bluuebunny/crossref_metadata_2025_split huggingface dataset:
Anomalous Meltwater From Ice Sheets and Ice Shelves Is a Historical Forcing
Authors: Schmidt Gavin. A. , Romanou Anastasia , Roach Lettie A. , Mankoff Kenneth D. , Li Qian , Rye Craig D. , Kelley Maxwell , Marshall John C. , Busecke Julius J. M. 
Published: December 2023

AbstractRecent mass loss from ice sheets and ice shelves is now persistent and prolonged enough that it impacts downstream oceanographic conditions. To demonstrate this, we use an ensemble of coupled GISS‐E2.1‐G simulations forced with historical estimates of anomalous freshwater, in addition to other climate forcings, from 1990 through 2019. There are detectable differences in zonal‐mean sea surface temperatures (SST) and sea ice in the Southern Ocean, and in regional sea level around Antarctica and in the western North Atlantic. These impacts mostly improve the model's representation of historical changes, including reversing the forced trends in Antarctic sea ice. The changes in SST may have implications for estimates of the SST pattern effect on climate sensitivity and for cloud feedbacks. We conclude that the changes are sufficiently large that model groups should strive to include more accurate estimates of these drivers in all‐forcing historical simulations in future coupled model intercomparisons.
Energy Conversion by a Twisted Magnetic Structure at Magnetopause Boundary Layer: MMS Observations
Authors: Du C. X. , Fu H. S. , Wang Z. , Cao J. B. , Liu Y. Y. , Fu W. D. 
Published: December 2023

AbstractThe Earth's magnetopause is an ion‐scale boundary that separates the magnetosphere from the shocked solar wind. At such boundary, energy‐conversion processes frequently occur. Previous studies suggested that such energy conversions are related to the magnetic reconnection process. Here, we report a new mechanism that the coaction between the twisted magnetic structure and lower‐hybrid waves can also drive energy conversion (J⋅ E, J is current density and E is electric field) at the magnetopause boundary layer, by using high‐resolution measurements of the four Magnetospheric Multiscale spacecraft. We find that such energy conversion is efficient (with magnitude up to 20 nW/m3) and is attributed to an intense current filament (j ≈ 3,800 nA/m2) and a fluctuating electric field driven by lower‐hybrid waves. With the help of the First‐Order Taylor Expansion method, we find that the intense current filament is driven by a twisted magnetic structure at electron scale. Our study improves the understanding of energy‐conversion processes at the Earth's magnetopause.
Cortical microstructural associations with CSF amyloid and pTau
Authors: Nir Talia M. , Villalón-Reina Julio E. , Salminen Lauren E. , Haddad Elizabeth , Zheng Hong , Thomopoulos Sophia I. , Jack Clifford R. , Weiner Michael W. , Thompson Paul M. , Jahanshad Neda ,   for the Alzheimer’s Disease Neuroimaging Initiative (ADNI)
Published: December 2023

AbstractDiffusion MRI (dMRI) can be used to probe microstructural properties of brain tissue and holds great promise as a means to non-invasively map Alzheimer’s disease (AD) pathology. Few studies have evaluated multi-shell dMRI models such as neurite orientation dispersion and density imaging (NODDI) and mean apparent propagator (MAP)-MRI in cortical gray matter where many of the earliest histopathological changes occur in AD. Here, we investigated the relationship between CSF pTau181 and Aβ1–42 burden and regional cortical NODDI and MAP-MRI indices in 46 cognitively unimpaired individuals, 18 with mild cognitive impairment, and two with dementia (mean age: 71.8 ± 6.2 years) from the Alzheimer’s Disease Neuroimaging Initiative. We compared findings to more conventional cortical thickness measures. Lower CSF Aβ1–42 and higher pTau181 were associated with cortical dMRI measures reflecting less hindered or restricted diffusion and greater diffusivity. Cortical dMRI measures, but not cortical thickness measures, were more widely associated with Aβ1–42 than pTau181 and better distinguished Aβ+ from Aβ- participants than pTau+ from pTau- participants. dMRI associations mediated the relationship between CSF markers and delayed logical memory performance, commonly impaired in early AD. dMRI metrics sensitive to early AD pathogenesis and microstructural damage may be better measures of subtle neurodegeneration in comparison to standard cortical thickness and help to elucidate mechanisms underlying cognitive decline.
Feasibility of a novel wearable thermal device for management of bothersome hot flashes in patients with prostate cancer
Authors: Peeke Pamela , Billes Sonja K. , Vetter Andrew , Naghavi Nader , Le Diana , Smith Matthew , Morgans Alicia K. 
Published: December 2023

Abstract
Background
This single-arm prospective study evaluated the feasibility of a novel wrist-worn thermal device that applies cooling to the inside of the wrist for management of bothersome hot flashes in prostate cancer survivors.

Methods
57 individuals were enrolled and instructed to use the thermal device as needed for management of hot flashes for 4 weeks. The primary outcome was thermal device usage (hours and sessions per day). Additional outcomes included the change in Hot Flash Related Daily Interference Scale (HFRDIS, range 0–10) and Patient Reported Outcomes Measurement Information System Sleep Disturbance 4a (PROMIS SD T-score, range 0–100) and Sleep-Related Impairment 8a (PROMIS SRI T-score, range 0–100). Study procedures were conducted remotely from May to Dec 2021 in the US.

Results
44 participants completed the study and 39 had retrievable usage data. The mean ± SD age was 67 ± 6 years and 5 ± 5 years since cancer diagnosis. The baseline mean ± SD HFRDIS score of 4.3 ± 2.0 indicated moderate hot flash interference in this population. During the study, participants used the thermal device (mean ± SD) 3.2 ± 2.5 hours/day and 7.6 ± 3.6 sessions/day. Most (67%) participants reported using the device 7 days and 7 nights each week. Statistically significant improvements from baseline at Week 4 were observed for HFRDIS (mean ± SE change: −1.1 ± 0.3), PROMIS SD (−6.0 ± 1.0), and PROMIS SRI (−5.5 ± 1.2) scores (all p < 0.001). The majority (69%) of participants reported that the thermal device was effective at helping them manage hot flashes. No adverse events were reported.

Conclusions
Results support the feasibility of using the thermal device for management of bothersome hot flashes in prostate cancer survivors. Future randomized controlled studies are warranted to evaluate the impact of the thermal device on frequency and severity of hot flashes, sleep quality, fatigue, and overall quality of life.
Chlorpromazine affects glioblastoma bioenergetics by interfering with pyruvate kinase M2
Authors: Abbruzzese Claudia , Matteoni Silvia , Matarrese Paola , Signore Michele , Ascione Barbara , Iessi Elisabetta , Gurtner Aymone , Sacconi Andrea , Ricci-Vitiani Lucia , Pallini Roberto , Pace Andrea , Villani Veronica , Polo Andrea , Costantini Susan , Budillon Alfredo , Ciliberto Gennaro , Paggi Marco G. 
Published: December 2023

AbstractGlioblastoma (GBM) is the most frequent and lethal brain tumor, whose therapeutic outcome - only partially effective with current schemes - places this disease among the unmet medical needs, and effective therapeutic approaches are urgently required. In our attempts to identify repositionable drugs in glioblastoma therapy, we identified the neuroleptic drug chlorpromazine (CPZ) as a very promising compound. Here we aimed to further unveil the mode of action of this drug. We performed a supervised recognition of the signal transduction pathways potentially influenced by CPZ via Reverse-Phase Protein microArrays (RPPA) and carried out an Activity-Based Protein Profiling (ABPP) followed by Mass Spectrometry (MS) analysis to possibly identify cellular factors targeted by the drug. Indeed, the glycolytic enzyme PKM2 was identified as one of the major targets of CPZ. Furthermore, using the Seahorse platform, we analyzed the bioenergetics changes induced by the drug. Consistent with the ability of CPZ to target PKM2, we detected relevant changes in GBM energy metabolism, possibly attributable to the drug’s ability to inhibit the oncogenic properties of PKM2. RPE-1 non-cancer neuroepithelial cells appeared less responsive to the drug. PKM2 silencing reduced the effects of CPZ. 3D modeling showed that CPZ interacts with PKM2 tetramer in the same region involved in binding other known activators. The effect of CPZ can be epitomized as an inhibition of the Warburg effect and thus malignancy in GBM cells, while sparing RPE-1 cells. These preclinical data enforce the rationale that allowed us to investigate the role of CPZ in GBM treatment in a recent multicenter Phase II clinical trial.
Competition and evolutionary selection among core regulatory motifs in gene expression control
Authors: Gyorgy Andras 
Published: December 2023

AbstractGene products that are beneficial in one environment may become burdensome in another, prompting the emergence of diverse regulatory schemes that carry their own bioenergetic cost. By ensuring that regulators are only expressed when needed, we demonstrate that autoregulation generally offers an advantage in an environment combining mutation and time-varying selection. Whether positive or negative feedback emerges as dominant depends primarily on the demand for the target gene product, typically to ensure that the detrimental impact of inevitable mutations is minimized. While self-repression of the regulator curbs the spread of these loss-of-function mutations, self-activation instead facilitates their propagation. By analyzing the transcription network of multiple model organisms, we reveal that reduced bioenergetic cost may contribute to the preferential selection of autoregulation among transcription factors. Our results not only uncover how seemingly equivalent regulatory motifs have fundamentally different impact on population structure, growth dynamics, and evolutionary outcomes, but they can also be leveraged to promote the design of evolutionarily robust synthetic gene circuits.
Global distribution and dynamics of muddy coasts
Authors: Hulskamp Romy , Luijendijk Arjen , van Maren Bas , Moreno-Rodenas Antonio , Calkoen Floris , Kras Etiënne , Lhermitte Stef , Aarninkhof Stefan 
Published: December 2023

AbstractMuddy coasts provide ecological habitats, supply food and form a natural coastal defence. Relative sea level rise, changing wave energy and human interventions will increase the pressure on muddy coastal zones. For sustainable coastal management it is key to obtain information on the geomorphology of and historical changes along muddy areas. So far, little is known about the distribution and behaviour of muddy coasts at a global scale. In this study we present a global scale assessment of the occurrence of muddy coasts and rates of coastline change therein. We combine publicly available satellite imagery and coastal geospatial datasets, to train an automated classification method to identify muddy coasts. We find that 14% of the world’s ice-free coastline is muddy, of which 60% is located in the tropics. Furthermore, the majority of the world’s muddy coasts are eroding at rates exceeding 1 m/yr over the last three decades.
Crystal-facet-dependent surface transformation dictates the oxygen evolution reaction activity in lanthanum nickelate
Authors: Füngerlings Achim , Wohlgemuth Marcus , Antipin Denis , van der Minne Emma , Kiens Ellen Marijn , Villalobos Javier , Risch Marcel , Gunkel Felix , Pentcheva Rossitza , Baeumer Christoph 
Published: December 2023

AbstractElectrocatalysts are the cornerstone in the transition to sustainable energy technologies and chemical processes. Surface transformations under operation conditions dictate the activity and stability. However, the dependence of the surface structure and transformation on the exposed crystallographic facet remains elusive, impeding rational catalyst design. We investigate the (001), (110) and (111) facets of a LaNiO3−δ electrocatalyst for water oxidation using electrochemical measurements, X-ray spectroscopy, and density functional theory calculations with a Hubbard U term. We reveal that the (111) overpotential is ≈ 30−60 mV lower than for the other facets. While a surface transformation into oxyhydroxide-like NiOO(H) may occur for all three orientations, it is more pronounced for (111). A structural mismatch of the transformed layer with the underlying perovskite for (001) and (110) influences the ratio of Ni2+ and Ni3+ to Ni4+ sites during the reaction and thereby the binding energy of reaction intermediates, resulting in the distinct catalytic activities of the transformed facets.
GNTD: reconstructing spatial transcriptomes with graph-guided neural tensor decomposition informed by spatial and functional relations
Authors: Song Tianci , Broadbent Charles , Kuang Rui 
Published: December 2023

AbstractSpatially-resolved RNA profiling has now been widely used to understand cells’ structural organizations and functional roles in tissues, yet it is challenging to reconstruct the whole spatial transcriptomes due to various inherent technical limitations in tissue section preparation and RNA capture and fixation in the application of the spatial RNA profiling technologies. Here, we introduce a graph-guided neural tensor decomposition (GNTD) model for reconstructing whole spatial transcriptomes in tissues. GNTD employs a hierarchical tensor structure and formulation to explicitly model the high-order spatial gene expression data with a hierarchical nonlinear decomposition in a three-layer neural network, enhanced by spatial relations among the capture spots and gene functional relations for accurate reconstruction from highly sparse spatial profiling data. Extensive experiments on 22 Visium spatial transcriptomics datasets and 3 high-resolution Stereo-seq datasets as well as simulation data demonstrate that GNTD consistently improves the imputation accuracy in cross-validations driven by nonlinear tensor decomposition and incorporation of spatial and functional information, and confirm that the imputed spatial transcriptomes provide a more complete gene expression landscape for downstream analyses of cell/spot clustering for tissue segmentation, and spatial gene expression clustering and visualizations.
Topological structures and syntenic conservation in sea anemone genomes
Authors: Zimmermann Bob , Montenegro Juan D. , Robb Sofia M. C. , Fropf Whitney J. , Weilguny Lukas , He Shuonan , Chen Shiyuan , Lovegrove-Walsh Jessica , Hill Eric M. , Chen Cheng-Yi , Ragkousi Katerina , Praher Daniela , Fredman David , Schultz Darrin , Moran Yehu , Simakov Oleg , Genikhovich Grigory , Gibson Matthew C. , Technau Ulrich 
Published: December 2023

AbstractThere is currently little information about the evolution of gene clusters, genome architectures and karyotypes in early branching animals. Slowly evolving anthozoan cnidarians can be particularly informative about the evolution of these genome features. Here we report chromosome-level genome assemblies of two related anthozoans, the sea anemones Nematostella vectensis and Scolanthus callimorphus. We find a robust set of 15 chromosomes with a clear one-to-one correspondence between the two species. Both genomes show chromosomal conservation, allowing us to reconstruct ancestral cnidarian and metazoan chromosomal blocks, consisting of at least 19 and 16 ancestral linkage groups, respectively. We show that, in contrast to Bilateria, the Hox and NK clusters of investigated cnidarians are largely disintegrated, despite the presence of staggered hox/gbx expression in Nematostella. This loss of microsynteny conservation may be facilitated by shorter distances between cis-regulatory sequences and their cognate transcriptional start sites. We find no clear evidence for topologically associated domains, suggesting fundamental differences in long-range gene regulation compared to vertebrates. These data suggest that large sets of ancestral metazoan genes have been retained in ancestral linkage groups of some extant lineages; yet, higher order gene regulation with associated 3D architecture may have evolved only after the cnidarian-bilaterian split.
Hyperbolic exciton polaritons in a van der Waals magnet
Authors: Ruta Francesco L. , Zhang Shuai , Shao Yinming , Moore Samuel L. , Acharya Swagata , Sun Zhiyuan , Qiu Siyuan , Geurs Johannes , Kim Brian S. Y. , Fu Matthew , Chica Daniel G. , Pashov Dimitar , Xu Xiaodong , Xiao Di , Delor Milan , Zhu X-Y. , Millis Andrew J. , Roy Xavier , Hone James C. , Dean Cory R. , Katsnelson Mikhail I. , van Schilfgaarde Mark , Basov D. N. 
Published: December 2023

AbstractExciton polaritons are quasiparticles of photons coupled strongly to bound electron-hole pairs, manifesting as an anti-crossing light dispersion near an exciton resonance. Highly anisotropic semiconductors with opposite-signed permittivities along different crystal axes are predicted to host exotic modes inside the anti-crossing called hyperbolic exciton polaritons (HEPs), which confine light subdiffractionally with enhanced density of states. Here, we show observational evidence of steady-state HEPs in the van der Waals magnet chromium sulfide bromide (CrSBr) using a cryogenic near-infrared near-field microscope. At low temperatures, in the magnetically-ordered state, anisotropic exciton resonances sharpen, driving the permittivity negative along one crystal axis and enabling HEP propagation. We characterize HEP momentum and losses in CrSBr, also demonstrating coupling to excitonic sidebands and enhancement by magnetic order: which boosts exciton spectral weight via wavefunction delocalization. Our findings open new pathways to nanoscale manipulation of excitons and light, including routes to magnetic, nonlocal, and quantum polaritonics.
Grassland intensification effects cascade to alter multifunctionality of wetlands within metaecosystems
Authors: Guo Yuxi , Boughton Elizabeth H. , Bohlman Stephanie , Bernacchi Carl , Bohlen Patrick J. , Boughton Raoul , DeLucia Evan , Fauth John E. , Gomez-Casanovas Nuria , Jenkins David G. , Lollis Gene , Miller Ryan S. , Quintana-Ascencio Pedro F. , Sonnier Grégory , Sparks Jed , Swain Hilary M. , Qiu Jiangxiao 
Published: December 2023

AbstractSustainable agricultural intensification could improve ecosystem service multifunctionality, yet empirical evidence remains tenuous, especially regarding consequences for spatially coupled ecosystems connected by flows across ecosystem boundaries (i.e., metaecosystems). Here we aim to understand the effects of land-use intensification on multiple ecosystem services of spatially connected grasslands and wetlands, where management practices were applied to grasslands but not directly imposed to wetlands. We synthesize long-term datasets encompassing 53 physical, chemical, and biological indicators, comprising >11,000 field measurements. Our results reveal that intensification promotes high-quality forage and livestock production in both grasslands and wetlands, but at the expense of water quality regulation, methane mitigation, non-native species invasion resistance, and biodiversity. Land-use intensification weakens relationships among ecosystem services. The effects on grasslands cascade to alter multifunctionality of embedded natural wetlands within the metaecosystems to a similar extent. These results highlight the importance of considering spatial flows of resources and organisms when studying land-use intensification effects on metaecosystems as well as when designing grassland and wetland management practices to improve landscape multifunctionality.
Sex-dimorphic neuroprotective effect of CD163 in an α-synuclein mouse model of Parkinson’s disease
Authors: Ferreira Sara A. , Li Conghui , Klæstrup Ida H. , Vitic Zagorka , Rasmussen Rikke K. , Kirkegaard Asger , Toft Gitte U. , Betzer Cristine , Svendsen Pia , Jensen Poul H. , Luo Yonglun , Etzerodt Anders , Moestrup Søren K. , Romero-Ramos Marina 
Published: December 2023

AbstractAlpha-synuclein (α-syn) aggregation and immune activation represent hallmark pathological events in Parkinson’s disease (PD). The PD-associated immune response encompasses both brain and peripheral immune cells, although little is known about the immune proteins relevant for such a response. We propose that the upregulation of CD163 observed in blood monocytes and in the responsive microglia in PD patients is a protective mechanism in the disease. To investigate this, we used the PD model based on intrastriatal injections of murine α-syn pre-formed fibrils in CD163 knockout (KO) mice and wild-type littermates. CD163KO females revealed an impaired and differential early immune response to α-syn pathology as revealed by immunohistochemical and transcriptomic analysis. After 6 months, CD163KO females showed an exacerbated immune response and α-syn pathology, which ultimately led to dopaminergic neurodegeneration of greater magnitude. These findings support a sex-dimorphic neuroprotective role for CD163 during α-syn-induced neurodegeneration.
In vitro production of cat-restricted Toxoplasma pre-sexual stages
Authors: Antunes Ana Vera , Shahinas Martina , Swale Christopher , Farhat Dayana C. , Ramakrishnan Chandra , Bruley Christophe , Cannella Dominique , Robert Marie G. , Corrao Charlotte , Couté Yohann , Hehl Adrian B. , Bougdour Alexandre , Coppens Isabelle , Hakimi Mohamed-Ali 
Published: December 2023

AbstractSexual reproduction of Toxoplasma gondii, confined to the felid gut, remains largely uncharted owing to ethical concerns regarding the use of cats as model organisms. Chromatin modifiers dictate the developmental fate of the parasite during its multistage life cycle, but their targeting to stage-specific cistromes is poorly described1,2. Here we found that the transcription factors AP2XII-1 and AP2XI-2 operate during the tachyzoite stage, a hallmark of acute toxoplasmosis, to silence genes necessary for merozoites, a developmental stage critical for subsequent sexual commitment and transmission to the next host, including humans. Their conditional and simultaneous depletion leads to a marked change in the transcriptional program, promoting a full transition from tachyzoites to merozoites. These in vitro-cultured pre-gametes have unique protein markers and undergo typical asexual endopolygenic division cycles. In tachyzoites, AP2XII-1 and AP2XI-2 bind DNA as heterodimers at merozoite promoters and recruit MORC and HDAC3 (ref. 1), thereby limiting chromatin accessibility and transcription. Consequently, the commitment to merogony stems from a profound epigenetic rewiring orchestrated by AP2XII-1 and AP2XI-2. Successful production of merozoites in vitro paves the way for future studies on Toxoplasma sexual development without the need for cat infections and holds promise for the development of therapies to prevent parasite transmission.