bluuebunny/crossref_metadata_2025 huggingface dataset:
DarSIA: An Open-Source Python Toolbox for Two-Scale Image Processing of Dynamics in Porous Media
Authors: Nordbotten Jan Martin , Benali Benyamine , Both Jakub Wiktor , Brattekås Bergit , Storvik Erlend , Fernø Martin A.
Published: September 2023

Understanding porous media flow is inherently a multi-scale challenge, where at the core lies the aggregation of pore-level processes to a continuum, or Darcy-scale, description. This challenge is directly mirrored in image processing, where pore-scale grains and interfaces may be clearly visible in the image, yet continuous Darcy-scale parameters may be what are desirable to quantify. Classical image processing is poorly adapted to this setting, as most techniques do not explicitly utilize the fact that the image contains explicit physical processes. Here, we extend classical image processing concepts to what we define as “physical images” of porous materials and processes within them. This is realized through the development of a new open-source image analysis toolbox specifically adapted to time-series of images of porous materials.
Gesturing in plain sight: dialogical enactments of sustainable futures as being and doing in the world
Authors: Colucci-Gray Laura
Published: September 2023

Addressing the critical question posed by Gudrun Jonsdottir and Anne Kristine Byhring who are asking what place for a common future in the science classroom, this paper focuses on and expands on the construct of dialogical space. Not simply as an abstract concept to describe the presence of divergent ideas or the exchange of idioms, but a space filled with metaphors and material artefacts that exist in the world. On this basis, science education takes seriously the affordances of sensorial perception in space, as physical and material doings, arising from and deeply concerned with the lived experiences of people. By making visible the material relations that give life to human experience, and by giving life to different imaginations, science education can thus become profoundly dialogical: turning away from the expectation of sameness, it houses in itself the invitation of taking authorship and to give form, that being a narrative, a personal journey, or a different way of looking at the world. This is what I call gesturing in plain sight, a science education that critically engages with material artefacts and their relations; one that inhabits the realm of the symbolic and the experiential, and one that speaks to sustainable futures in general, repurposing and reconceiving the work of science education in particular.
Public Wrongs and Power Relations in Non-Democratic & Illiberal Polities
Authors: Hanafy Hend
Published: September 2023

One of the influential contributions to criminalisation theories is Duff’s work on public wrongs, which offers a thin master principle of criminalisation, proposing that we have a reason to criminalise a type of conduct if it constitutes a public wrong; one that violates a polity’s civil order and forms part of that polity’s proper business. The nature of the civil order, the scope of its proper business, and the distinction between the public and private realms of wrongs are context-relative to each polity, structured by their legal, institutional, and informal values and ways of life. Such a context-relative view led to problematic criminalisation examples raised by Duff and his critics. This article engages more fully with the relativism of the civil order and public wrongs in non-democratic and illiberal contexts. It draws on examples such as Saudi Arabi and Iran, and Beetham’s work on the legitimation of power to argue that conceptualising the civil order as an undifferentiated whole that represents a polity’s chosen way of life overlooks the ways in which the civil order’s values and practices are shaped by relations of power and exclusion rules and processes. This, in turn, exposes the theory to the risk of mirroring and legitimising unequal relations of power and impeding efforts to change them. This is also due to the theory’s lack of proper normative guidance on the legitimacy of criminalisation. The potential commitment to – instead of a preference for – democracy and guarantees of equality and freedoms might help strengthen the theory normatively, but it is insufficient to guard against the raised problems.
Geodesics of norms on the contactomorphisms group of $${\mathbb {R}}^{2n}\times S^1$$
Authors: Arlove Pierre-Alexandre
Published: September 2023

We prove that some paths of contactomorphisms of$${\mathbb {R}}^{2n}\times S^1$$R2n×S1endowed with its standard contact structure are geodesics for different norms defined on the identity component of the group of compactly supported contactomorphisms and its universal cover. We characterize these geodesics by giving conditions on the Hamiltonian functions that generate them. For every norm considered we show that the norm of a contactomorphism that is the time-one of such a geodesic can be expressed in terms of the maximum of the absolute value of the corresponding Hamiltonian function. In particular we recover the fact that these norms are unbounded.
Deep Learning Approaches Applied to Image Classification of Renal Tumors: A Systematic Review
Authors: Amador Sandra , Beuschlein Felix , Chauhan Vedant , Favier Judith , Gil David , Greenwood Phillip , de Krijger R. R. , Kroiss Matthias , Ortuño-Miquel Samanta , Patocs Attila , Stell Anthony , Walch Axel
Published: September 2023

Renal cancer is one of the ten most common cancers in the population that affects 65,000 new patients a year. Nowadays, to predict pathologies or classify tumors, deep learning (DL) methods are effective in addition to extracting high-performance features and dealing with segmentation tasks. This review has focused on the different studies related to the application of DL techniques for the detection or segmentation of renal tumors in patients. From the bibliographic search carried out, a total of 33 records were identified in Scopus, PubMed and Web of Science. The results derived from the systematic review give a detailed description of the research objectives, the types of images used for analysis, the data sets used, whether the database used is public or private, and the number of patients involved in the studies. The first paper where DL is applied compared to other types of tumors was in 2019 which is relatively recent. Public collection and sharing of data sets are of utmost importance to increase research in this field as many studies use private databases. We can conclude that future research will identify many benefits, such as unnecessary incisions for patients and more accurate diagnoses. As research in this field grows, the amount of open data is expected to increase.
Preoperative prediction of pancreatic neuroendocrine tumor grade based on 68Ga-DOTATATE PET/CT
Authors: Ma Jiao , Wang Xiaoyong , Tang Mingsong , Zhang Chunyin
Published: September 2023

Objective

To establish a prediction model for preoperatively predicting grade 1 and grade 2/3 tumors in patients with pancreatic neuroendocrine tumors (PNETs) based on 68Ga-DOTATATE PET/CT.

Methods

Clinical data of 41 patients with PNETs were included in this study. According to the pathological results, they were divided into grade 1 and grade 2/3. 68Ga-DOTATATE PET/CT images were collected within one month before surgery. The clinical risk factors and significant radiological features were filtered, and a clinical predictive model based on these clinical and radiological features was established. 3D slicer was used to extracted 107 radiomic features from the region of interest (ROI) of 68Ga-dotata PET/CT images. The Pearson correlation coefficient (PCC), recursive feature elimination (REF) based five-fold cross validation were adopted for the radiomic feature selection, and a radiomic score was computed subsequently. The comprehensive model combining the clinical risk factors and the rad-score was established as well as the nomogram. The performance of above clinical model and comprehensive model were evaluated and compared.

Results

Adjacent organ invasion, N staging, and M staging were the risk factors for PNET grading (p < 0.05). 12 optimal radiomic features (3 PET radiomic features, 9 CT radiomic features) were screen out. The clinical predictive model achieved an area under the curve (AUC) of 0.785. The comprehensive model has better predictive performance (AUC = 0.953).

Conclusion

We proposed a comprehensive nomogram model based on 68Ga-DOTATATE PET/CT to predict grade 1 and grade 2/3 of PNETs and assist personalized clinical diagnosis and treatment plans for patients with PNETs.
Postmortem redistribution of drugs: a literature review
Authors: Abdelaal Ghadeer M. M. , Hegazy Nagah I. , Etewa Rasha L. , Elmesallamy Ghada E. A.
Published: September 2023

Postmortem drug analysis is crucial in identifying the potential cause and manner of death. However, it is threatened by a significant phenomenon called postmortem redistribution (PMR), which refers to the alterations in drug levels occurring after death. This review aims to describe the PMR phenomenon, the mechanisms involved in the PMR of drugs, the various methods used to predict it, and various artifacts of postmortem drug concentrations. Several mechanisms, including passive diffusion from solid organs that act as drug reservoirs to the surrounding tissues, cadaveric changes after death (e.g., cell death, blood coagulation, hypostasis, and movements), and the putrefactive process, can result in artifacts of postmortem drug concentrations. The drug’s chemical and pharmacokinetic properties (such as acidic/basic properties, lipophilicity, protein binding, high volume of distribution, and residual metabolic activity) are additional factors. Several markers, including cardiac blood-to-peripheral blood ratio (C/P), liver-to-peripheral blood ratio (L/P), amino acid markers such as methionine, quantitative structure–activity relationship (QSAR) approach, and F factor, have been proposed for interpreting the liability of drugs to PMR. Several artifacts may affect the reliability of postmortem drug analysis. Peripheral blood is preferred for postmortem drug sample collection. Numerous laboratories evaluate the redistribution potential of drugs after death using the C/P concentration ratio. Nevertheless, the L/P concentration ratio is proposed to be a more reliable marker for PMR determination.
Whole-brain Optical Imaging: A Powerful Tool for Precise Brain Mapping at the Mesoscopic Level
Authors: Jiang Tao , Gong Hui , Yuan Jing
Published: September 2023

The mammalian brain is a highly complex network that consists of millions to billions of densely-interconnected neurons. Precise dissection of neural circuits at the mesoscopic level can provide important structural information for understanding the brain. Optical approaches can achieve submicron lateral resolution and achieve “optical sectioning” by a variety of means, which has the natural advantage of allowing the observation of neural circuits at the mesoscopic level. Automated whole-brain optical imaging methods based on tissue clearing or histological sectioning surpass the limitation of optical imaging depth in biological tissues and can provide delicate structural information in a large volume of tissues. Combined with various fluorescent labeling techniques, whole-brain optical imaging methods have shown great potential in the brain-wide quantitative profiling of cells, circuits, and blood vessels. In this review, we summarize the principles and implementations of various whole-brain optical imaging methods and provide some concepts regarding their future development.
What Mindfulness, and for Whom? And Why Might it Work?
Authors: Sedlmeier Peter
Published: September 2023

This comment on “Mindfulness for global public health: Critical analysis and agenda” by Doug Oman focuses on the difficulties associated with the current use and understanding of the term mindfulness. In particular, I argue that the current lack of agreement on what mindfulness practice is, or, perhaps more realistically, what mindfulness practices are, and how their effects can be explained might jeopardize such an integration process in the long run. In the literature, one can find widely differing conceptions of what constitutes a mindfulness practice. Moreover, there is clear evidence that different mindfulness practices can yield quite different effects. This holds for the comparison of “mindfulness packages” but also for comparisons of single components of these packages, and for incremental combinations of components. There is also strong evidence that mindfulness practices do not work equally well for different purposes and different people. These differential effects need to be elaborated and explained. Unfortunately, theoretical models for mindfulness practices are also still quite heterogeneous. As a first step, researchers and practitioners could be very specific about what they mean by mindfulness practice or even use alternative terms for different practices. Moreover, they could stay open to alternative forms of meditation and put as much theory as possible into their research to eventually find out when, how, and why specific mindfulness practices (and packages thereof) work and for whom.
Reuse of Steel in the Construction Industry: Challenges and Opportunities
Authors: Kanyilmaz Alper , Birhane Mussie , Fishwick Roy , del Castillo Carlos
Published: September 2023

The construction industry plays a critical role in tackling the challenges of climate change, carbon emissions, and resource consumption. To achieve a low-emission built environment, urgent action is required to reduce the carbon emissions associated with steel production and construction processes. Reusing structural steel elements could make a significant impact in this direction, but there are five key challenges to overcome: limited material availability, maximizing different reusable materials from demolition, lack of adequate design rules and standards, high upfront costs and overlooked carbon impact of the demolition prior to construction, and the need to engage and coordinate the complete construction ecosystem. This article described these barriers and proposed solutions to them by leveraging the digital technologies and artificial intelligence. The proposed solutions aim to promote reuse practices, facilitate the development of certification and regulation for reuse, and minimize the environmental impact of steel construction. The solutions explored here can also be extended to other construction materials.
The Interrelation Between Emotional Impulsivity, Craving, and Symptoms Severity in Behavioral Addictions and Related Conditions: a Theory-Driven Systematic Review
Authors: López-Guerrero José , Navas Juan F. , Perales José C. , Rivero Francisco J. , Muela Ismael
Published: September 2023

Purpose of Review

Here, we systematically review all available evidence on the triadic relationship between positive and negative urgency, craving, and severity of symptoms of candidate behavioral addictions.

Recent Findings

Current theoretical models attribute a central importance to craving in the chronification and prognosis of behavioral addictions and other problematic non-substance-related behavioral patterns. Craving, in turn, has been convincingly shown to be an affect-laden state, and its control can be conceptualized as partially resulting from emotion regulation mechanisms. However, some gaps remain: first, there is no consensus on the predominantly appetitive or aversive nature of craving; and, second, although positive and negative urgency have been proposed as proxies to incidental emotion regulation mechanisms, their direct or indirect role in craving regulation and severity of problematic behaviors is still poorly known.

According to our results, craving emerges as a central construct, partially resulting from emotion dysregulation as assessed by urgency. The preponderance of positive urgency shown by most studies in this review also reinforces the view of positive emotions as a ‘trojan horse’ in addictive processes. Negative urgency, in turn, seems to be a complication factor that could underlie gambling addiction and other related mental health conditions. Most studies, however, are about gambling behavior, with the few studies in other domains precluding firm conclusions about the differences or similarities between them.
Food Addiction and Impulsivity in Clinical Populations by Gender: a Systematic Review
Authors: Gaspar-Pérez Anahí , Paslakis Georgios , Rosinska Magda , Munguía Lucero , Jiménez-Murcia Susana , Szilágyi Anna , Miranda-Olivos Romina , Camacho-Barcia Lucia , Reque Cristina Ballero , Pászthy Bea , Fernández-Aranda Fernando
Published: September 2023

Purpose of Review

Food addiction (FA) has been found to be associated with impulsivity, mainly urgency (negative and positive) and lack of perseverance. The present systematic review aimed to identify differences in impulsivity by gender and current implications of treatment regarding FA and impulsivity in clinical populations. The search was conducted in PubMed, Scopus, and Web of Science (WOS) databases, using the following search terms: “food addiction” and “impuls*.” Studies were included if they were written in English, had an observational design (e.g., cross-sectional, longitudinal, case-control), and used a quantitative methodology, without a limited search period to avoid selection bias.

Recent Findings

We included twenty-nine articles that aimed to examine whether there is a relationship between FA and impulsivity in clinical populations. Looking at gender differences, attentional and motor impulsivity were found to be related to FA in samples of women with obesity, whereas in the only study in a sample of men with obesity, cognitive and non-planning impulsivity appeared to be more associated with FA. Moreover, we identified three studies on the effects of interventions which included motivational, psychosocial, nutritional, and mindfulness components to address impulsivity and FA in cohorts with overweight/obesity and with substance use disorder (SUD). While some studies reported decreased levels of impulsivity, in other studies only FA decreased, and only one study showed significant changes in both FA and impulsivity after treatment.

Further research is needed to better understand the association between impulsivity and FA. Specifically, more studies with male populations could provide further evidence on how to better tailor treatment designs.
Optimization of castor bean (Ricinus communis L.) cultivation methods using biostimulants in an arid climate
Authors: Esmaeilian Yaser , Babaeian Mahdi , Caballero-Calvo Andrés
Published: September 2023

In arid areas, low soil fertility, an imbalance of nutrients, and the inability of crops to absorb some nutrients are among the main constraints on crop production. The use of biological fertilizers and biostimulants can be a suitable solution. A 2-year field experiment was conducted as a factorial experiment based on a randomized complete block design with three replications to study the response of castor bean to arbuscular mycorrhizal fungi (AMF) and amino acid biostimulant (AAB) (foliar, soil, and combined application methods). Findings showed that plants inoculated with AMF had better performance: the biological and seed yields were increased by an average of 20.9 and 26.4% over the 2 years of the experiment. The yield components showed a 14.0 to 18.6% increase, and the water productivity (WP) was improved by 13.9%. The seed oil content was increased by 5.1%: linoleic acid, an oil fatty acid, showed the highest response, with an increase of 10.0%. Among the AAB treatments, the combined application method (CAM) brought the best results. The highest increases in biological and seed yields (68.4 and 63.2%, respectively) were obtained from the CAM treatment. The WP was improved by 67.8% and the seed oil content showed an increase of 9.4%. Among the fatty acids, the highest increase (24.4%) belonged to linoleic acid. The results show a positive and significant response of castor beans to biostimulants, which indicates that replacing chemicals with biological fertilizers could be a promising approach to the cultivation of castor beans in arid climates.
Large simplicial complexes: universality, randomness, and ampleness
Authors: Farber Michael
Published: September 2023

The paper surveys recent progress in understanding geometric, topological and combinatorial properties of large simplicial complexes, focusing mainly on ampleness, connectivity and universality (Even-Zohar et al. in Eur J Math 8(1):1–32, 2022; Farber and Mead in Topol Appl 272(22):107065, 2020; Farber et al. in J Appl Comput Topol 5(2):339–356, 2021). In the first part of the paper we concentrate on r-ample simplicial complexes which are high dimensional analogues of the r-e.c. graphs introduced originally by Erdős and Rényi (Acta Math Acad Sci Hungar 14:295–315, 1963), see also Bonato (Contrib Discrete Math 4(1):40–53, 2009). The class of r-ample complexes is useful for applications since these complexes allow extensions of subcomplexes of certain type in all possible ways; besides, r-ample complexes exhibit remarkable robustness properties. We discuss results about the existence of r-ample complexes and describe their probabilistic and deterministic constructions. The properties of random simplicial complexes in medial regime (Farber and Mead 2020) are important for this discussion since these complexes are ample, in certain range. We prove that the topological complexity of a random simplicial complex in the medial regime satisfies $$\textsf{TC}(X)\le 4$$

TC
(
X
)
≤
4

, with probability tending to 1 as $$n\rightarrow \infty $$

n
→
∞

. There exists a unique (up to isomorphism) $$\infty $$
∞
-ample complex on countable set of vertexes (the Rado complex), and the second part of the paper surveys the results about universality, homogeneity, indestructibility and other important properties of this complex. The Appendix written by J.A. Barmak discusses connectivity of conic and ample complexes.
Market impact and efficiency in cryptoassets markets
Authors: Barucci Emilio , Giuffra Moncayo Giancarlo , Marazzina Daniele
Published: September 2023

We analyze markets for cryptoassets (cryptocurrencies and stablecoins), investigating market impact and efficiency through the lens of the market order flow. We provide evidence that markets where cryptoassets are exchanged between themselves play a central role on price formation and are more efficient than markets where cryptocurrencies are exchanged with the US dollar. For the first set of markets we observe some evidence of the presence of insiders/contrarians, instead in the latter we observe the predominance of herding and trend-followers.
Besov regularity of inhomogeneous parabolic PDEs
Authors: Schneider Cornelia , Szemenyei Flóra Orsolya
Published: September 2023

We study the regularity of solutions of parabolic partial differential equations with inhomogeneous boundary conditions on polyhedral domains $$D\subset \mathbb {R}^3$$

D
⊂

R

3

in the specific scale $$\ B^{\alpha }_{\tau ,\tau }, \ \frac{1}{\tau }=\frac{\alpha }{3}+\frac{1}{p}\ $$

B

τ
,
τ

α

,

1
τ

=

α
3

+

1
p

of Besov spaces. The regularity of the solution in this scale determines the order of approximation that can be achieved by adaptive numerical schemes. We show that for all cases under consideration the Besov regularity is high enough to justify the use of adaptive algorithms. Our results are in good agreement with the forerunner (Dahlke and Schneider in Anal Appl 17:235–291, 2019), where parabolic equations with homogeneous boundary conditions were investigated.
Fluctuation-mediated orbital rotation of microparticles in non-coaxially counter-propagating optical tweezers
Authors: Setoura Kenji , kakimoto Takayasu , Miyasaka Hiroshi , Ito Syoji
Published: September 2023

We have demonstrated in the present report that dielectric microparticles exhibited orbital rotation in the light field of non-coaxially configured two counter-propagating laser beams both in numerical simulations and experiments. A series of computational simulations indicated that when irradiated with two non-coaxially counter-propagating parallel laser beams with the same intensity distributions in the absence of thermal (Brownian) motion, a microparticle did not exhibit orbital rotation due to the symmetry of the optical field. However, the computations predicted that a microparticle exhibited one directional orbital rotation in the presence of thermal motion because of the symmetry breaking of the optical force acting on the particle. This spontaneous orbital rotation was experimentally demonstrated for 1-µm dielectric particles in water at room temperature.

Graphical abstract
Life and Language Beyond Earth
Authors: Hickey Raymond
Published: September 2023

Have you ever wondered whether we are alone in the universe, or if life forms on other planets might exist? If they do exist, how might their languages have evolved? Could we ever understand them, and indeed learn to communicate with them? This highly original, thought-provoking book takes us on a fascinating journey over billions of years, from the formation of galaxies and solar systems, to the appearance of planets in the habitable zones of their parent stars, and then to how biology and, ultimately, human life arose on our own planet. It delves into how our brains and our language developed, in order to explore the likelihood of communication beyond Earth and whether it would evolve along similar lines. In the process, fascinating insights from the fields of astronomy, evolutionary biology, palaeoanthropology, neuroscience and linguistics are uncovered, shedding new light on life as we know it on Earth, and beyond.
Rapid Expansion of Fixed Nitrogen Deficit in the Eastern Pacific Ocean Revealed by 50‐Year Time Series
Authors: Evans Natalya , Tichota Juliana , Ruef Wendi , Moffett James , Devol Allan
Published: September 2023

Climate change is expected to increase the strength of ocean Oxygen Deficient Zones (ODZs), but we lack a detailed understanding of the temporal or spatial variability of these ODZs. A 50‐year time series in the Eastern Tropical North Pacific (ETNP) ODZ revealed that it has strengthened by 30% from 1994 to 2019. We subdivided the ODZ into a core and a deep layer based on potential density and revealed that different processes control the magnitude of fixed nitrogen loss between these regions. We postulate that the depth of the upper ETNP ODZ water mass, the 13°C Water, influences the organic carbon supply to the core ODZ and therefore its strength. We correlated the maximum fixed nitrogen loss in the core ODZ with a nearby sedimentary nitrogen isotope record and found that this recent increase in the magnitude of fixed nitrogen loss occurred only a few times over the last 1,200 years. Using this correlation, we derived the first confidence interval for the natural variability of the maximum fixed nitrogen loss within the ETNP ODZ, which has a range of 3.3 μmol kg−1 (p = 0.01). While the current increase is only comparable to two previous events, it is within the confidence interval for natural variability (p = 0.03). The deep ODZ also strengthened from 2016 to 2019 by approximately 30%, but this increase occurred more rapidly than the core ODZ, and this dramatic increase was not observed over the rest of the 40 years. Climate‐driven intensification could lead to unprecedented changes in the ETNP ODZ within the next decade.
Exploring Just How Extreme Future Storms Could Get
Authors: Stanley Sarah
Published: September 2023

A novel approach to storm simulations could help prepare for increasingly heavy precipitation events.
Sources and Fate of Sedimentary Organic Matter in the Western Mediterranean Sea
Authors: Ausín Blanca , Bossert Gina , Krake Nicola , Paradis Sarah , Haghipour Negar , Durrieu de Madron Xavier , Alonso Belén , Eglinton Timothy
Published: September 2023

Marine sediments comprise the primary long‐term sink of organic matter (OM) in marine systems. Disentangling the diverse origins of OM and the influence of the main processes that determine organic carbon (OC) fate at a global scale has proven difficult due to limited spatial data coverage. Thus, comprehensive studies of the spatial distribution of the content and geochemical characteristics of sedimentary OM at basin scales provide fundamental knowledge on the role of marine sediments in the global carbon cycle. Here, we shed light on the origin of OM and the underlying mechanisms that determine its fate in a semi‐enclosed basin by examining the spatial patterns in the isotopic and elemental composition of OM in 149 core‐top samples from the Western Mediterranean Sea and the adjacent Atlantic Ocean sector. Our results reveal an apparent SW‐NE gradient that reverses in the Gulf of Lions in most geochemical and sedimentological features. Changes in the OC content and ẟ13C and Δ14C signatures are ascribed to spatial variations in marine primary productivity and the influence of varying discharge of rivers and well‐developed canyons that favor the cross‐shelf transport of terrestrial (and petrogenic) OC. Our results also suggest the potential influence of two other mechanisms on the geochemical signatures of OM: (a) lateral transport of allochthonous OC and selective degradation of labile OM, which potentially occurs across the studied area having a greater impact toward the north‐eastern region, and (b) OM protection via association with mineral surfaces, potentially having a greater influence toward the south‐western basins.
Model‐Dependent Atlantic Multidecadal Variability Modulations on North Pacific Sea Surface Temperature Variability and Decadal Prediction
Authors: Lv Zhen , Yang Jun‐Chao , Zhang Yu , Lin Xiaopei
Published: September 2023

Previous studies suggested that Atlantic Multidecadal Variability (AMV) modulations on pan‐Pacific sea surface temperature (SST) variability and prediction are model‐dependent. These results were mainly based on SST forcing experiments in which AMV‐related Atlantic SST anomalies were prescribed. However, the AMV itself is also model‐dependent, but its influences on the Pacific remain unclear. Here, we use multi‐model fully coupled experiments from the Coupled Model Intercomparison Project Phase 6 (CMIP6), along with observations, to study the model‐dependent AMV trans‐basin effects. We found that AMV strength is a key factor: Stronger (Weaker) model AMV than observations overestimates (underestimates) SST response and decadal prediction skills, mainly in the North Pacific. The reason is that stronger positive phased AMV, for example, leads to higher sea level pressure anomalies over the North Pacific, which lifts sea surface height and deepens thermocline to warm SST. Our study highlights the necessity to improve simulations of AMV strength.
Local Infrasound Monitoring of Lava Eruptions at Nyiragongo Volcano (D.R. Congo) Using Urban and Near‐Source Stations
Authors: Barrière Julien , Oth Adrien , d’Oreye Nicolas , Subira Josué , Smittarello Delphine , Brenot Hugues , Theys Nicolas , Smets Benoît
Published: September 2023

During eruptions, volcanoes produce air‐pressure waves inaudible for the human ear called infrasound, which are very helpful for detecting early signs of magma at the surface. Compared to violent ash‐rich explosions, recording more discrete atmospheric disturbances from effusive eruptions remains a practical challenge depending on the distance to the source. At Nyiragongo volcano (D.R. Congo), towering above a 1‐million urban area, we analyzed local infrasonic records between January 2018 and April 2022. An acoustic signature from this open‐vent volcano is detected up to the volcano observatory facilities in Goma city center about 17 km from its crater. We compared infrasound signals with space‐based observations of the intra‐crater activity (SO2 emissions, thermal anomalies, crater depth/radius). We thus obtain a comprehensive picture of Nyiragongo's eruptive activity during this period, encompassing the drainage of its lava lake during its third known flank eruption on 22 May 2021.
Electron Heating and Associated Electrostatic Waves in Magnetic Flux Rope Embedded Within Super‐Alfvén Plasma Flow
Authors: Chen Z. Z. , Wang J. , Liu C. M. , Yu J. , He Z. G. , Liu N. G. , Cui J. , Cao J. B.
Published: September 2023

Magnetic flux ropes (MFRs) are significant regions for the production of energetic electrons in space and astrophysical plasmas. However, the research on electron heating and acceleration driven by turbulence in MFRs is still quite rare. Utilizing in‐situ measurements from MMS satellite, we study electron heating and associated electrostatic waves in an ion‐scale MFR within terrestrial super‐Alfvén plasma flow. Lower‐hybrid drift waves, generated locally in this MFR, can contribute to the perpendicular heating through their electrostatic potential accelerating electrons. The parallel heating is attributed to antiparallel propagating electron beams. These beams excite the broadband electrostatic waves that can interact with electrons and thermalize electrons. Our study promotes understanding of electron energization driven by plasma waves and wave‐particle interaction in MFRs.
P and S Wave Anisotropic Tomography of the Banda Subduction Zone
Authors: Hua Yuanyuan , Zhao Dapeng , Xu Yi‐Gang
Published: September 2023

In subduction zones with slab‐slab interactions, the pattern of mantle convection is very complex and still unclear. In this study, we jointly invert a large number of P and S wave arrival time data of local earthquakes for 3‐D isotropic and anisotropic velocity structures of the Banda subduction zone. Along the curved Banda arc, the subducting Indo‐Australian slab is detected clearly as a high‐velocity zone, and its azimuthal anisotropy changes along the arc strike, representing fossil anisotropy within the slab and modified anisotropy by the subduction processes. Around the northern edge of the Banda slab, a semi‐toroidal pattern of anisotropy appears in low‐velocity anomalies, representing mantle flow extruded from the Banda arc and escaped from a gap of the Banda‐Molucca slab toward the northeast. Our 3‐D anisotropic tomography uncovers the mantle convection pattern induced by the slab‐slab interactions, shedding new light on the complex dynamical processes in this curved subduction zone.
Properties of Whistler Waves’ Ducting in Plasmas With Systems of Small‐Scale Density Depletions
Authors: Zudin I. Yu. , Zaboronkova T. M. , Gushchin M. E. , Korobkov S. V. , Krafft C.
Published: September 2023

The ducting of whistler waves by systems of small‐scale field‐aligned plasma density depletions is studied. Similarly to our previous paper (Zudin et al., 2019, https://doi.org/10.1029/2019ja026637), we carry out analytical calculations and numerical simulations for the parameters of an active experiment in which very low frequency whistler waves emitted by a ground‐based transmitter at a frequency of 18 kHz were received onboard the DEMETER satellite at 700 km above the SURA heating facility. Random‐sized density depletions with a level around 10%–20% and perpendicular sizes ranging from 10 m up to about 300 m are considered. The properties of ducted waves are determined by the perpendicular size of individual depletions. Particularly, depletions with a width of more then d0 ∼ 100 m form separate ducting structures, that is, coupled waveguides capable of exchanging energy by means of mode overlap. Depletions with a width of less than d0 ∼ 100 m form a common waveguide structure, whose properties are equivalent to those of a wider irregularity with a smoothed density profile. Two important differences are revealed in ducting properties of density depletions compared to density enhancements considered in Zudin et al. (2019, https://doi.org/10.1029/2019ja026637). First, depletions support highly oblique Gendrin mode waves, rather than quasi‐longitudinal whistlers as in the case of density enhancements. Second, the characteristic perpendicular size d0 ∼ 100 m of density depletions separating the regimes of “coupled waveguides” and of “equivalent ducting structure” with smoothed density profile is by an order of magnitude smaller than for density enhancements of the same 10–20% relative level.
Blocking insulin-like growth factor 1 receptor signaling pathway inhibits neuromuscular junction regeneration after botulinum toxin-A treatment
Authors: Ishihara Hiroki , Otani Yoshinori , Tanaka Kazuki , Miyajima Hisao , Ngo Huy Xuan , Fujitani Masashi
Published: September 2023

Botulinum toxin-A (BTX) administration into muscle is an established treatment for conditions with excessive muscle contraction. However, botulinum therapy has short-term effectiveness, and high-dose injection of BTX could induce neutralizing antibodies against BTX. Therefore, prolonging its effects could be beneficial in a clinical situation. Insulin-like growth factor-1 receptor (IGF1R) and its ligands, insulin-like growth factor (IGF) -I and II, regulate the physiological and pathological processes of the nervous system. It has been suggested that IGF1R is involved in the process after BTX administration, but the specific regeneration mechanism remains unclear. Therefore, this study aimed to determine how inhibition of IGF1R signaling pathway affects BTX-induced muscle paralysis. The results showed that anti-IGF1R antibody administration inhibited the recovery from BTX-induced neurogenic paralysis, and the synaptic components at the neuromuscular junction (NMJ), mainly post-synaptic components, were significantly affected by the antibody. In addition, the wet weight or frequency distribution of the cross-sectional area of the muscle fibers was regulated by IGF1R, and sequential antibody administration following BTX treatment increased the number of Pax7+-satellite cells in the gastrocnemius (GC) muscle, independent of NMJ recovery. Moreover, BTX treatment upregulated mammalian target of rapamycin (mTOR)/S6 kinase signaling pathway, HDAC4, Myog, Fbxo32/MAFbx/Atrogin-1 pathway, and transcription of synaptic components, but not autophagy. Finally, IGF1R inhibition affected only mTOR/S6 kinase translational signaling in the GC muscle. In conclusion, the IGF1R signaling pathway is critical for NMJ regeneration via specific translational signals. IGF1R inhibition could be highly beneficial in clinical practice by decreasing the number of injections and total dose of BTX due to the prolonged duration of the effect.
LncRNA Neat1 targets NonO and miR-128-3p to promote antigen-specific Th17 cell responses and autoimmune inflammation
Authors: Chen Sisi , Wang Jiali , Zhang Kailang , Ma Binyun , Li Xiaorong , Wei Ruihua , Nian Hong
Published: September 2023

Long non-coding RNAs (lncRNAs) interaction with RNA-Binding proteins (RBPs) plays an important role in immunological processes. The generation of antigen-specific Th17 cells is closely associated with autoimmune pathogenesis. However, the function of lncRNA-RBP interactions in the regulation of pathogenic Th17 cell responses during autoimmunity remains poorly understood. Here, we found that lncRNA Neat1, highly expressed in Th17 cells, promoted antigen-specific Th17 cell responses. Both global and CD4+ T cell-specific knockdown of Neat1 protected mice against the development of experimental autoimmune uveitis (EAU). Mechanistically, Neat1 regulated RNA-Binding protein NonO, thus relieving IL-17 and IL-23R from NonO-mediated transcriptional repression and supporting antigen-specific Th17 cell responses. In addition, Neat1 also modulated miR-128-3p/NFAT5 axis to increase the expression of IL-17 and IL-23R, leading to augmented Th17 cell responses. Our findings elucidate a previously unrecognized mechanistic insight into the action of Neat1 in promoting antigen-specific Th17 responses and autoimmunity, and may facilitate the development of therapeutic targets for T cell-mediated autoimmune diseases.
ATP7B R778L mutant hepatocytes resist copper toxicity by activating autophagy and inhibiting necroptosis
Authors: Tang Shan , Liang Chen , Hou Wei , Hu Zhongjie , Chen Xinyue , Zhao Jing , Zhang Wei , Duan Zhongping , Bai Li , Zheng Sujun
Published: September 2023

Wilson’s disease (WD) is an inherited disease characterized by copper metabolism disorder caused by mutations in the adenosine triphosphatase copper transporting β gene (ATP7B). Currently, WD cell and animal model targeting the most common R778L mutation in Asia is lacking. In addition, the mechanisms by which hepatocytes resist copper toxicity remain to be further elucidated. In this study, we aimed to construct a novel WD cell model with R778L mutation and dissected the molecular basics of copper resistance. A novel HepG2 cell line stably expressing the ATP7B R778L gene (R778L cell) was constructed. The expression of necroptosis- and autophagy-related molecules was detected by PCR and Western blot (WB) in wild-type (WT) HepG2 and R778L cells with or without CuSO4 treatment. In addition, we detected and compared the levels of autophagy and necroptosis in CuSO4-treated R778L cells with the activation and inhibition of autophagy. Moreover, the mRNA and protein levels of autophagy and necroptosis signaling molecules were compared in R778L cells with the overexpression and knockdown of Unc-51 Like Autophagy Activating Kinase 1 (ULK1) and Autophagy Related 16 Like 1 (ATG16L1). We successfully constructed an R778L mutation HepG2 cell line. CuSO4 triggered the enhanced expression of autophagy and necroptosis signaling molecules in WT HepG2 cells and R778L cells. Remarkably, higher levels of autophagy and necroptosis were observed in R778L cells compared with those in WT cells. Autophagy activation led to weakened necroptosis mediated by RIPK3 and MLKL, conversely, autophagy inhibition brought about enhanced necroptosis. At the molecular level, ULK1- and ATG16L1 overexpression resulted in reduced necroptosis levels and vice versa. ULK1- and ATG16L1-mediated autophagy activation protects hepatocytes against RIPK3- and MLKL-mediated necroptosis in our new WD cell model treated with CuSO4. Targeted therapy by autophagy activation or necroptosis inhibition may be a novel and effective strategy to treat WD.
Integrating end-to-end learning with deep geometrical potentials for ab initio RNA structure prediction
Authors: Li Yang , Zhang Chengxin , Feng Chenjie , Pearce Robin , Lydia Freddolino P. , Zhang Yang
Published: September 2023

RNAs are fundamental in living cells and perform critical functions determined by their tertiary architectures. However, accurate modeling of 3D RNA structure remains a challenging problem. We present a novel method, DRfold, to predict RNA tertiary structures by simultaneous learning of local frame rotations and geometric restraints from experimentally solved RNA structures, where the learned knowledge is converted into a hybrid energy potential to guide RNA structure assembly. The method significantly outperforms previous approaches by >73.3% in TM-score on a sequence-nonredundant dataset containing recently released structures. Detailed analyses showed that the major contribution to the improvements arise from the deep end-to-end learning supervised with the atom coordinates and the composite energy function integrating complementary information from geometry restraints and end-to-end learning models. The open-source DRfold program with fast training protocol allows large-scale application of high-resolution RNA structure modeling and can be further improved with future expansion of RNA structure databases.
Performance of tumour microenvironment deconvolution methods in breast cancer using single-cell simulated bulk mixtures
Authors: Tran Khoa A. , Addala Venkateswar , Johnston Rebecca L. , Lovell David , Bradley Andrew , Koufariotis Lambros T. , Wood Scott , Wu Sunny Z. , Roden Daniel , Al-Eryani Ghamdan , Swarbrick Alexander , Williams Elizabeth D. , Pearson John V. , Kondrashova Olga , Waddell Nicola
Published: September 2023

Cells within the tumour microenvironment (TME) can impact tumour development and influence treatment response. Computational approaches have been developed to deconvolve the TME from bulk RNA-seq. Using scRNA-seq profiling from breast tumours we simulate thousands of bulk mixtures, representing tumour purities and cell lineages, to compare the performance of nine TME deconvolution methods (BayesPrism, Scaden, CIBERSORTx, MuSiC, DWLS, hspe, CPM, Bisque, and EPIC).Some methods are more robust in deconvolving mixtures with high tumour purity levels. Most methods tend to mis-predict normal epithelial for cancer epithelial as tumour purity increases, a finding that is validated in two independent datasets. The breast cancer molecular subtype influences this mis-prediction. BayesPrism and DWLS have the lowest combined numbers of false positives and false negatives, and have the best performance when deconvolving granular immune lineages. Our findings highlight the need for more single-cell characterisation of rarer cell types, and suggest that tumour cell compositions should be considered when deconvolving the TME.
Ustilago maydis PR-1-like protein has evolved two distinct domains for dual virulence activities
Authors: Lin Yu-Han , Xu Meng-Yun , Hsu Chuan-Chih , Damei Florensia Ariani , Lee Hui-Chun , Tsai Wei-Lun , Hoang Cuong V. , Chiang Yin-Ru , Ma Lay-Sun
Published: September 2023

The diversification of effector function, driven by a co-evolutionary arms race, enables pathogens to establish compatible interactions with hosts. Structurally conserved plant pathogenesis-related PR-1 and PR-1-like (PR-1L) proteins are involved in plant defense and fungal virulence, respectively. It is unclear how fungal PR-1L counters plant defense. Here, we show that Ustilago maydis UmPR-1La and yeast ScPRY1, with conserved phenolic resistance functions, are Ser/Thr-rich region mediated cell-surface localization proteins. However, UmPR-1La has gained specialized activity in sensing phenolics and eliciting hyphal-like formation to guide fungal growth in plants. Additionally, U. maydis hijacks maize cathepsin B-like 3 (CatB3) to release functional CAPE-like peptides by cleaving UmPR-1La’s conserved CNYD motif, subverting plant CAPE-primed immunity and promoting fungal virulence. Surprisingly, CatB3 avoids cleavage of plant PR-1s, despite the presence of the same conserved CNYD motif. Our work highlights that UmPR-1La has acquired additional dual roles to suppress plant defense and sustain the infection process of fungal pathogens.
Loss of microglial MCT4 leads to defective synaptic pruning and anxiety-like behavior in mice
Authors: Monsorno Katia , Ginggen Kyllian , Ivanov Andranik , Buckinx An , Lalive Arnaud L. , Tchenio Anna , Benson Sam , Vendrell Marc , D’Alessandro Angelo , Beule Dieter , Pellerin Luc , Mameli Manuel , Paolicelli Rosa Chiara
Published: September 2023

Microglia, the innate immune cells of the central nervous system, actively participate in brain development by supporting neuronal maturation and refining synaptic connections. These cells are emerging as highly metabolically flexible, able to oxidize different energetic substrates to meet their energy demand. Lactate is particularly abundant in the brain, but whether microglia use it as a metabolic fuel has been poorly explored. Here we show that microglia can import lactate, and this is coupled with increased lysosomal acidification. In vitro, loss of the monocarboxylate transporter MCT4 in microglia prevents lactate-induced lysosomal modulation and leads to defective cargo degradation. Microglial depletion of MCT4 in vivo leads to impaired synaptic pruning, associated with increased excitation in hippocampal neurons, enhanced AMPA/GABA ratio, vulnerability to seizures and anxiety-like phenotype. Overall, these findings show that selective disruption of the MCT4 transporter in microglia is sufficient to alter synapse refinement and to induce defects in mouse brain development and adult behavior.