bluuebunny/crossref_metadata_2025_split huggingface dataset:
Single‐Hemisphere Oxygen Outflow From Earth's Subauroral Zone
Authors: Liu Z.‐Y. , Zong Q.‐G. , Zhou X.‐Z. , Fu S.‐Y. , Hu Z.‐J. , Liu J.‐J. , Yue C. 
Published: July 2024

AbstractBesides the cusp, polar cap, and auroral oval, the nightside subauroral zone has also recently been reported as a source region of the ionospheric oxygen outflows. However, the detailed mass and energy sources of these ions remain open questions. Here, we address this issue from the perspective of the response of conjugate hemispheres. Investigation of Van Allen Probes data demonstrates a notable preference of oxygen outflows from the nightside subauroral zone from the sunlit hemisphere. This characteristic eliminates the possibility of nightside auroral precipitation playing a significant role, as it is more prominent in darkness. Instead, it highlights sunlight‐induced ionization as the mass source and enhanced plasma waves from the magnetotail as the energy source. The results presented here further support the nightside subauroral zone as an independent source of magnetospheric oxygen ions.
Patient adherence in orthodontics: a scoping review
Authors: van der Bie Ronald Max , Bos Annemieke , Bruers Jan Joseph Mathieu , Jonkman Ronald Edwin Gaston 
Published: July 2024

ABSTRACT
Background
Patient adherence is a key factor in achieving orthodontic treatment success. Despite an evolution in orthodontic healthcare, no recent comprehensive reviews are available on patient adherence in orthodontics. This scoping review provides an evidence-based overview of the literature available on multiple aspects of patient adherence in orthodontics, during both active treatment as well as during the retention phase. Knowledge gaps identified in the literature are listed.

Methods
The protocol for this scoping review was registered in the Open Science Framework (https://doi.org/10.17605/OSF.IO/EC6QD). Electronic databases and reference lists of relevant studies were searched up to 9 February 2023. The inclusion criteria were studies investigating any form of patient adherence in orthodontics published in English from 2006 onwards. The exclusion criteria were studies investigating adherence in the following patients: those with an intellectual or physical disability that could affect their ability to coincide with their therapist’s recommendations and advice, those with oral cleft and craniofacial conditions, and those treated solely for obstructive sleep apnoea. Non-peer-reviewed studies and case reports were also excluded.

Results
A total of 3284 articles were identified, 60 of which met the criteria for final inclusion.

Conclusions
There is no conclusive evidence on which factors have a significant impact on patient adherence and how patient adherence can be promoted. The degree of patient adherence is generally not compared to achieved treatment results or stability of treatment results, making it difficult to provide clear statements about the impact of the degree of adherence on desired treatment results or orthodontic stability.
Mitophagy-related regulated cell death: molecular mechanisms and disease implications
Authors: Yang Molin , Wei Xiang , Yi Xin , Jiang Ding-Sheng 
Published: July 2024

AbstractDuring oxidative phosphorylation, mitochondria continuously produce reactive oxygen species (ROS), and untimely ROS clearance can subject mitochondria to oxidative stress, ultimately resulting in mitochondrial damage. Mitophagy is essential for maintaining cellular mitochondrial quality control and homeostasis, with activation involving both ubiquitin-dependent and ubiquitin-independent pathways. Over the past decade, numerous studies have indicated that different forms of regulated cell death (RCD) are connected with mitophagy. These diverse forms of RCD have been shown to be regulated by mitophagy and are implicated in the pathogenesis of a variety of diseases, such as tumors, degenerative diseases, and ischemia‒reperfusion injury (IRI). Importantly, targeting mitophagy to regulate RCD has shown excellent therapeutic potential in preclinical trials, and is expected to be an effective strategy for the treatment of related diseases. Here, we present a summary of the role of mitophagy in different forms of RCD, with a focus on potential molecular mechanisms by which mitophagy regulates RCD. We also discuss the implications of mitophagy-related RCD in the context of various diseases.
Introducing carbon assimilation in yeasts using photosynthetic directed endosymbiosis
Authors: Gao Yang-le , Cournoyer Jay , De Bidhan C. , Wallace Catherine L. , Ulanov Alexander V. , La Frano Michael R. , Mehta Angad P. 
Published: July 2024

Abstract
Conversion of heterotrophic organisms into partially or completely autotrophic organisms is primarily accomplished by extensive metabolic engineering and laboratory evolution efforts that channel CO2 into central carbon metabolism. Here, we develop a directed endosymbiosis approach to introduce carbon assimilation in budding yeasts. Particularly, we engineer carbon assimilating and sugar-secreting photosynthetic cyanobacterial endosymbionts within the yeast cells, which results in the generation of yeast/cyanobacteria chimeras that propagate under photosynthetic conditions in the presence of CO2 and in the absence of feedstock carbon sources like glucose or glycerol. We demonstrate that the yeast/cyanobacteria chimera can be engineered to biosynthesize natural products under the photosynthetic conditions. Additionally, we expand our directed endosymbiosis approach to standard laboratory strains of yeasts, which transforms them into photosynthetic yeast/cyanobacteria chimeras. We anticipate that our studies will have significant implications for sustainable biotechnology, synthetic biology, and experimentally studying the evolutionary adaptation of an additional organelle in yeast.
A multiomic atlas of the aging hippocampus reveals molecular changes in response to environmental enrichment
Authors: Pérez Raúl F. , Tezanos Patricia , Peñarroya Alfonso , González-Ramón Alejandro , Urdinguio Rocío G. , Gancedo-Verdejo Javier , Tejedor Juan Ramón , Santamarina-Ojeda Pablo , Alba-Linares Juan José , Sainz-Ledo Lidia , Roberti Annalisa , López Virginia , Mangas Cristina , Moro María , Cintado Reyes Elisa , Muela Martínez Pablo , Rodríguez-Santamaría Mar , Ortea Ignacio , Iglesias-Rey Ramón , Castilla-Silgado Juan , Tomás-Zapico Cristina , Iglesias-Gutiérrez Eduardo , Fernández-García Benjamín , Sanchez-Mut Jose Vicente , Trejo José Luis , Fernández Agustín F. , Fraga Mario F. 
Published: July 2024

AbstractAging involves the deterioration of organismal function, leading to the emergence of multiple pathologies. Environmental stimuli, including lifestyle, can influence the trajectory of this process and may be used as tools in the pursuit of healthy aging. To evaluate the role of epigenetic mechanisms in this context, we have generated bulk tissue and single cell multi-omic maps of the male mouse dorsal hippocampus in young and old animals exposed to environmental stimulation in the form of enriched environments. We present a molecular atlas of the aging process, highlighting two distinct axes, related to inflammation and to the dysregulation of mRNA metabolism, at the functional RNA and protein level. Additionally, we report the alteration of heterochromatin domains, including the loss of bivalent chromatin and the uncovering of a heterochromatin-switch phenomenon whereby constitutive heterochromatin loss is partially mitigated through gains in facultative heterochromatin. Notably, we observed the multi-omic reversal of a great number of aging-associated alterations in the context of environmental enrichment, which was particularly linked to glial and oligodendrocyte pathways. In conclusion, our work describes the epigenomic landscape of environmental stimulation in the context of aging and reveals how lifestyle intervention can lead to the multi-layered reversal of aging-associated decline.
Hippocampal connectivity patterns echo macroscale cortical evolution in the primate brain
Authors: Eichert Nicole , DeKraker Jordan , Howard Amy F. D. , Huszar Istvan N. , Zhu Silei , Sallet Jérôme , Miller Karla L. , Mars Rogier B. , Jbabdi Saad , Bernhardt Boris C. 
Published: July 2024

AbstractWhile the hippocampus is key for human cognitive abilities, it is also a phylogenetically old cortex and paradoxically considered evolutionarily preserved. Here, we introduce a comparative framework to quantify preservation and reconfiguration of hippocampal organisation in primate evolution, by analysing the hippocampus as an unfolded cortical surface that is geometrically matched across species. Our findings revealed an overall conservation of hippocampal macro- and micro-structure, which shows anterior-posterior and, perpendicularly, subfield-related organisational axes in both humans and macaques. However, while functional organisation in both species followed an anterior-posterior axis, we observed a marked reconfiguration in the latter across species, which mirrors a rudimentary integration of the default-mode-network in non-human primates. Here we show that microstructurally preserved regions like the hippocampus may still undergo functional reconfiguration in primate evolution, due to their embedding within heteromodal association networks.
Surface properties of the seas of Titan as revealed by Cassini mission bistatic radar experiments
Authors: Poggiali Valerio , Brighi Giancorrado , Hayes Alexander G. , Nicholson Phil D. , MacKenzie Shannon , Lalich Daniel E. , Bonnefoy Léa E. , Oudrhiri Kamal , Lorenz Ralph D. , Soderblom Jason M. , Tortora Paolo , Zannoni Marco 
Published: July 2024

AbstractSaturn’s moon Titan was explored by the Cassini spacecraft from 2004 to 2017. While Cassini revealed a lot about this Earth-like world, its radar observations could only provide limited information about Titan’s liquid hydrocarbons seas Kraken, Ligeia and Punga Mare. Here, we show the results of the analysis of the Cassini mission bistatic radar experiments data of Titan’s polar seas. The dual-polarized nature of bistatic radar observations allow independent estimates of effective relative dielectric constant and small-scale roughness of sea surface, which were not possible via monostatic radar data. We find statistically significant variations in effective dielectric constant (i.e., liquid composition), consistent with a latitudinal dependence in the methane-ethane mixing-ratio. The results on estuaries suggest lower values than the open seas, compatible with methane-rich rivers entering seas with higher ethane content. We estimate small-scale roughness of a few millimeters from the almost purely coherent scattering from the sea surface, hinting at the presence of capillary waves. This roughness is concentrated near estuaries and inter-basin straits, perhaps indicating active tidal currents.
Multi-omics analysis of green lineage osmotic stress pathways unveils crucial roles of different cellular compartments
Authors: Vilarrasa-Blasi Josep , Vellosillo Tamara , Jinkerson Robert E. , Fauser Friedrich , Xiang Tingting , Minkoff Benjamin B. , Wang Lianyong , Kniazev Kiril , Guzman Michael , Osaki Jacqueline , Barrett-Wilt Gregory A. , Sussman Michael R. , Jonikas Martin C. , Dinneny José R. 
Published: July 2024

AbstractMaintenance of water homeostasis is a fundamental cellular process required by all living organisms. Here, we use the single-celled green alga Chlamydomonas reinhardtii to establish a foundational understanding of osmotic-stress signaling pathways through transcriptomics, phosphoproteomics, and functional genomics approaches. Comparison of pathways identified through these analyses with yeast and Arabidopsis allows us to infer their evolutionary conservation and divergence across these lineages. 76 genes, acting across diverse cellular compartments, were found to be important for osmotic-stress tolerance in Chlamydomonas through their functions in cytoskeletal organization, potassium transport, vesicle trafficking, mitogen-activated protein kinase and chloroplast signaling. We show that homologs for five of these genes have conserved functions in stress tolerance in Arabidopsis and reveal a novel PROFILIN-dependent stage of acclimation affecting the actin cytoskeleton that ensures tissue integrity upon osmotic stress. This study highlights the conservation of the stress response in algae and land plants, and establishes Chlamydomonas as a unicellular plant model system to dissect the osmotic stress signaling pathway.
OmicVerse: a framework for bridging and deepening insights across bulk and single-cell sequencing
Authors: Zeng Zehua , Ma Yuqing , Hu Lei , Tan Bowen , Liu Peng , Wang Yixuan , Xing Cencan , Xiong Yuanyan , Du Hongwu 
Published: July 2024

AbstractSingle-cell sequencing is frequently affected by “omission” due to limitations in sequencing throughput, yet bulk RNA-seq may contain these ostensibly “omitted” cells. Here, we introduce the single cell trajectory blending from Bulk RNA-seq (BulkTrajBlend) algorithm, a component of the OmicVerse suite that leverages a Beta-Variational AutoEncoder for data deconvolution and graph neural networks for the discovery of overlapping communities. This approach effectively interpolates and restores the continuity of “omitted” cells within single-cell RNA sequencing datasets. Furthermore, OmicVerse provides an extensive toolkit for both bulk and single cell RNA-seq analysis, offering seamless access to diverse methodologies, streamlining computational processes, fostering exquisite data visualization, and facilitating the extraction of significant biological insights to advance scientific research.
Closing Kok’s cycle of nature’s water oxidation catalysis
Authors: Guo Yu , He Lanlan , Ding Yunxuan , Kloo Lars , Pantazis Dimitrios A. , Messinger Johannes , Sun Licheng 
Published: July 2024

AbstractThe Mn4CaO5(6) cluster in photosystem II catalyzes water splitting through the Si state cycle (i = 0–4). Molecular O2 is formed and the natural catalyst is reset during the final S3 → (S4) → S0 transition. Only recently experimental breakthroughs have emerged for this transition but without explicit information on the S0-state reconstitution, thus the progression after O2 release remains elusive. In this report, our molecular dynamics simulations combined with density functional calculations suggest a likely missing link for closing the cycle, i.e., restoring the first catalytic state. Specifically, the formation of closed-cubane intermediates with all hexa-coordinate Mn is observed, which would undergo proton release, water dissociation, and ligand transfer to produce the open-cubane structure of the S0 state. Thereby, we theoretically identify the previously unknown structural isomerism in the S0 state that acts as the origin of the proposed structural flexibility prevailing in the cycle, which may be functionally important for nature’s water oxidation catalysis.
Unidirectional guided-wave-driven metasurfaces for arbitrary wavefront control
Authors: Li Shiqing , Tsakmakidis Kosmas L. , Jiang Tao , Shen Qian , Zhang Hang , Yan Jinhua , Sun Shulin , Shen Linfang 
Published: July 2024

AbstractMetasurfaces are capable of fully reshaping the wavefronts of incident beams in desired manners. However, the requirement for external light excitation and the resonant nature of their meta-atoms, make challenging their on-chip integration. Here, we introduce the concept and design of a fresh class of metasurfaces, driven by unidirectional guided waves, capable of arbitrary wavefront control based on the unique dispersion properties of unidirectional guided waves rather than resonant meta-atoms. Upon experimentally demonstrating the feasibility of our designs in the microwave regime, we numerically validate the introduced principle through the design of several microwave meta-devices using metal-air-gyromagnetic unidirectional surface magneto-plasmons, agilely converting unidirectional guided modes into the wavefronts of 3D Bessel beams, focused waves, and controllable vortex beams. We, further, numerically demonstrate sub-diffraction focusing, which is beyond the capability of conventional metasurfaces. Our unfamiliar yet practical designs may enable full, broadband manipulation of electromagnetic waves on deep subwavelength scales.
Membrane protein MHZ3 regulates the on-off switch of ethylene signaling in rice
Authors: Li Xin-Kai , Huang Yi-Hua , Zhao Rui , Cao Wu-Qiang , Lu Long , Han Jia-Qi , Zhou Yang , Zhang Xun , Wu Wen-Ai , Tao Jian-Jun , Wei Wei , Zhang Wan-Ke , Chen Shou-Yi , Ma Biao , Zhao He , Yin Cui-Cui , Zhang Jin-Song 
Published: July 2024

AbstractEthylene regulates plant growth, development, and stress adaptation. However, the early signaling events following ethylene perception, particularly in the regulation of ethylene receptor/CTRs (CONSTITUTIVE TRIPLE RESPONSE) complex, remains less understood. Here, utilizing the rapid phospho-shift of rice OsCTR2 in response to ethylene as a sensitive readout for signal activation, we revealed that MHZ3, previously identified as a stabilizer of ETHYLENE INSENSITIVE 2 (OsEIN2), is crucial for maintaining OsCTR2 phosphorylation. Genetically, both functional MHZ3 and ethylene receptors prove essential for OsCTR2 phosphorylation. MHZ3 physically interacts with both subfamily I and II ethylene receptors, e.g., OsERS2 and OsETR2 respectively, stabilizing their association with OsCTR2 and thereby maintaining OsCTR2 activity. Ethylene treatment disrupts the interactions within the protein complex MHZ3/receptors/OsCTR2, reducing OsCTR2 phosphorylation and initiating downstream signaling. Our study unveils the dual role of MHZ3 in fine-tuning ethylene signaling activation, providing insights into the initial stages of the ethylene signaling cascade.
Phase interface engineering enables state-of-the-art half-Heusler thermoelectrics
Authors: Zhang Yihua , Peng Guyang , Li Shuankui , Wu Haijun , Chen Kaidong , Wang Jiandong , Zhao Zhihao , Lyu Tu , Yu Yuan , Zhang Chaohua , Zhang Yang , Ma Chuansheng , Guo Shengwu , Ding Xiangdong , Sun Jun , Liu Fusheng , Hu Lipeng 
Published: July 2024

AbstractIn thermoelectric, phase interface engineering proves effective in reducing the lattice thermal conductivity via interface scattering and amplifying the density-of-states effective mass by energy filtering. However, the indiscriminate introduction of phase interfaces inevitably leads to diminished carrier mobility. Moreover, relying on a singular energy barrier is insufficient for comprehensive filtration of low-energy carriers throughout the entire temperature range. Addressing these challenges, we advocate the establishment of a composite phase interface using atomic layer deposition (ALD) technology. This design aims to effectively decouple the interrelated thermoelectric parameters in ZrNiSn. The engineered coherent dual-interface energy barriers substantially enhance the density-of-states effective mass across the entire temperature spectrum while preser carrier mobility. Simultaneously, the strong interface scattering on phonons is crucial for curtailing lattice thermal conductivity. Consequently, a 40-cycles TiO2 coating on ZrNi1.03Sn0.99Sb0.01 achieves an unprecedented zT value of 1.3 at 873 K. These findings deepen the understanding of coherent composite-phase interface engineering.
Molecularly specific detection towards trace nitrogen dioxide by utilizing Schottky-junction-based Gas Sensor
Authors: Xu Shipu , Zhou Xuehan , Xu Shidang , Zhang Yan , Shi Yiwen , Cong Xuzhong , Xu Qijia , Tian Ye , Jiang Ying , Guo Hanjie , Zhao Jinkui , Sun Fengqiang , Peng Hailin 
Published: July 2024

AbstractTrace NO2 detection is essential for the production and life, where the sensing strategy is appropriate for rapid detection but lacks molecular specificity. This investigation proposes a sensing mechanism dominated by surface-scattering to achieve the molecularly-specific detection. Two-dimensional Bi2O2Se is firstly fabricated into a Schottky-junction-based gas-sensor. Applied with an alternating excitation, the sensor simultaneously outputs multiple response signals (i.e., resistance, reactance, and the impedance angle). Their response times are shorter than 200 s at room temperature. In NO2 sensing, these responses present the detection limit in ppt range and the sensitivity is up to 16.8 %·ppb−1. This NO2 sensitivity presents orders of magnitude higher than those of the common gases within the exhaled breath. The impedance angle is involved in the principle component analysis together with the other two sensing signals. Twelve kinds of typical gases containing NO2 are acquired with molecular characteristics. The change in dipole moment of the target molecule adsorbed is demonstrated to correlate with the impedance angle via surface scattering. The proposed mechanism is confirmed to output ultra-sensitive sensing responses with the molecular characteristic.
First-principles predictions of HfO2-based ferroelectric superlattices
Authors: Mukherjee Binayak , Fedorova Natalya S. , Íñiguez-González Jorge 
Published: July 2024

AbstractThe metastable nature of the ferroelectric phase of HfO2 is a significant impediment to its industrial application as a functional ferroelectric material. In fact, no polar phases exist in the bulk phase diagram of HfO2, which shows a dominant non-polar monoclinic ground state. As a consequence, ferroelectric orthorhombic HfO2 is stabilized either kinetically or via epitaxial strain. Here, we propose an alternative approach, demonstrating the feasibility of thermodynamically stabilizing polar HfO2 in superlattices with other simple oxides. Using the composition and stacking direction of the superlattice as design parameters, we obtain heterostructures that can be fully polar, fully antipolar or mixed, with improved thermodynamic stability compared to the orthorhombic polar HfO2 in bulk form. Our results suggest that combining HfO2 with an oxide that does not have a monoclinic ground state generally drives the superlattice away from this non-polar phase, favoring the stability of the ferroelectric structures that minimize the elastic and electrostatic penalties. As such, these diverse and tunable superlattices hold promise for various applications in thin-film ferroelectric devices
A neural modeling approach to study mechanisms underlying the heterogeneity of visual spatial frequency sensitivity in schizophrenia
Authors: Dugan Caroline , Zikopoulos Basilis , Yazdanbakhsh Arash 
Published: July 2024

AbstractPatients with schizophrenia exhibit abnormalities in spatial frequency sensitivity, and it is believed that these abnormalities indicate more widespread dysfunction and dysregulation of bottom-up processing. The early visual system, including the first-order Lateral Geniculate Nucleus of the thalamus (LGN) and the primary visual cortex (V1), are key contributors to spatial frequency sensitivity. Medicated and unmedicated patients with schizophrenia exhibit contrasting changes in spatial frequency sensitivity, thus making it a useful probe for examining potential effects of the disorder and antipsychotic medications in neural processing. We constructed a parameterized, rate-based neural model of on-center/off-surround neurons in the early visual system to investigate the impacts of changes to the excitatory and inhibitory receptive field subfields. By incorporating changes in both the excitatory and inhibitory subfields that are associated with pathophysiological findings in schizophrenia, the model successfully replicated perceptual data from behavioral/functional studies involving medicated and unmedicated patients. Among several plausible mechanisms, our results highlight the dampening of excitation and/or increase in the spread and strength of the inhibitory subfield in medicated patients and the contrasting decreased spread and strength of inhibition in unmedicated patients. Given that the model was successful at replicating results from perceptual data under a variety of conditions, these elements of the receptive field may be useful markers for the imbalances seen in patients with schizophrenia.