peer review was perceived as the most influential factor in reducing delineation difficulty (mean score 4.59 ± 0.58), followed by contouring training (mean score 4.48 ± 0.58) and training on artificial intelligence (AI) (mean score 4.35 ± 0.48).

Conclusion:
The introduction of peer review, training and AI could facilitate the delineation of OARs.
Hydrothermal Seepage of Altered Crustal Formation Water Seaward of the Middle America Trench, Offshore Costa Rica
Authors: Parsons Patrice K. F. , Wheat C. Geoffrey , Fisher Andrew T. , Silver Eli A. , Hutnak Michael 
Published: January 2024

AbstractChemical compositions of sediment pore waters are presented from 13 piston and gravity cores that were collected on ∼24 Ma crust of the Cocos Plate seaward of the Middle America Trench and near the onset of crustal faulting from subduction. Cores were collected mainly within a 1.75 km2 area overlying a buried basement topographic high that supports an elevated heat flux, consistent with seawater transport within the upper volcanic crust. Systematic variations in pore water chemical profiles indicate upward seepage speeds (up to 1.7 cm yr−1 providing a net flux of 0.1 L s−1), constrain the chemical composition of the formation water within the underlying upper basaltic basement, and elucidate diagenetic reactions in the sediment. Relative to seawater, formation water has an elevated temperature (70–80°C) and concentrations or values of Ca, chlorinity, Sr, Ba, Li, Fe, Mn, Si, Cs, D/H, and Mo, and lower concentrations or values of Mg, Na, sulfate, alkalinity, TCO2, K, B, F, phosphate, 87Sr/86Sr, δ13C, δ18O, U, and Rb. Although this site is located only 30 km from the trench axis, there is no chemical evidence for subduction‐related hydrologic influences. Instead, the data are explained by a combination of seawater‐basalt reactions within the upper basement and diffusive exchange with overlying sediment, as part of a shallow, ridge‐flank hydrothermal system. It is unclear why this site has an elevated heat flux relative to neighboring crust, but this may result from variations in crustal properties or modification related to flexural faulting outboard of the trench.
Remote Sensing Measurements at a Rural Site in China: Implications for Satellite NO2 and HCHO Measurement Uncertainty and Emissions From Fires
Authors: Chong Kezhen , Wang Yuhang , Liu Cheng , Gao Yang , Boersma K. Folkert , Tang Jianhui , Wang Xinming 
Published: January 2024

AbstractNitrogen dioxide (NO2) and formaldehyde (HCHO) play vital roles in atmospheric photochemical processes. Their tropospheric vertical column density (TVCD) distributions have been monitored by satellite instruments. Evaluation of these observations is essential for applying these observations to study photochemistry. Assessing satellite products using observations at rural sites, where local emissions are minimal, is particularly useful due in part to the spatial homogeneity of trace gases. In this study, we evaluate OMI and TROPOMI NO2 and HCHO TVCDs using multi‐axis differential optical absorption spectroscopy (MAX‐DOAS) measurements at a rural site in the east coast of the Shandong province, China in spring 2018 during the Ozone Photochemistry and Export from China Experiment (OPECE) measurement campaign. On days not affected by local burning, we found generally good agreement of NO2 data after using consistent a priori profiles in satellite and MAX‐DOAS retrievals and accounting for low biases in scattering weights in one of the OMI products. In comparison, satellite HCHO products exhibited weaker correlations with MAX‐DOAS data, in contrast to satellite NO2 products. However, TROPOMI HCHO products showed significantly better agreement with MAX‐DOAS measurements compared to OMI data. Furthermore, case studies of the vertical profiles measured by MAX‐DOAS on burning days revealed large enhancements of nitrous acid (HONO), NO2, and HCHO in the upper boundary layer, accompanied with considerable variability, particularly in HONO enhancements.
Activation of Ca2+ phosphatase Calcineurin regulates Parkin translocation to mitochondria and mitophagy in flies
Authors: Marchesan Elena , Nardin Alice , Mauri Sofia , Bernardo Greta , Chander Vivek , Di Paola Simone , Chinellato Monica , von Stockum Sophia , Chakraborty Joy , Herkenne Stephanie , Basso Valentina , Schrepfer Emilie , Marin Oriano , Cendron Laura , Medina Diego L. , Scorrano Luca , Ziviani Elena 
Published: January 2024

AbstractSelective removal of dysfunctional mitochondria via autophagy is crucial for the maintenance of cellular homeostasis. This event is initiated by the translocation of the E3 ubiquitin ligase Parkin to damaged mitochondria, and it requires the Serine/Threonine-protein kinase PINK1. In a coordinated set of events, PINK1 operates upstream of Parkin in a linear pathway that leads to the phosphorylation of Parkin, Ubiquitin, and Parkin mitochondrial substrates, to promote ubiquitination of outer mitochondrial membrane proteins. Ubiquitin-decorated mitochondria are selectively recruiting autophagy receptors, which are required to terminate the organelle via autophagy. In this work, we show a previously uncharacterized molecular pathway that correlates the activation of the Ca2+-dependent phosphatase Calcineurin to Parkin translocation and Parkin-dependent mitophagy. Calcineurin downregulation or genetic inhibition prevents Parkin translocation to CCCP-treated mitochondria and impairs stress-induced mitophagy, whereas Calcineurin activation promotes Parkin mitochondrial recruitment and basal mitophagy. Calcineurin interacts with Parkin, and promotes Parkin translocation in the absence of PINK1, but requires PINK1 expression to execute mitophagy in MEF cells. Genetic activation of Calcineurin in vivo boosts basal mitophagy in neurons and corrects locomotor dysfunction and mitochondrial respiratory defects of a Drosophila model of impaired mitochondrial functions. Our study identifies Calcineurin as a novel key player in the regulation of Parkin translocation and mitophagy.
Inhibition of NRF2 enhances the acute myeloid leukemia cell death induced by venetoclax via the ferroptosis pathway
Authors: Yu Xibao , Wang Yan , Tan Jiaxiong , Li Yuchen , Yang Pengyue , Liu Xuan , Lai Jing , Zhang Yue , Cai Letong , Gu Yinfeng , Xu Ling , Li Yangqiu 
Published: January 2024

AbstractVenetoclax, an inhibitor that selectively targets B cell lymphoma-2 (BCL-2) that has been approved for treating adult acute myeloid leukemia (AML) in combination with hypomethylating agents. However, its short duration of response and emergence of resistance are significant issues. In this study, we found that the sensitivity of AML cells to venetoclax was considerably enhanced by ML385, an inhibitor of the ferroptosis factor nuclear transcription factor erythroid 2-related factor 2 (NRF2). Using AML samples, we verified that NRF2 and its target gene ferritin heavy chain 1 (FTH1) were highly expressed in patients with AML and correlated with poor prognosis. Downregulation of NRF2 could inhibit FTH1 expression and significantly enhance the venetoclax-induced labile iron pool and lipid peroxidation. By contrast, NRF2 overexpression or administration of the reactive oxygen species inhibitor N-acetylcysteine and vitamin E could effectively suppress the anti-AML effects of ML385+venetoclax. Furthermore, the ferroptosis inducer erastin increased the anti-AML effects of venetoclax. Our study demonstrated that NRF2 inhibition could enhance the AML cell death induced by venetoclax via the ferroptosis pathway. Thus, the combination of ML385 with venetoclax may offer a favorable strategy for AML treatment.
Long-term intake of Lactobacillus helveticus enhances bioavailability of omega-3 fatty acids in the mouse retina
Authors: Lapaquette Pierre , Terrat Sébastien , Proukhnitzky Lil , Martine Lucy , Grégoire Stéphane , Buteau Bénédicte , Cabaret Stéphanie , Rieu Aurélie , Bermúdez-Humarán Luis G. , Gabrielle Pierre-Henry , Creuzot-Garcher Catherine , Berdeaux Olivier , Acar Niyazi , Bringer Marie-Agnès 
Published: January 2024

AbstractOmega-3 (n-3) polyunsaturated fatty acids (PUFAs), particularly docosahexaenoic acid (DHA), are required for the structure and function of the retina. Several observational studies indicate that consumption of a diet with relatively high levels of n-3 PUFAs, such as those provided by fish oils, has a protective effect against the development of age-related macular degeneration. Given the accumulating evidence showing the role of gut microbiota in regulating retinal physiology and host lipid metabolism, we evaluated the potential of long-term dietary supplementation with the Gram-positive bacterium Lactobacillus helveticus strain VEL12193 to modulate the retinal n-3 PUFA content. A set of complementary approaches was used to study the impact of such a supplementation on the gut microbiota and host lipid/fatty acid (FA) metabolism. L. helveticus-supplementation was associated with a decrease in retinal saturated FAs (SFAs) and monounsaturated FAs (MUFAs) as well as an increase in retinal n-3 and omega-6 (n-6) PUFAs. Interestingly, supplementation with L. helveticus enriched the retina in C22:5n-3 (docosapentaenoic acid, DPA), C22:6n-3 (DHA), C18:2n-6 (linoleic acid, LA) and C20:3n-6 (dihomo gamma-linolenic acid, DGLA). Long-term consumption of L. helveticus also modulated gut microbiota composition and some changes in OTUs abundance correlated with the retinal FA content. This study provides a proof of concept that targeting the gut microbiota could be an effective strategy to modulate the retinal FA content, including that of protective n-3 PUFAs, thus opening paths for the design of novel preventive and/or therapeutical strategies for retinopathies.
The corrosion mechanism of lead-glazed pottery in Han dynasty
Authors: Zhang Kexin , Wu Chen , Zhao Jing , Yu Wendi , Zhao Meng 
Published: January 2024

AbstractAncient pottery, having endured prolonged burial in soil, invariably underwent the process of glaze corrosion. The micromorphology and structural composition of four lead-glazed pottery fragments dating back to the Han Dynasty, excavated in the Qinhan New Town within Xixian New area of Xi’an are elucidated by comprehensive analysis method. The results reveal that the corrosion products predominantly comprised PbCO3, Pb3(PO4)2, CaCO3, and Ca3(PO4)2. Concurrently, the presence of organic substances exhibiting characteristic self-excitation fluorescence in the cracks of the sample is identified through fluorescence microscopy and Fourier infrared spectroscopy. Through a comparative analysis of well-preserved and severely corroded samples, taking into account compositional analysis, observations of corrosion morphology, and the characteristics of corrosion products, it is deduced that the primary corrosion mechanisms involve chemical corrosion, microbial corrosion, and crack corrosion. This study provides a comprehensive depiction of glaze corrosion process inherent to lead-glazed pottery and establishes corresponding corrosion models.
Non-Hermitian topology in a multi-terminal quantum Hall device
Authors: Ochkan Kyrylo , Chaturvedi Raghav , Könye Viktor , Veyrat Louis , Giraud Romain , Mailly Dominique , Cavanna Antonella , Gennser Ulf , Hankiewicz Ewelina M. , Büchner Bernd , van den Brink Jeroen , Dufouleur Joseph , Fulga Ion Cosma 
Published: January 2024

AbstractQuantum devices characterized by non-Hermitian topology are predicted to show highly robust and potentially useful properties for precision sensing and signal amplification. However, realizing them has remained a daunting experimental task, as non-Hermiticity is often associated with gain and loss, which would require precise tailoring to produce the signatures of non-trivial topology. Here, instead of gain and loss, we use the non-reciprocity of quantum Hall edge states to directly observe non-Hermitian topology in a multi-terminal quantum Hall ring. Our transport measurements evidence a robust, non-Hermitian skin effect, characterized by currents and voltages showing an exponential profile that persists across Hall plateau transitions away from the regime of maximum non-reciprocity. Our observation of non-Hermitian topology in a quantum device introduces a scalable experimental approach to construct and investigate generic non-Hermitian systems.
KARR-seq reveals cellular higher-order RNA structures and RNA–RNA interactions
Authors: Wu Tong , Cheng Anthony Youzhi , Zhang Yuexiu , Xu Jiayu , Wu Jinjun , Wen Li , Li Xiao , Liu Bei , Dou Xiaoyang , Wang Pingluan , Zhang Linda , Fei Jingyi , Li Jianrong , Ouyang Zhengqing , He Chuan 
Published: January 2024

AbstractRNA fate and function are affected by their structures and interactomes. However, how RNA and RNA-binding proteins (RBPs) assemble into higher-order structures and how RNA molecules may interact with each other to facilitate functions remain largely unknown. Here we present KARR-seq, which uses N3-kethoxal labeling and multifunctional chemical crosslinkers to covalently trap and determine RNA–RNA interactions and higher-order RNA structures inside cells, independent of local protein binding to RNA. KARR-seq depicts higher-order RNA structure and detects widespread intermolecular RNA–RNA interactions with high sensitivity and accuracy. Using KARR-seq, we show that translation represses mRNA compaction under native and stress conditions. We determined the higher-order RNA structures of respiratory syncytial virus (RSV) and vesicular stomatitis virus (VSV) and identified RNA–RNA interactions between the viruses and the host RNAs that potentially regulate viral replication.