bluuebunny/crossref_metadata_2025_split huggingface dataset:
The challenging history of other Earths
Authors: Graney Christopher M. 
Published: August 2023

AbstractThis paper provides an overview of recent historical research regarding scientifically-informed challenges to the idea that the stars are other suns orbited by other inhabited earths – an idea that came to be known as ‘the Plurality of Worlds’. Johannes Kepler in the 17th century, Jacques Cassini in the 18th and William Whewell in the 19th each argued against ‘pluralism’ based on what in their respective times was solid science. Nevertheless, pluralism remained popular despite these and other scientific challenges. This history will be of interest to the astronomical community so that it is better positioned to avoid difficulties should the historical trajectory of pluralism continue, especially as it persists in the popular imagination.
Discontinuous Igneous Addition Along the Eastern North American Margin Beneath the East Coast Magnetic Anomaly
Authors: Brandl Collin C. , Worthington Lindsay L. , Magnani M. Beatrice , Shillington Donna J. , Luckie Thomas W. 
Published: August 2023

AbstractDetailed models of crustal structure at volcanic passive margins offer insight into the role of magmatism and the distribution of igneous addition during continental rifting. The Eastern North American Margin (ENAM) is a volcanic passive margin that formed during the breakup of Pangea ∼200 Myr ago. The offshore, margin‐parallel East Coast Magnetic Anomaly (ECMA) is thought to mark the locus of syn‐rift magmatism. Previous widely spaced margin‐perpendicular studies seismically imaged igneous addition as seaward dipping reflectors (SDRs) and high velocity lower crust (HVLC; >7.2 km/s) beneath the ECMA. Along‐strike imaging is necessary to more accurately determine the distribution and volume of igneous addition during continental breakup. We use wide‐angle, marine active‐source seismic data from the 2014–2015 ENAM Community Seismic Experiment to determine crustal structure beneath a ∼370‐km‐long section of the ECMA. P‐wave velocity models based on data from short‐period ocean bottom seismometers reveal a ∼21‐km‐thick crust with laterally variable lower crust velocities ranging from 6.9 to 7.5 km/s. Sections with HVLC (>7.2 km/s) alternate with two ∼30‐km‐wide areas where the average velocities are less than 7.0 km/s. This variable structure indicates that HVLC is discontinuous along the margin, reflecting variable amounts of intrusion along‐strike. Our results suggest that magmatism during rifting was segmented. The HVLC discontinuities roughly align with locations of Mid‐Atlantic Ridge fracture zones, which may suggest that rift segmentation influenced later segmentation of the Mid‐Atlantic Ridge.
Re-audit of the use of flumazenil following midazolam-induced conscious sedation
Authors: Rosli Muhammad Syafiq Asyraf , Heidari Ellie 
Published: August 2023

Abstract
Introduction
Flumazenil is an antagonist drug of Benzodiazepam (BDZ) that has been used as a reversal agent of midazolam-induced conscious sedation (CS) in both emergency and elective procedures. For CS procedure, a high-quality record keeping and clinical justification prior to admission of flumazenil are recommended. Clinical Audit (CA) enables clinicians to evaluate the quality and standard of recorded clinical procedures.

Methods
This re-audit investigated the reasons for the use of flumazenil and record keeping’s quality with particular emphasis on CS. In this retrospective reaudit, the authors looked at the patients’ records who had received dental care under CS in the Sedation and Special Care Department of (SSCD), United Kingdom from January to June 2022.

Results
Out of 665 patients who received midazolam-induced CS, 21 patients were administered IV Flumazenil. The commonest reason (9, 42.8%) was due to prolonged recovery.

Conclusion
This re-audit highlighted the need for administrating flumazenil in certain patient groups, and/or circumstances (not emergency). The importance of maintaining high-quality record keeping is discussed.
MAVS signaling is required for preventing persistent chikungunya heart infection and chronic vascular tissue inflammation
Authors: Noval Maria G. , Spector Sophie N. , Bartnicki Eric , Izzo Franco , Narula Navneet , Yeung Stephen T. , Damani-Yokota Payal , Dewan M. Zahidunnabi , Mezzano Valeria , Rodriguez-Rodriguez Bruno A. , Loomis Cynthia , Khanna Kamal M. , Stapleford Kenneth A. 
Published: August 2023

AbstractChikungunya virus (CHIKV) infection has been associated with severe cardiac manifestations, yet, how CHIKV infection leads to heart disease remains unknown. Here, we leveraged both mouse models and human primary cardiac cells to define the mechanisms of CHIKV heart infection. Using an immunocompetent mouse model of CHIKV infection as well as human primary cardiac cells, we demonstrate that CHIKV directly infects and actively replicates in cardiac fibroblasts. In immunocompetent mice, CHIKV is cleared from cardiac tissue without significant damage through the induction of a local type I interferon response from both infected and non-infected cardiac cells. Using mice deficient in major innate immunity signaling components, we found that signaling through the mitochondrial antiviral-signaling protein (MAVS) is required for viral clearance from the heart. In the absence of MAVS signaling, persistent infection leads to focal myocarditis and vasculitis of the large vessels attached to the base of the heart. Large vessel vasculitis was observed for up to 60 days post infection, suggesting CHIKV can lead to vascular inflammation and potential long-lasting cardiovascular complications. This study provides a model of CHIKV cardiac infection and mechanistic insight into CHIKV-induced heart disease, underscoring the importance of monitoring cardiac function in patients with CHIKV infections.
Genetic risk, adherence to healthy lifestyle and acute cardiovascular and thromboembolic complications following SARS-COV-2 infection
Authors: Xie Junqing , Feng Yuliang , Newby Danielle , Zheng Bang , Feng Qi , Prats-Uribe Albert , Li Chunxiao , Wareham Nicholas J. , Paredes R. , Prieto-Alhambra Daniel 
Published: August 2023

AbstractCurrent understanding of determinants for COVID-19-related cardiovascular and thromboembolic (CVE) complications primarily covers clinical aspects with limited knowledge on genetics and lifestyles. Here, we analysed a prospective cohort of 106,005 participants from UK Biobank with confirmed SARS-CoV-2 infection. We show that higher polygenic risk scores, indicating individual’s hereditary risk, were linearly associated with increased risks of post-COVID-19 atrial fibrillation (adjusted HR 1.52 [95% CI 1.44 to 1.60] per standard deviation increase), coronary artery disease (1.57 [1.46 to 1.69]), venous thromboembolism (1.33 [1.18 to 1.50]), and ischaemic stroke (1.27 [1.05 to 1.55]). These genetic associations are robust across genders, key clinical subgroups, and during Omicron waves. However, a prior composite healthier lifestyle was consistently associated with a reduction in all outcomes. Our findings highlight that host genetics and lifestyle independently affect the occurrence of CVE complications in the acute infection phrase, which can guide tailored management of COVID-19 patients and inform population lifestyle interventions to offset the elevated cardiovascular burden post-pandemic.
Neoadjuvant Afatinib for stage III EGFR-mutant non-small cell lung cancer: a phase II study
Authors: Bian Dongliang , Sun Liangdong , Hu Junjie , Duan Liang , Xia Haoran , Zhu Xinsheng , Sun Fenghuan , Zhang Lele , Yu Huansha , Xiong Yicheng , Huang Zhida , Zhao Deping , Song Nan , Yang Jie , Bao Xiao , Wu Wei , Huang Jie , He Wenxin , Zhu Yuming , Jiang Gening , Zhang Peng 
Published: August 2023

AbstractAfatinib, an irreversible ErbB-family blocker, could improve the survival of advanced epidermal growth factor receptor (EGFR)-mutant non-small cell lung cancer patients (NSCLCm+). This phase II trial (NCT04201756) aimed to assess the feasibility of neoadjuvant Afatinib treatment for stage III NSCLCm+. Forty-seven patients received neoadjuvant Afatinib treatment (40 mg daily). The primary endpoint was objective response rate (ORR). Secondary endpoints included pathological complete response (pCR) rate, pathological downstaging rate, margin-free resection (R0) rate, event-free survival, disease-free survival, progression-free survival, overall survival, treatment-related adverse events (TRAEs). The ORR was 70.2% (95% CI: 56.5% to 84.0%), meeting the pre-specified endpoint. The major pathological response (MPR), pCR, pathological downstaging, and R0 rates were 9.1%, 3.0%, 57.6%, and 87.9%, respectively. The median survivals were not reached. The most common TRAEs were diarrhea (78.7%) and rash (78.7%). Only three patients experienced grade 3/4 TRAEs. Biomarker analysis and tumor microenvironment dynamics by bulk RNA sequencing were included as predefined exploratory endpoints. CISH expression was a promising marker for Afatinib response (AUC = 0.918). In responders, compared to baseline samples, increasing T-cell- and B-cell-related features were observed in post-treatment tumor and lymph-node samples, respectively. Neoadjuvant Afatinib is feasible for stage III NSCLC+ patients and leads to dynamic changes in the tumor microenvironment.
Functional annotation of proteins for signaling network inference in non-model species
Authors: Van den Broeck Lisa , Bhosale Dinesh Kiran , Song Kuncheng , Fonseca de Lima Cássio Flavio , Ashley Michael , Zhu Tingting , Zhu Shanshuo , Van De Cotte Brigitte , Neyt Pia , Ortiz Anna C. , Sikes Tiffany R. , Aper Jonas , Lootens Peter , Locke Anna M. , De Smet Ive , Sozzani Rosangela 
Published: August 2023

AbstractMolecular biology aims to understand cellular responses and regulatory dynamics in complex biological systems. However, these studies remain challenging in non-model species due to poor functional annotation of regulatory proteins. To overcome this limitation, we develop a multi-layer neural network that determines protein functionality directly from the protein sequence. We annotate kinases and phosphatases in Glycine max. We use the functional annotations from our neural network, Bayesian inference principles, and high resolution phosphoproteomics to infer phosphorylation signaling cascades in soybean exposed to cold, and identify Glyma.10G173000 (TOI5) and Glyma.19G007300 (TOT3) as key temperature regulators. Importantly, the signaling cascade inference does not rely upon known kinase motifs or interaction data, enabling de novo identification of kinase-substrate interactions. Conclusively, our neural network shows generalization and scalability, as such we extend our predictions to Oryza sativa, Zea mays, Sorghum bicolor, and Triticum aestivum. Taken together, we develop a signaling inference approach for non-model species leveraging our predicted kinases and phosphatases.
Shallow-water hydrothermal venting linked to the Palaeocene–Eocene Thermal Maximum
Authors: Berndt Christian , Planke Sverre , Alvarez Zarikian Carlos A. , Frieling Joost , Jones Morgan T. , Millett John M. , Brinkhuis Henk , Bünz Stefan , Svensen Henrik H. , Longman Jack , Scherer Reed P. , Karstens Jens , Manton Ben , Nelissen Mei , Reed Brandon , Faleide Jan Inge , Huismans Ritske S. , Agarwal Amar , Andrews Graham D. M. , Betlem Peter , Bhattacharya Joyeeta , Chatterjee Sayantani , Christopoulou Marialena , Clementi Vincent J. , Ferré Eric C. , Filina Irina Y. , Guo Pengyuan , Harper Dustin T. , Lambart Sarah , Mohn Geoffroy , Nakaoka Reina , Tegner Christian , Varela Natalia , Wang Mengyuan , Xu Weimu , Yager Stacy L. 
Published: August 2023

AbstractThe Palaeocene–Eocene Thermal Maximum (PETM) was a global warming event of 5–6 °C around 56 million years ago caused by input of carbon into the ocean and atmosphere. Hydrothermal venting of greenhouse gases produced in contact aureoles surrounding magmatic intrusions in the North Atlantic Igneous Province have been proposed to play a key role in the PETM carbon-cycle perturbation, but the precise timing, magnitude and climatic impact of such venting remains uncertain. Here we present seismic data and the results of a five-borehole transect sampling the crater of a hydrothermal vent complex in the Northeast Atlantic. Stable carbon isotope stratigraphy and dinoflagellate cyst biostratigraphy reveal a negative carbon isotope excursion coincident with the appearance of the index taxon Apectodinium augustum in the vent crater, firmly tying the infill to the PETM. The shape of the crater and stratified sediments suggests large-scale explosive gas release during the initial phase of vent formation followed by rapid, but largely undisturbed, diatomite-rich infill. Moreover, we show that these vents erupted in very shallow water across the North Atlantic Igneous Province, such that volatile emissions would have entered the atmosphere almost directly without oxidation to CO2 and at the onset of the PETM.
Household and plot-level survey data on adoption, outcomes, and perceptions of early sown wheat and zero tillage in Northwest India
Authors: Naeher Dominik , Albanna Basma , Kumar Abhijeet , Vollmer Sebastian 
Published: August 2023

AbstractThis study collected evidence on the use of early sown wheat varieties and complementary zero tillage technologies in Northwest India. Detailed information on farmers’ knowledge, adoption decisions, personal experience, and perceptions of early sown wheat and zero tillage technologies were collected at the household level using different survey tools. Additional information on agricultural practices during the Rabi Season 2021/22 were collected at the plot level and geocoded. Overall, the dataset comprises responses from 1206 wheat farmers in 70 villages across 7 districts in Punjab and Haryana that were collected between September and October 2022. The villages were selected using stratified random sampling based on a sampling frame of 1722 communities that had been identified as predominantly wheat growing areas based on remote-sensing data from satellite images. The dataset provides rich information that may be used for assessing the diffusion and impact of recently developed wheat varieties designed for early sowing, identifying barriers to the wider adoption of these technologies, and informing policy making aimed at improving adoption and usage decisions of agricultural innovations.
A chromosome-level genome assembly for the astaxanthin-producing microalga Haematococcus pluvialis
Authors: Bian Chao , Liu Chenglong , Zhang Guiying , Tao Ming , Huang Danqiong , Wang Chaogang , Lou Sulin , Li Hui , Shi Qiong , Hu Zhangli 
Published: August 2023

AbstractThe green microalga Haematococcus pluvialis can synthesize high amounts of astaxanthin, which is a valuable antioxidant that has been utilized in human health, cosmetics, and aquaculture. To illustrate detailed molecular clues to astaxanthin yield, we performed PacBio HIFI along with Hi-C sequencing to construct an improved chromosome-level haplotypic genome assembly with 32 chromosomes and a genome size of 316.0 Mb. Its scaffold N50 (942.6 kb) and contig N50 (304.8 kb) have been upgraded remarkably from our previous genome draft, and a total of 32,416 protein-coding genes were predicted. We also established a high-evidence phylogenetic tree from seven representative algae species, with the main aim to calculate their divergence times and identify expanded/contracted gene families. We also characterized genome-wide localizations on chromosomes of some important genes such as five BKTs (encoding beta-carotene ketolases) that are putatively involved in astaxanthin production. In summary, we reported the first chromosome-scale map of H. pluvialis, which provides a valuable genetic resource for in-depth biomedical investigations on this momentous green alga and commercial astaxanthin bioproduction.
Structure prediction of novel isoforms from uveal melanoma by AlphaFold
Authors: Zhang Zhe , Li Chen , Li Qian , Su Xiaoming , Li Jiayi , Zhu Lili , Lin Xinhua , Shen Jianfeng 
Published: August 2023

AbstractAlternative splicing is an important mechanism that enhances protein functional diversity. To date, our understanding of alternative splicing variants has been based on mRNA transcript data, but due to the difficulty in predicting protein structures, protein tertiary structures have been largely unexplored. However, with the release of AlphaFold, which predicts three-dimensional models of proteins, this challenge is rapidly being overcome. Here, we present a dataset of 315 predicted structures of abnormal isoforms in 18 uveal melanoma patients based on second- and third-generation transcriptome-sequencing data. This information comprises a high-quality set of structural data on recurrent aberrant isoforms that can be used in multiple types of studies, from those aimed at revealing potential therapeutic targets to those aimed at recognizing of cancer neoantigens at the atomic level.
Forecasting Brassica napus production under climate change with a mechanistic species distribution model
Authors: Borges Cláudia Eduarda , Von dos Santos Veloso Ronnie , da Conceição Crislaine Alves , Mendes Débora Sampaio , Ramirez-Cabral Nadiezhda YZ , Shabani Farzin , Shafapourtehrany Mahyat , Nery Marcela Carlota , da Silva Ricardo Siqueira 
Published: August 2023

AbstractBrassica napus, a versatile crop with significant socioeconomic importance, serves as a valuable source of nutrition for humans and animals while also being utilized in biodiesel production. The expansion potential of B. napus is profoundly influenced by climatic variations, yet there remains a scarcity of studies investigating the correlation between climatic factors and its distribution. This research employs CLIMEX to identify the current and future ecological niches of B. napus under the RCP 8.5 emission scenario, utilizing the Access 1.0 and CNRM-CM5 models for the time frame of 2040–2059. Additionally, a sensitivity analysis of parameters was conducted to determine the primary climatic factors affecting B. napus distribution and model responsiveness. The simulated outcomes demonstrate a satisfactory alignment with the known current distribution of B. napus, with 98% of occurrence records classified as having medium to high climatic suitability. However, the species displays high sensitivity to thermal parameters, thereby suggesting that temperature increases could trigger shifts in suitable and unsuitable areas for B. napus, impacting regions such as Canada, China, Brazil, and the United States.
Investigation of internal damage evolution in gneiss considering water softening
Authors: Sun Changhai , Xie Bingxin , Wang Rui , Deng Xianghui , Wu Jin 
Published: August 2023

AbstractIn soft rock tunnels, there are often large deformations during construction, especially when the groundwater seepage and softens the surrounding rock. For achieving the purpose of studying the softening effect of water immersion on strength and stability of surrounding rock, 15 rock samples were selected for physical and mechanical tests under 5 conditions: natural state and free immersion for 1, 3, 6, and 9 months, and nuclear magnetic resonance technology(NMR) was also adopted to test the internal pore structure of specimens with different immersion durations, thus the micro structure features of the gneiss, such as the NMR relaxation time T2 spectrum distribution, porosity, and pore volume ratio of different pore sizes under water softening were then obtained. The NMR results shows that the longer the free immersion duration of the rock sample, the greater the porosity; at the same time, the number of micropores in the rock gradually decreases under the interaction of water and rock, and the mesopores increase slightly first and then decrease all the time. The number of macropores is gradually increasing. When the immersion duration is 6 months, the number of macropores begins to increase significantly, and the mechanical properties of the specimens begin to drop significantly. By 9 months, the proportion of macropores in the rock has reached 57.6%. The results showed that the number growth of macropores is the root cause of the macroscopic failure of rock sample. The study results have significance for on-site construction in water-rich areas.
Spatio-temporal activation patterns of neuronal population evoked by optostimulation and the comparison to electrical microstimulation
Authors: Margalit Shany Nivinsky , Slovin Hamutal 
Published: August 2023

AbstractOptostimulation and electrical microstimulation are well-established techniques that enable to artificially stimulate the brain. While the activation patterns evoked by microstimulation in cortical network are well characterized, much less is known for optostimulation. Specifically, the activation maps of neuronal population at the membrane potential level and direct measurements of these maps were barely reported. In addition, only a few studies compared the activation patterns evoked by microstimulation and optostimulation. In this study we addressed these issues by applying optostimulation in the barrel cortex of anesthetized rats after a short (ShortExp) or a long (LongExp) opsin expression time and compared it to microstimulation. We measured the membrane potential of neuronal populations at high spatial (meso-scale) and temporal resolution using voltage-sensitive dye imaging. Longer optostimulation pulses evoked higher neural responses spreading over larger region relative to short pulses. Interestingly, similar optostimulation pulses evoked stronger and more prolonged population response in the LongExp vs. the ShortExp condition. Finally, the spatial activation patterns evoked in the LongExp condition showed an intermediate state, with higher resemblance to the microstimulation at the stimulation site. Therefore, short microstimulation and optostimulation can induce wide spread activation, however the effects of optostimulation depend on the opsin expression time.
Self-evaluation of automated vehicles based on physics, state-of-the-art motion prediction and user experience
Authors: Stockem Novo Anne , Hürten Christian , Baumann Robin , Sieberg Philipp 
Published: August 2023

AbstractLegal restrictions allow to give full control to automated vehicles for longer time periods either in restricted areas or when moving with reduced speed. Although being technically feasible for a wide range of driving scenarios, the restrictions are still in place due to the lack of a clear safety strategy. An essential step towards safety is the introduction of a self-monitoring component. In this study, a self-evaluation concept is presented which assesses a system based on a physics-defined minimum prediction horizon for state-of-the-art Deep Learning-based trajectory prediction models. Since User Experience is a key metric for car manufacturers, a further manoeuvre constraint is added to the model. We emphasize the generalizability of the presented assessment concept, however, in order to demonstrate feasibility in practical use, three specific scenarios are discussed. The results are gained with real data from publicly available driving campaigns as well as synthetically generated simulation data. Two exemplary models, a simple LSTM-based model and VectorNet, a prominent motion prediction model, are evaluated. A quantitative assessment shows a lack of training data in the public datasets for vehicle speeds > 25 m/s in order to offer safe driving above such vehicle speeds.