bluuebunny/crossref_metadata_2025_split huggingface dataset:
Augmenting a Spanish clinical dataset for transformer-based linking of negations and their out-of-scope references
Authors: Tamayo-Herrera Antonio Jesús , Burgos Diego A. , Gelbukh Alexander 
Published: May 2024

AbstractA negated statement consists of three main components: the negation cue, the negation scope, and the negation reference. The negation cue is the indicator of negation, while the negation scope defines the extent of the negation. The negation reference, which may or may not be within the negation scope, is the part of the statement being negated. Although there has been considerable research on the negation cue and scope, little attention has been given to identifying negation references outside the scope, even though they make up almost half of all negations. In this study, our goal is to identify out-of-scope references (OSRs) to restore the meaning of truncated negated statements identified by negation detection systems. To achieve this, we augment the largest available Spanish clinical dataset by adding annotations for OSRs. Additionally, we fine-tune five robust BERT-based models using transfer learning to address negation detection, uncertainty detection, and OSR identification and linking with their respective negation scopes. Our best model achieves state-of-the-art performance in negation detection while also establishing a competitive baseline for OSR identification (Macro F1 = 0.56) and linking (Macro F1 = 0.86). We support these findings with relevant statistics from the newly annotated dataset and an extensive review of existing literature.
La résistance interne chez Nicole Oresme. Étude sur saPhysiqueet son commentaire latin au traitéDu ciel
Authors: Laverdière Yanick 
Published: May 2024

RésuméAfin d'encourager la réflexion sur l'impact de la résistance interne dans la théorie du mouvement au XIVesiècle, je propose d'examiner ici l’évolution du concept chez l'universitaire parisien Nicole Oresme. Dans saPhysique, le penseur présente une position qui ne paraît pas tout à fait aboutie et qui soulève quelques questions en lien avec les qualités motrices des différents éléments constituant les mobiles. Cette situation devient d'autant plus évidente lorsque sa position change, plus tard, dans ses questions sur le traitéDu ciel. Oresme semble alors encore moins enclin à accepter l'idée d'une résistance interne dans le mouvement.
Conflict Escalation Done Wrong? The Free City of Regensburg Seizes Ehrenfels Castle, 13 April 1417
Authors: Kaar Alexandra 
Published: May 2024

AbstractThis article examines the various modes of conflict management used by the free city of Regensburg and the local nobleman Hans I Staufer of Ehrenfels during a prolonged dispute over revenues from 1413 to 1418. In the early years of this feud, both parties utilized nonviolent methods such as legal action and arbitration, which were occasionally accompanied by minor military interventions. In April 1417, however, the Regensburg councilors broke with convention and decided to escalate the conflict with their feud opponent by capturing his ancestral castle, Ehrenfels, near Beratzhausen in the Upper Palatinate region. Using both urban account books and documentary evidence, the case study investigates the reasons behind the councilors' decision to launch this ostentatious military attack, their objectives in seizing Ehrenfels castle, and the impact of their show of force on the ongoing conflict. It portrays late medieval Central European towns as potent military actors and argues for a more systematic integration of economic considerations and cost-benefit calculations into our picture of late medieval feuding.
The Real-Time Impact of the War on Russian Imports: A Synthetic Control Method Approach
Authors: Mancini Michele , Conteduca Francesco Paolo , Borin Alessandro 
Published: May 2024

AbstractIn response to the invasion of Ukraine, the EU and most other advanced economies imposed extensive sanctions on Russia, intending to harm its production capabilities and hinder its economic activities by restricting its access to international trade and financial markets. This paper develops an empirical framework based on the synthetic control method to assess the impact of the war and the following sanctions on bilateral and sectoral exports to Russia almost in real time. The war and the following sanctions reduced aggregate exports to Russia by a third between March and December 2022, with the effects being stronger for sanctioning countries than for non-sanctioning ones, albeit with substantial country-level heterogeneity within each group. Exports to Russia in high-tech sectors – relatively more targeted by trade sanctions – have been disproportionately affected.
The 2021 La Palma (Canary Islands) Eruption Ending Forecast Through Magma Pressure Drop
Authors: Charco M. , González P. J. , Pallero J. L. G. , García‐Cañada L. , del Fresno C. , Rodríguez‐Ortega A. 
Published: May 2024

AbstractForecast of eruptive activity is a core challenge in volcanology. Here, we present an actual forecast for the end of the 2021 La Palma eruption. Using continuous GNSS data, we identified a co‐eruptive quasi‐exponential deflation trend. Assuming mass conservation, magma upflow from an overpressurized reservoir drives the eruptive process. The forecast was carried out during the eruption, however there was uncertainty in the key percentage of drop in driving pressure necessary to stop this eruption. In hindcast, we explore how forecast uncertainty reduces with increase in ingested near‐real time data. We conclude that precise forecasts could have been possible, but only after twice a characteristic exponential decay time‐scale, providing error estimates of 45% of the actual duration. We verify the mass conservation assumption using eruptive material volumes and propose that the eruption dynamics was controlled by a main reservoir at a depth close to Moho discontinuity beneath Cumbre Vieja volcano.
Topographic Controls on Pyroclastic Density Current Hazard at Aluto Volcano (Ethiopia) Identified Using a Novel Zero‐Censored Gaussian Process Emulator
Authors: Tierz Pablo , Spiller Elaine T. , Clarke Ben A. , Dessalegn Firawalin , Bekele Yewubinesh , Lewi Elias , Yirgu Gezahegn , Wolpert Robert L. , Loughlin Susan C. , Calder Eliza S. 
Published: May 2024

AbstractAluto volcano (Central Ethiopia) displays a complex, hybrid topography, combining elements typical of caldera systems (e.g., a central, flat caldera floor) and stratovolcanoes (e.g., relatively high and steep, radial flanks, related to eruptions occurring clustered in space). The most recent known eruptions at Aluto have commonly generated column‐collapse pyroclastic density currents (PDCs), a hazardous phenomenon that can pose a significant risk to inhabited areas on and around the volcano. In order to analyze and quantify the role that Aluto's complex topography has on PDC hazard, we apply a versatile probabilistic strategy, which merges the TITAN2D model for PDCs with a novel zero‐censored Gaussian Process (zGP) emulator, enabling robust uncertainty quantification at tractable computational costs. Results from our analyses indicate a critical role of the eruptive vent location, but also highlight a complex interplay between the topography and PDC volume and mobility. The relative importance of each factor reciprocally depends on the other factors. Thus, large PDCs (≥0.1–0.5 km3) can diminish the influence of topography over proximal regions of flow propagation, but PDCs respond to large‐ and small‐scale topographic features over medial to distal areas, and the zGP captures processes like PDC channelization and overbanking. The novel zGP can be applied to other PDC models and can enable specific investigations of PDC dynamics, topographic interactions, and PDC hazard at many volcanic systems worldwide. Potentially, it could also be used during volcanic crises, when time constraints usually only permit computation of scenario‐based hazard assessments.
Verification of Long‐Term Ensemble Evapotranspiration Hindcast Using a Conditional Nonlinear Optimal Parameter Perturbation Ensemble Prediction Method on the Tibetan Plateau
Authors: Sun Guodong , Mu Mu , Zhang Qiyu , Ren Qiujie , You Qinglong 
Published: May 2024

AbstractIn this research, a conditional nonlinear optimal perturbation related to parameters (CNOP‐P) method is employed to propose an ensemble prediction method titled as the conditional nonlinear optimal perturbation related to parameters ensemble prediction (CNOP‐PEP) method. Within the CNOP‐PEP method, all ensemble members are generated by the CNOP‐P method. To explore the operability and validity of the CNOP‐PEP method, long‐term evapotranspiration (ET) hindcast skill is evaluated at 13 sites on the Tibetan Plateau (TP) during the period of 2001–2018 with a land surface model. Two traditional ensemble prediction methods (the stochastically perturbed parameters (SPP) method and the one‐at‐a‐time (OAT) method) are also applied to assess the ET hindcast skills. The numerical results indicate that the CNOP‐PEP method shows the best hindcast skill for estimated ET at 13 stations on the TP among the three methods (CNOP‐PEP, OAT, and SPP methods) during the period of 2001–2018. This suggests that the CNOP‐PEP method is helpful and effective for long‐term and interannual hydrological predictions, such as long‐term and interannual ET predictions. The numerical results also indicate that ensemble members with certain special properties of fast‐growing types should be selected to implement ensemble prediction compared to these ordinary and traditional samples. The CNOP‐PEP method could supply special samples to improve the ensemble prediction and hindcast skill of hydrological cycle.
A Non‐Magnetized Chondrite Parent Body Revealed by Paleomagnetic Investigation of LL6 Chondrite NWA 14180
Authors: Li Haijun , Wang Huapei , Wen Chen , Cao Ting , Liu Jiabo 
Published: May 2024

AbstractMagnetic records from meteorites provide valuable information about the formation and evolution of the solar system and planets. The parent planetesimals of chondrites are typically considered to be undifferentiated based on their primary chemical composition and texture. However, recent paleomagnetic investigations of various chondrites indicate that they carry a primary remanence generated by a dynamo, suggesting partial differentiation of their parent planetesimals. The presence of a dynamo within the parent planetesimal of LL chondrites remains uncertain due to the ambiguous origin of the remanent magnetism. Here, we report petrographic, paleomagnetic, and rock magnetic properties for the novel LL6 chondrite NWA 14180. The high metamorphic temperature experienced by NWA 14180 could have removed the pre‐accretionary remanence. The fusion crust baked‐contact test suggests that NWA 14180 preserves primary magnetic information about its parent body. Alternating field demagnetization results from interior subsamples reveal distinct low‐ and medium‐coercivity components that may represent a viscous remanent magnetization acquired in the geomagnetic field. No natural remanent magnetization was unblocked in the high coercivity range, implying that NWA 14180 cooled in zero‐field conditions. Therefore, we suggest that the parent body of NWA 14180 did not have a dynamo. Furthermore, this result suggests that the LL chondrite parent planetesimal accreted later and was smaller in size than other chondrite classes.
The Temperature of the Deep Ocean Is a Robust Proxy for Global Mean Surface Temperature During the Cenozoic
Authors: Evans David , Brugger Julia , Inglis Gordon N. , Valdes Paul 
Published: May 2024

AbstractReconstructing global mean surface temperature (GMST) is one of the key contributions that paleoclimate science can make in addressing societally relevant questions and is required to determine equilibrium climate sensitivity (ECS). GMST has been derived from the temperature of the deep ocean (Td), with previous work suggesting a simple Td‐GMST scaling factor of 1 prior to the Pliocene. However, this factor lacks a robust mechanistic basis, and indeed, is intuitively difficult to envisage given that polar amplification is a ubiquitous feature of past warm climate states and deep water overwhelmingly forms at high latitudes. Here, we interrogate whether and crucially, why, this relationship exists using a suite of curated data compilations and two sets of paleoclimate model simulations. We show that models and data are in full agreement that a 1:1 relationship is a good approximation. Taken together, the two sets of climate models suggest that (a) a lower sensitivity of SST in the season of deep water formation than high latitude mean annual SST in response to climate forcing, and moreover (b) a greater degree of land versus ocean surface warming are the two processes that act to counterbalance a possible polar amplification‐derived bias on Td‐derived GMST. Using this knowledge, we provide a new Cenozoic record of GMST. Our estimates are substantially warmer than similar previous efforts for much of the Paleogene and are thus consistent with a substantially higher‐than‐modern ECS during deep‐time high CO2 climate states.
Using Convex Optimization to Efficiently Apportion Tracer and Pollutant Sources From Point Concentration Observations
Authors: Barnes Richard , Lipp Alex G. 
Published: May 2024

AbstractRivers transport elements, minerals, chemicals, and pollutants produced in their upstream basins. A sample from a river is a mixture of all of its upstream sources, making it challenging to pinpoint the contribution from each individual source. Here, we show how a nested sample design and convex optimization can be used to efficiently unmix downstream samples of a well‐mixed, conservative tracer in a steady state system into the contributions of their upstream sources. Our approach is significantly faster than previous methods. We represent the river's sub‐catchments, defined by sampling sites, using a directed acyclic graph. This graph is used to build a convex optimization problem which, thanks to its convexity, can be quickly solved to global optimality—in under a second on desktop hardware for data sets of ∼100 samples or fewer. Uncertainties in the upstream predictions can be generated using Monte Carlo resampling. We provide an open‐source implementation of this approach in Python. The inputs required are straightforward: a table containing sample locations and observed tracer concentrations, along with a D8 flow‐direction raster map. As a case study, we use this method to map the elemental geochemistry of sediment sources for rivers draining the Cairngorms mountains, UK. This method could be extended to non‐conservative and non‐steady state tracers. We also show, theoretically, how multiple tracers could be simultaneously inverted to recover upstream run‐off or erosion rates as well as source concentrations. Overall, this approach can provide valuable insights to researchers in various fields, including water quality, geochemical exploration, geochemistry, hydrology, and wastewater epidemiology.
The Beginning of a Wilson Cycle in an Accretionary Orogen: The Mongol–Okhotsk Ocean Opened Assisted by a Devonian Mantle Plume
Authors: Zhu Mingshuai , Pastor–Galán Daniel , Smit Matthijs A. , Sanchir Dorjgochoo , Zhang Fuqin , Liu Chenghao , Luo Ye , Miao Laicheng 
Published: May 2024

AbstractThe opening of oceans within accretionary orogens is important for understanding the Wilson cycle. The Mongol–Okhotsk Ocean (MOO) began opening within the early Paleozoic accretionary collage of the Central Asian Orogenic Belt (CAOB), representing a world‐class example to constrain the geodynamic history of ocean opening in accretionary orogens, but the kinematics and mechanisms associated to this process are highly debated. We report on a newly‐discovered bimodal volcanic suite and associated volcanic‐sediments that comprise part of the Altay‐Sayan Rift System, which indicate a widespread Early Devonian extensional event within the CAOB. This extension regime is attributed to a Devonian mantle plume, which is thought to have impinged upon and weakened the lithosphere of the Early Paleozoic collage, and drove the opening of the MOO. Opening of the MOO suggests continent breakup in accretionary orogens tends to focus along intervening weak orogenic lithosphere between the rigid microcontinents.
Exploiting sweet relief for preeclampsia by targeting autophagy-lysosomal machinery and proteinopathy
Authors: Huang Zheping , Cheng Shibin , Jash Sukanta , Fierce Jamie , Agudelo Anthony , Higashiyama Takanobu , Hanna Nazeeh , Nakashima Akitoshi , Saito Shigeru , Padbury James , Schuster Jessica , Sharma Surendra 
Published: May 2024

AbstractThe etiology of preeclampsia (PE), a severe complication of pregnancy with several clinical manifestations and a high incidence of maternal and fetal morbidity and mortality, remains unclear. This issue is a major hurdle for effective treatment strategies. We recently demonstrated that PE exhibits an Alzheimer-like etiology of impaired autophagy and proteinopathy in the placenta. Targeting of these pathological pathways may be a novel therapeutic strategy for PE. Stimulation of autophagy with the natural disaccharide trehalose and its lacto analog lactotrehalose in hypoxia-exposed primary human trophoblasts restored autophagy, inhibited the accumulation of toxic protein aggregates, and restored the ultrastructural features of autophagosomes and autolysosomes. Importantly, trehalose and lactotrehalose inhibited the onset of PE-like features in a humanized mouse model by normalizing autophagy and inhibiting protein aggregation in the placenta. These disaccharides restored the autophagy-lysosomal biogenesis machinery by increasing nuclear translocation of the master transcriptional regulator TFEB. RNA-seq analysis of the placentas of mice with PE indicated the normalization of the PE-associated transcriptome profile in response to trehalose and lactotrehalose. In summary, our results provide a novel molecular rationale for impaired autophagy and proteinopathy in patients with PE and identify treatment with trehalose and its lacto analog as promising therapeutic options for this severe pregnancy complication.
The phenotype of MEGF8-related Carpenter syndrome (CRPT2) is refined through the identification of eight new patients
Authors: Watts Laura M. , Bertoli Marta , Attie-Bitach Tania , Roux Natalie , Rausell Antonio , Paschal Cate R. , Zambonin Jessica L. , Curry Cynthia J. , Martin Blanche , Tooze Rebecca S. , Hawkes Lara , Kini Usha , Twigg Stephen R. F. , Wilkie Andrew O. M. 
Published: May 2024

AbstractCarpenter syndrome (CRPTS) is a rare autosomal recessive condition caused by biallelic variants in genes that encode negative regulators of hedgehog signalling (RAB23 [CRPT1] or, more rarely, MEGF8 [CRPT2]), and is characterised by craniosynostosis, polysyndactyly, and other congenital abnormalities. We describe a further six families comprising eight individuals with MEGF8-associated CRPT2, increasing the total number of reported cases to fifteen, and refine the phenotype of CRPT2 compared to CRPT1. The core features of craniosynostosis, polysyndactyly and (in males) cryptorchidism are almost universal in both CRPT1 and CRPT2. However, laterality defects are present in nearly half of those with MEGF8-associated CRPT2, but are rare in RAB23-associated CRPT1. Craniosynostosis in CRPT2 commonly involves a single midline suture in comparison to the multi-suture craniosynostosis characteristic of CRPT1. No patient to date has carried two MEGF8 gene alterations that are both predicted to lead to complete loss-of-function, suggesting that a variable degree of residual MEGF8 activity may be essential for viability and potentially contributing to variable phenotypic severity. These data refine the phenotypic spectrum of CRPT2 in comparison to CRPT1 and more than double the number of likely pathogenic MEGF8 variants in this rare disorder.
Bioinformatics leading to conveniently accessible, helix enforcing, bicyclic ASX motif mimics (BAMMs)
Authors: Mi Tianxiong , Nguyen Duyen , Gao Zhe , Burgess Kevin 
Published: May 2024

AbstractHelix mimicry provides probes to perturb protein-protein interactions (PPIs). Helical conformations can be stabilized by joining side chains of non-terminal residues (stapling) or via capping fragments. Nature exclusively uses capping, but synthetic helical mimics are heavily biased towards stapling. This study comprises: (i) creation of a searchable database of unique helical N-caps (ASX motifs, a protein structural motif with two intramolecular hydrogen-bonds between aspartic acid/asparagine and following residues); (ii) testing trends observed in this database using linear peptides comprising only canonical L-amino acids; and, (iii) novel synthetic N-caps for helical interface mimicry. Here we show many natural ASX motifs comprise hydrophobic triangles, validate their effect in linear peptides, and further develop a biomimetic of them, Bicyclic ASX Motif Mimics (BAMMs). BAMMs are powerful helix inducing motifs. They are synthetically accessible, and potentially useful to a broad section of the community studying disruption of PPIs using secondary structure mimics.
Structures of the mumps virus polymerase complex via cryo-electron microscopy
Authors: Li Tianhao , Liu Mingdong , Gu Zhanxi , Su Xin , Liu Yunhui , Lin Jinzhong , Zhang Yu , Shen Qing-Tao 
Published: May 2024

AbstractThe viral polymerase complex, comprising the large protein (L) and phosphoprotein (P), is crucial for both genome replication and transcription in non-segmented negative-strand RNA viruses (nsNSVs), while structures corresponding to these activities remain obscure. Here, we resolved two L–P complex conformations from the mumps virus (MuV), a typical member of nsNSVs, via cryogenic-electron microscopy. One conformation presents all five domains of L forming a continuous RNA tunnel to the methyltransferase domain (MTase), preferably as a transcription state. The other conformation has the appendage averaged out, which is inaccessible to MTase. In both conformations, parallel P tetramers are revealed around MuV L, which, together with structures of other nsNSVs, demonstrates the diverse origins of the L-binding X domain of P. Our study links varying structures of nsNSV polymerase complexes with genome replication and transcription and points to a sliding model for polymerase complexes to advance along the RNA templates.
Liver ACOX1 regulates levels of circulating lipids that promote metabolic health through adipose remodeling
Authors: Lu Dongliang , He Anyuan , Tan Min , Mrad Marguerite , El Daibani Amal , Hu Donghua , Liu Xuejing , Kleiboeker Brian , Che Tao , Hsu Fong-Fu , Bambouskova Monika , Semenkovich Clay F. , Lodhi Irfan J. 
Published: May 2024

AbstractThe liver gene expression of the peroxisomal β-oxidation enzyme acyl-coenzyme A oxidase 1 (ACOX1), which catabolizes very long chain fatty acids (VLCFA), increases in the context of obesity, but how this pathway impacts systemic energy metabolism remains unknown. Here, we show that hepatic ACOX1-mediated β-oxidation regulates inter-organ communication involved in metabolic homeostasis. Liver-specific knockout of Acox1 (Acox1-LKO) protects mice from diet-induced obesity, adipose tissue inflammation, and systemic insulin resistance. Serum from Acox1-LKO mice promotes browning in cultured white adipocytes. Global serum lipidomics show increased circulating levels of several species of ω−3 VLCFAs (C24-C28) with previously uncharacterized physiological role that promote browning, mitochondrial biogenesis and Glut4 translocation through activation of the lipid sensor GPR120 in adipocytes. This work identifies hepatic peroxisomal β-oxidation as an important regulator of metabolic homeostasis and suggests that manipulation of ACOX1 or its substrates may treat obesity-associated metabolic disorders.