bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Predictability of Marine Heatwaves With Random Forests
Authors: Giamalaki K. , Beaulieu C. , Prochaska J. X. 
Published: November 2022

AbstractMarine heatwaves (MHWs) have increased in frequency and duration over the last century and are expected to intensify in the future. Such events have become an increasing threat for marine ecosystems and subsequently the economies and populations that rely on them. Here we apply random forests to assess skill in forecasting MHWs onset and severity at multiple prediction lead times. Random forests models are trained on a range of atmospheric and oceanic conditions to identify precursors of MHWs. The best performing random forest model accurately captures (76%) MHW presence/absence in the northeast Pacific and is capable of forecasting realistic extreme sea surface temperature patterns at weekly lead times. However, the total accuracy drops to 38% when forecasting MHW severity. Machine learning algorithms affirm further exploration as forecasting tools and have the potential to accelerate our predictive ability and preparedness against upcoming extreme climate changes.
Cobalamin Co‐Limits Phytoplankton and Bacterial Biomass and Activity in Eastern Mediterranean Coastal Waters
Authors: Rahav Eyal , Silverman Jacob 
Published: November 2022

AbstractIn this study, we examined the response of phytoplankton and heterotrophic bacteria to B12 amendments in microcosm experiments in the coastal southeastern Mediterranean Sea (SEMS) during the summer, where ambient levels of dissolved B12 ranged from as low as ∼2 pmol L−1 to 60 pmol L−1 (median 5.3 pmol L−1). Additions of B12 (20 pmol L−1) to surface seawater triggered a 4‐fold increase in NO3+NO2 uptake compared to unamended seawater, resulting in proliferation of mainly pico/nano‐eukaryotic phytoplankton (∼30%) and increase in primary and bacterial productivity (40%–50%). Complimentary experiments that tested the combined effects of nutrient (NO3 and PO4) and B12 additions suggest that phytoplankton were primarily NO3 and B12 co‐limited, whereas heterotrophic bacteria were PO4 and B12 co‐limited. These results provide valuable information about the marine distribution of nutrient limitation in low nutrients low chlorophyll (LNLC) environments such as the SEMS, and how bacterioplankton might respond to environmental perturbations.
Does Uranus' Asymmetric Magnetic Field Produce a Relatively Weak Proton Radiation Belt?
Authors: Masters A. , Ioannou C. , Rayns N. 
Published: November 2022

AbstractSince the Voyager 2 flyby in 1986 the radiation belts of Uranus have presented a problem for physicists. The observations indicate the electron radiation belt is far more intense than the proton radiation belt, and while the electron intensities are close to the upper theoretical limit, proton intensities are well below. Here we propose the relatively weak proton radiation belt could be due to Uranus' asymmetric magnetic field. We model test particle motion through the field to show that perturbations arising from asymmetry are greater the larger the particle gyroradius, predominantly affecting 100‐keV protons. For these particles, more rapid changes in maximum distance from the planet during a bounce motion promote trajectory evolution into regions where they could be lost through impact with the rings, impact with the atmosphere, or to the distant magnetosphere and solar wind. We suggest this could explain a relatively weak proton radiation belt at Uranus.
Common Error Patterns in the Regional Atmospheric Circulation Simulated by the CMIP Multi‐Model Ensemble
Authors: Brands Swen 
Published: November 2022

AbstractThe ability of global climate models to reproduce recurrent regional atmospheric circulation types is introduced as an overarching concept to explore potential dependencies between these models. If this approach is applied on a sufficiently large spatial domain, the similarity of the resulting error pattern can be compared from one model to another. By computing a pattern correlation matrix for a large multi‐model ensemble from the Coupled Model Intercomparison Project Phases 5 and 6, groups of comparatively strong correlation coefficients are obtained for those models working with similar atmospheric components. Thereby, frequent shared error patterns are found within the ensemble, which also occur for nominally different atmospheric component models. The error pattern correlation coefficients describing these similarities are nearly unrelated to model performance and can be used as statistical dependency weights.
Depth‐Varying Friction on a Ramp‐Flat Fault Illuminated by ∼3‐Year InSAR Observations Following the 2017 Mw 7.3 Sarpol‐e Zahab Earthquake
Authors: Guo Zelong , Motagh Mahdi , Hu Jyr‐Ching , Xu Guangyu , Haghighi Mahmud Haghshenas , Bahroudi Abbas , Fathian Aram , Li Shaoyang 
Published: November 2022

AbstractWe use interferometric synthetic aperture radar observations to investigate the fault geometry and afterslip evolution within 3 years after a mainshock. The postseismic observations favor a ramp‐flat structure in which the flat angle should be lower than 10°. The postseismic deformation is dominated by afterslip, while the viscoelastic response is negligible. A multisegment, stress‐driven afterslip model (hereafter called the SA‐2 model) with depth‐varying frictional properties better explains the spatiotemporal evolution of the postseismic deformation than a two‐segment, stress‐driven afterslip model (hereafter called the SA‐1 model). Although the SA‐2 model does not improve the misfit significantly, this multisegment fault with depth‐varying friction is more physically plausible given the depth‐varying mechanical stratigraphy in the region. Compared to the kinematic afterslip model, the mechanical afterslip models with friction variation tend to underestimate early postseismic deformation to the west, which may indicate more complex fault friction than we expected. Both the kinematic and stress‐driven models can resolve downdip afterslip, although it could be affected by data noise and model resolution. The transition depth of the sedimentary cover basement interface inferred by afterslip models is ∼12 km in the seismogenic zone, which coincides with the regional stratigraphic profile. Because the coseismic rupture propagated along a basement‐involved fault while the postseismic slip may activate the frontal structures and/or shallower detachments in the sedimentary cover, the 2017 Sarpol‐e Zahab earthquake may have acted as a typical event that contributed to both thick‐ and thin‐skinned shortening of the Zagros in both seismic and aseismic ways.
A Multi‐Layer Linear Rossby Wave Dispersion Relation for Vertical Tilt of Mesoscale Eddies
Authors: Li Hong , Xu Fanghua , Wang Guihua , Shi Ruizi 
Published: November 2022

AbstractVertical tilt of mesoscale eddies has been frequently observed in world oceans. The observations of composite eddies, individual eddies from an oceanic reanalysis product, and idealized numerical experiments of mesoscale eddies all show that the eddy vertical tilt is gradually increased with time in eddy mature stage, implying that the eddy translation speed changes with depth. However, eddy vertical tilt cannot be explained by the classic linear Rossby wave dispersion relation, since the classic zonal translation speed () of linear Rossby waves is depth‐independent from the quasi‐geostrophic potential vorticity (QGPV) equation. To deduce a depth‐dependent linear Rossby wave dispersion relation, we solved the QGPV equation by assuming that the stratified water column in oceans can be separated into a number of fine layers with constant stratification in each layer, whereas the stratification changes among layers. A multi‐layer linear Rossby wave (MLRW) dispersion relation in stratified oceans is then deduced. The MLRW dispersion relation shows that changes with depth. In each layer, is proportional to stratification and layer thickness but inversely proportional to Earth's rotation. The estimated structure from the MLRW dispersion relation is consistent with the structure of eddies in numerical experiments and the observed composite eddies. Noticeably, there are some discrepancies between the theoretical estimates and those from observations and numerical simulations, primarily due to the sensitivity of the theoretical estimates to layer thickness. The study attempts to provide an approach to describe and predict mesoscale eddy vertical tilt.
Oncosuppressive miRNAs loaded in lipid nanoparticles potentiate targeted therapies in BRAF-mutant melanoma by inhibiting core escape pathways of resistance
Authors: Fattore Luigi , Cafaro Giordana , Di Martile Marta , Campani Virginia , Sacconi Andrea , Liguoro Domenico , Marra Emanuele , Bruschini Sara , Stoppoloni Daniela , Cirombella Roberto , De Nicola Francesca , Pallocca Matteo , Ruggiero Ciro F. , Castaldo Vittorio , Catizone Angiolina , Del Bufalo Donatella , Viglietto Giuseppe , Vecchione Andrea , Blandino Giovanni , Aurisicchio Luigi , Fanciulli Maurizio , Ascierto Paolo A. , De Rosa Giuseppe , Mancini Rita , Ciliberto Gennaro 
Published: November 2022

AbstractBRAF-mutated melanoma relapsing after targeted therapies is an aggressive disease with unmet clinical need. Hence the need to identify novel combination therapies able to overcome drug resistance. miRNAs have emerged as orchestrators of non-genetic mechanisms adopted by melanoma cells to challenge therapies. In this context we previously identified a subset of oncosuppressor miRNAs downregulated in drug-resistant melanomas. Here we demonstrate that lipid nanoparticles co-encapsulating two of them, miR-199-5p and miR-204-5p, inhibit tumor growth both in vitro and in vivo in combination with target therapy and block the development of drug resistance. Mechanistically they act by directly reducing melanoma cell growth and also indirectly by hampering the recruitment and reprogramming of pro-tumoral macrophages. Molecularly, we demonstrate that the effects on macrophages are mediated by the dysregulation of a newly identified miR-204-5p-miR-199b-5p/CCL5 axis. Finally, we unveiled that M2 macrophages programs are molecular signatures of resistance and predict response to therapy in patients. Overall, these findings have strong translational implications to propose new combination therapies making use of RNA therapeutics for metastatic melanoma patients.
Bioinformatics driven discovery of small molecule compounds that modulate the FOXM1 and PPARA pathway activities in breast cancer
Authors: Huang Shujun , Hu Pingzhao , Lakowski Ted M. 
Published: November 2022

AbstractOur previous studies demonstrated that the FOXM1 pathway is upregulated and the PPARA pathway downregulated in breast cancer (BC), and especially in the triple negative breast cancer (TNBC) subtype. Targeting the two pathways may offer potential therapeutic strategies to treat BC, especially TNBC which has the fewest effective therapies available among all BC subtypes. In this study we identified small molecule compounds that could modulate the PPARA and FOXM1 pathways in BC using two methods. In the first method, data were initially curated from the Connectivity Map (CMAP) database, which provides the gene expression profiles of MCF7 cells treated with different compounds as well as paired controls. We then calculated the changes in the FOXM1 and PPARA pathway activities from the compound-induced gene expression profiles under each treatment to identify compounds that produced a decreased activity in the FOXM1 pathway or an increased activity in the PPARA pathway. In the second method, the CMAP database tool was used to identify compounds that could reverse the expression pattern of the two pathways in MCF7 cells. Compounds identified as repressing the FOXM1 pathway or activating the PPARA pathway by the two methods were compared. We identified 19 common compounds that could decrease the FOXM1 pathway activity scores and reverse the FOXM1 pathway expression pattern, and 13 common compounds that could increase the PPARA pathway activity scores and reverse the PPARA pathway expression pattern. It may be of interest to validate these compounds experimentally to further investigate their effects on TNBCs.
Caspase-8 is required for HSV-1-induced apoptosis and promotes effective viral particle release via autophagy inhibition
Authors: Marino-Merlo Francesca , Klett Anusha , Papaianni Emanuela , Drago Selene Francesca Anna , Macchi Beatrice , Rincón María Gabriela , Andreola Federica , Serafino Annalucia , Grelli Sandro , Mastino Antonio , Borner Christoph 
Published: November 2022

AbstractRegulated cell death (RCD) plays an important role in the progression of viral replication and particle release in cells infected by herpes simplex virus-1 (HSV-1). However, the kind of RCD (apoptosis, necroptosis, others) and the resulting cytopathic effect of HSV-1 depends on the cell type and the species. In this study, we further investigated the molecular mechanisms of apoptosis induced by HSV-1. Although a role of caspase-8 has previously been suggested, we now clearly show that caspase-8 is required for HSV-1-induced apoptosis in a FADD-/death receptor-independent manner in both mouse embryo fibroblasts (MEF) and human monocytes (U937). While wild-type (wt) MEFs and U937 cells exhibited increased caspase-8 and caspase-3 activation and apoptosis after HSV-1 infection, respective caspase-8-deficient (caspase-8−/−) cells were largely impeded in any of these effects. Unexpectedly, caspase-8−/− MEF and U937 cells also showed less virus particle release associated with increased autophagy as evidenced by higher Beclin-1 and lower p62/SQSTM1 levels and increased LC3-I to LC3-II conversion. Confocal and electron microscopy revealed that HSV-1 stimulated a strong perinuclear multivesicular body response, resembling increased autophagy in caspase-8−/− cells, entrapping virions in cellular endosomes. Pharmacological inhibition of autophagy by wortmannin restored the ability of caspase-8−/− cells to release viral particles in similar amounts as in wt cells. Altogether our results support a non-canonical role of caspase-8 in both HSV-1-induced apoptosis and viral particle release through autophagic regulation.
Structural basis of tankyrase activation by polymerization
Authors: Pillay Nisha , Mariotti Laura , Zaleska Mariola , Inian Oviya , Jessop Matthew , Hibbs Sam , Desfosses Ambroise , Hopkins Paul C. R. , Templeton Catherine M. , Beuron Fabienne , Morris Edward P. , Guettler Sebastian 
Published: November 2022

AbstractThe poly-ADP-ribosyltransferase tankyrase (TNKS, TNKS2) controls a wide range of disease-relevant cellular processes, including WNT–β-catenin signalling, telomere length maintenance, Hippo signalling, DNA damage repair and glucose homeostasis1,2. This has incentivized the development of tankyrase inhibitors. Notwithstanding, our knowledge of the mechanisms that control tankyrase activity has remained limited. Both catalytic and non-catalytic functions of tankyrase depend on its filamentous polymerization3–5. Here we report the cryo-electron microscopy reconstruction of a filament formed by a minimal active unit of tankyrase, comprising the polymerizing sterile alpha motif (SAM) domain and its adjacent catalytic domain. The SAM domain forms a novel antiparallel double helix, positioning the protruding catalytic domains for recurring head-to-head and tail-to-tail interactions. The head interactions are highly conserved among tankyrases and induce an allosteric switch in the active site within the catalytic domain to promote catalysis. Although the tail interactions have a limited effect on catalysis, they are essential to tankyrase function in WNT–β-catenin signalling. This work reveals a novel SAM domain polymerization mode, illustrates how supramolecular assembly controls catalytic and non-catalytic functions, provides important structural insights into the regulation of a non-DNA-dependent poly-ADP-ribosyltransferase and will guide future efforts to modulate tankyrase and decipher its contribution to disease mechanisms.
The encoding of touch by somatotopically aligned dorsal column subdivisions
Authors: Turecek Josef , Lehnert Brendan P. , Ginty David D. 
Published: November 2022

AbstractThe somatosensory system decodes a range of tactile stimuli to generate a coherent sense of touch. Discriminative touch of the body depends on signals conveyed from peripheral mechanoreceptors to the brain through the spinal cord dorsal column and its brainstem target, the dorsal column nuclei (DCN)1,2. Models of somatosensation emphasize that fast-conducting low-threshold mechanoreceptors (LTMRs) innervating the skin drive the DCN3,4. However, postsynaptic dorsal column (PSDC) neurons within the spinal cord dorsal horn also collect mechanoreceptor signals and form a second major input to the DCN5–7. The significance of PSDC neurons and their contributions to the coding of touch have remained unclear since their discovery. Here we show that direct LTMR input to the DCN conveys vibrotactile stimuli with high temporal precision. Conversely, PSDC neurons primarily encode touch onset and the intensity of sustained contact into the high-force range. LTMR and PSDC signals topographically realign in the DCN to preserve precise spatial detail. Different DCN neuron subtypes have specialized responses that are generated by distinct combinations of LTMR and PSDC inputs. Thus, LTMR and PSDC subdivisions of the dorsal column encode different tactile features and differentially converge in the DCN to generate specific ascending sensory processing streams.
Organization of residential space, site function variability, and seasonality of activities among MIS 5 Iberian Neandertals
Authors: Deschamps Marianne , Martín-Lerma Ignacio , Linares-Matás Gonzalo , Zilhão João 
Published: November 2022

AbstractWhether ethnoarcheological models of hunter-gatherer mobility, landscape use, and structuration of the inhabited space are relevant to the archeology of Neandertals and the Middle Paleolithic remains controversial. The thin lenses of hearth-associated stone tools and faunal remains excavated in sub-complex AS5 of Cueva Antón (Murcia, Spain) significantly advance these debates. Dated to 77.8–85.1 ka, these living floors are interstratified in river-accumulated sands and were buried shortly after abandonment by low-energy inundation events, with minimal disturbance and negligible palimpsest formation. Stone tools were made and ergonomically modified to fit tasks; their spatial distributions and use-wear reveal hearth-focused activities and a division of the inhabited space into resting and working areas. Site function varied with season of the year: units III-i/j1 and III-i/j2-3 record winter visits focused on filleting and hide processing, while woodworking predominated in unit III-b/d, which subsumes visits to the site over the course of at least one winter, one spring, and one summer. These snapshots of Neandertal behavior match expectations derived from the ethnographic and Upper Paleolithic records for the lifeways of hunter-gatherers inhabiting temperate regions with a markedly seasonal climate.
Arc discharge rapid synthesis of engineered copper oxides nano shapes with potent antibacterial activity against multi-drug resistant bacteria
Authors: Elwakil Bassma H. , Toderas M. , El-Khatib Mostafa 
Published: November 2022

AbstractNowadays Nano metals have received an eminent compromise of attention. Even though different nanostructure of same metal maybe gives different results in wide range applications. Copper oxide (CuO-NPs) and Copper Nano wires (CuO-NWs) were prepared in controlled size via the alternating current Arc discharge process. Deionized water and argon gas were the chosen dielectric medium during the process to obtain 2 different forms of copper oxides. By changing the dielectric material from deionized water to argon gas the shape of CuO nanoparticles changed from spherical (CuO-NPs) to wires (CuO-NWS). The yield prepared depicted the purity of the prepared CuO, and their diameters were about 10 ± 5 nm and 30 ± 3 nm for CuO-NWs and CuO-NPs respectively. In vitro cytotoxic effect of the prepared CuO-NWs & CuO-NPs using human normal lung fibroblast cell line (WI-38 cells) revealed that CuO-NWs & CuO-NPs CC50 values were 458.8 and 155.6 µg/mL respectively. Both yields showed potent antibacterial activity against different multi-drug resistant Acinetobacter baumannii strains. A complete eradication of the bacterial growth was noticed after 4 Hrs incubation with CuO-NWs. Moreover, CuO-NWs showed superior antibacterial activity (with minimum inhibitory concentration reached 1.8 µg/mL) over CuO-NPs. The detailed antibacterial activity mechanism of CuO-NWs was further investigated; data proved the precipitation and adsorption of the nanoparticles on the bacterial cell surface leading to cell deformation with reactive oxygen species increment. The results explicated that the nanoparticles shape plays an essential role in the antibacterial activity. Rotational Arc discharge machine might be a promising tool to obtain various metal nanostructures with low cost and environmentally friendly with potent activity.
Detecting hierarchical organization of pervasive communities by modular decomposition of Markov chain
Authors: Okamoto Hiroshi , Qiu Xule 
Published: November 2022

AbstractConnecting nodes that contingently co-appear, which is a common process of networking in social and biological systems, normally leads to modular structure characterized by the absence of definite boundaries. This study seeks to find and evaluate methods to detect such modules, which will be called ‘pervasive’ communities. We propose a mathematical formulation to decompose a random walk spreading over the entire network into localized random walks as a proxy for pervasive communities. We applied this formulation to biological and social as well as synthetic networks to demonstrate that it can properly detect communities as pervasively structured objects. We further addressed a question that is fundamental but has been little discussed so far: What is the hierarchical organization of pervasive communities and how can it be extracted? Here we show that hierarchical organization of pervasive communities is unveiled from finer to coarser layers through discrete phase transitions that intermittently occur as the value for a resolution-controlling parameter is quasi-statically increased. To our knowledge, this is the first elucidation of how the pervasiveness and hierarchy, both hallmarks of community structure of real-world networks, are unified.