bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep‐Marine Brine Seeps Stimulate Microbial Nitrogen Cycling: Implications for the Formation of Sediment‐Hosted Ore Deposits
Authors: Stüeken Eva E. , Long Annabel , Rochelle‐Bates Nathan , Teske Andreas 
Published: July 2024

AbstractDeep‐marine brine seeps in the modern ocean are considered analogs for settings that favored the formation of sedimentary‐exhalative zinc and lead deposits in deep time. Microbial activity plays an important role in the accumulation of ore minerals, meaning that the extent of mineralization is at least indirectly dependent on nutrient fluxes. Here, we investigated the biogeochemical nitrogen cycle in shallow (15–50 cm) sediment cores from the Orca Basin brine pool and surrounding sites, as well as from an active brine seep area near Dead Crab Lake in the Gulf of Mexico, with the aim of constraining the effect of brine seepage on this bio‐essential element. We find high porewater ammonium concentrations in the millimolar range, paired with elevated ratios of organic carbon to nitrogen in sediments, which confirm previous hypotheses that the brine recycles ammonium from sedimentary strata back into the water column. Within Orca Basin, we note tentative evidence of microbial ammonium utilization. At the active seep, ammonium is mixed into the overlying water column and likely undergoes oxidation. Isotopic data from sediments and dissolved ammonium, paired with previously published genomic data, suggest the presence of dissimilatory nitrate reduction to ammonium at the brine‐seawater interface. We conclude that brine seeps can stimulate biological nitrogen metabolisms in multiple ways. Our results may help calibrate studies of biogeochemical cycles around brine seeps that are archived in the rock record.
Replica symmetry breaking in 1D Rayleigh scattering system: theory and validations
Authors: Qi Yifei , Ni Longqun , Ye Zhenyu , Zhang Jiaojiao , Bao Xingyu , Wang Pan , Rao Yunjiang , Raposo Ernesto P. , Gomes Anderson S. L. , Wang Zinan 
Published: July 2024

AbstractSpin glass theory, as a paradigm for describing disordered magnetic systems, constitutes a prominent subject of study within statistical physics. Replica symmetry breaking (RSB), as one of the pivotal concepts for the understanding of spin glass theory, means that under identical conditions, disordered systems can yield distinct states with nontrivial correlations. Random fiber laser (RFL) based on Rayleigh scattering (RS) is a complex disordered system, owing to the disorder and stochasticity of RS. In this work, for the first time, a precise theoretical model is elaborated for studying the photonic phase transition via the platform of RS-based RFL, in which we clearly reveal that, apart from the pump power, the photon phase variation in RFL is also an analogy to the temperature term in spin-glass phase transition, leading to a novel insight into the intrinsic mechanisms of photonic phase transition. In addition, based on this model and real-time high-fidelity detection spectral evolution, we theoretically predict and experimentally observe the mode-asymmetric characteristics of photonic phase transition in RS-based RFL. This finding contributes to a deeper understanding of the photonic RSB regime and the dynamics of RS-based RFL.
Anisotropy-free arrayed waveguide gratings on X-cut thin film lithium niobate platform of in-plane anisotropy
Authors: Yi Junjie , Guo Changjian , Ruan Ziliang , Chen Gengxin , Wei Haiqiang , Lu Liwang , Gong Shengqi , Pan Xiaofu , Shen Xiaowan , Guan Xiaowei , Dai Daoxin , Zhong Kangping , Liu Liu 
Published: July 2024

AbstractArrayed waveguide grating is a versatile and scalable integrated light dispersion device, which has been widely adopted in various applications, including, optical communications and optical sensing. Recently, thin-film lithium niobate emerges as a promising photonic integration platform, due to its ability of shrinking largely the size of typical lithium niobate based optical devices. This would also enable multifunctional photonic integrated chips on a single lithium niobate substrate. However, due to the intrinsic anisotropy of the material, to build an arrayed waveguide grating on X-cut thin-film lithium niobate has never been successful. Here, a universal strategy to design anisotropy-free dispersive components on a uniaxial in-plane anisotropic photonic integration platform is introduced for the first time. This leads to the first implementation of arrayed waveguide gratings on X-cut thin-film lithium niobate with various configurations and high-performances. The best insertion loss of 2.4 dB and crosstalk of −24.1 dB is obtained for the fabricated arrayed waveguide grating devices. Applications of such arrayed waveguide gratings as a wavelength router and in a wavelength-division multiplexed optical transmission system are also demonstrated.
3D printed energy devices: generation, conversion, and storage
Authors: Son Jin-ho , Kim Hongseok , Choi Yoonseob , Lee Howon 
Published: July 2024

AbstractThe energy devices for generation, conversion, and storage of electricity are widely used across diverse aspects of human life and various industry. Three-dimensional (3D) printing has emerged as a promising technology for the fabrication of energy devices due to its unique capability of manufacturing complex shapes across different length scales. 3D-printed energy devices can have intricate 3D structures for significant performance enhancement, which are otherwise impossible to achieve through conventional manufacturing methods. Furthermore, recent progress has witnessed that 3D-printed energy devices with micro-lattice structures surpass their bulk counterparts in terms of mechanical properties as well as electrical performances. While existing literature focuses mostly on specific aspects of individual printed energy devices, a brief overview collectively covering the wide landscape of energy applications is lacking. This review provides a concise summary of recent advancements of 3D-printed energy devices. We classify these devices into three functional categories; generation, conversion, and storage of energy, offering insight on the recent progress within each category. Furthermore, current challenges and future prospects associated with 3D-printed energy devices are discussed, emphasizing their potential to advance sustainable energy solutions.
Distinct synaptic mechanisms drive the behavioral response to acute stress and rapid correction by ketamine
Authors: Kim Ji-Woon , Kleinfelter Benjamin , Kavalali Ege T. , Monteggia Lisa M. 
Published: July 2024

AbstractPrevailing hypotheses on the mechanisms of antidepressant action posit that antidepressants directly counteract deficiencies in major neurotransmitter signaling systems that underlie depression. The rapidly acting antidepressant ketamine has been postulated to correct excess glutamatergic signaling via glutamatergic antagonism leading to the rescue of neuronal structural deficits and reversal of behavioral symptoms. We studied this premise using systemic administration of the acetylcholinesterase inhibitor physostigmine, which has been shown to rapidly elicit a shorter-term period of depressed mood in humans via cholinergic mechanisms. We observed that physostigmine induces acute stress in tandem with long term depression of glutamate release in the hippocampus of mice. However, ketamine rapidly acts to re-establish glutamatergic synaptic efficacy via postsynaptic signaling and behaviorally masks the reduction in passive coping induced by physostigmine. These results underscore the divergence of synaptic signaling mechanisms underlying mood changes and antidepressant action and highlight how distinct synaptic mechanisms may underlie neuropsychiatric disorders versus their treatment.
Cell signaling and transcriptional regulation of osteoblast lineage commitment, differentiation, bone formation, and homeostasis
Authors: Zhu Siyu , Chen Wei , Masson Alasdair , Li Yi-Ping 
Published: July 2024

AbstractThe initiation of osteogenesis primarily occurs as mesenchymal stem cells undergo differentiation into osteoblasts. This differentiation process plays a crucial role in bone formation and homeostasis and is regulated by two intricate processes: cell signal transduction and transcriptional gene expression. Various essential cell signaling pathways, including Wnt, BMP, TGF-β, Hedgehog, PTH, FGF, Ephrin, Notch, Hippo, and Piezo1/2, play a critical role in facilitating osteoblast differentiation, bone formation, and bone homeostasis. Key transcriptional factors in this differentiation process include Runx2, Cbfβ, Runx1, Osterix, ATF4, SATB2, and TAZ/YAP. Furthermore, a diverse array of epigenetic factors also plays critical roles in osteoblast differentiation, bone formation, and homeostasis at the transcriptional level. This review provides an overview of the latest developments and current comprehension concerning the pathways of cell signaling, regulation of hormones, and transcriptional regulation of genes involved in the commitment and differentiation of osteoblast lineage, as well as in bone formation and maintenance of homeostasis. The paper also reviews epigenetic regulation of osteoblast differentiation via mechanisms, such as histone and DNA modifications. Additionally, we summarize the latest developments in osteoblast biology spurred by recent advancements in various modern technologies and bioinformatics. By synthesizing these insights into a comprehensive understanding of osteoblast differentiation, this review provides further clarification of the mechanisms underlying osteoblast lineage commitment, differentiation, and bone formation, and highlights potential new therapeutic applications for the treatment of bone diseases.
Pig blastocyst-like structure models from embryonic stem cells
Authors: Xiang Jinzhu , Wang Hanning , Shi Bingbo , Li Jiajun , Liu Dong , Wang Kaipeng , Wang Zhuangfei , Min Qiankun , Zhao Chengchen , Pei Duanqing 
Published: July 2024

AbstractPluripotent stem cells have the potential to generate embryo models that can recapitulate developmental processes in vitro. Large animals such as pigs may also benefit from stem-cell-based embryo models for improving breeding. Here, we report the generation of blastoids from porcine embryonic stem cells (pESCs). We first develop a culture medium 4FIXY to derive pESCs. We develop a 3D two-step differentiation strategy to generate porcine blastoids from the pESCs. The resulting blastoids exhibit similar morphology, size, cell lineage composition, and single-cell transcriptome characteristics to blastocysts. These porcine blastoids survive and expand for more than two weeks in vitro under two different culture conditions. Large animal blastoids such as those derived from pESCs may enable in vitro modeling of early embryogenesis and improve livestock species’ breeding practices.
More efficient adaptation of cardiovascular response to repeated restraint in spontaneously hypertensive rats: the role of autonomic nervous system
Authors: Vavřínová Anna , Behuliak Michal , Vodička Martin , Bencze Michal , Ergang Peter , Vaněčková Ivana , Zicha Josef 
Published: July 2024

AbstractWe hypothesized that sympathetic hyperactivity and parasympathetic insuficiency in spontaneously hypertensive rats (SHR) underlie their exaggerated cardiovascular response to acute stress and impaired adaptation to repeated restraint stress exposure compared to Wistar-Kyoto rats (WKY). Cardiovascular responses to single (120 min) or repeated (daily 120 min for 1 week) restraint were measured by radiotelemetry and autonomic balance was evaluated by power spectral analysis of systolic blood pressure variability (SBPV) and heart rate variability (HRV). Baroreflex sensitivity (BRS) was measured by the pharmacological Oxford technique. Stress-induced pressor response and vascular sympathetic activity (low-frequency component of SBPV) were enhanced in SHR subjected to single restraint compared to WKY, whereas stress-induced tachycardia was similar in both strains. SHR exhibited attenuated cardiac parasympathetic activity (high-frequency component of HRV) and blunted BRS compared to WKY. Repeated restraint did not affect the stress-induced increase in blood pressure. However, cardiovascular response during the post-stress recovery period of the 7th restraint was reduced in both strains. The repeatedly restrained SHR showed lower basal heart rate during the dark (active) phase and slightly decreased basal blood pressure during the light phase compared to stress-naive SHR. SHR subjected to repeated restraint also exhibited attenuated stress-induced tachycardia, augmented cardiac parasympathetic activity, attenuated vascular sympathetic activity and improved BRS during the last seventh restraint compared to single-stressed SHR. Thus, SHR exhibited enhanced cardiovascular and sympathetic responsiveness to novel stressor exposure (single restraint) compared to WKY. Unexpectedly, the adaptation of cardiovascular and autonomic responses to repeated restraint was more effective in SHR.
Approximate encoding of quantum states using shallow circuits
Authors: Ben-Dov Matan , Shnaiderov David , Makmal Adi , Dalla Torre Emanuele G. 
Published: July 2024

AbstractQuantum algorithms and simulations often require the preparation of complex states through sequences of 2-qubit gates. For a generic quantum state, the number of required gates grows exponentially with the number of qubits, becoming unfeasible on near-term quantum devices. Here, we aim at creating an approximate encoding of the target state using a limited number of gates. As a first step, we consider a quantum state that is efficiently represented classically, such as a one-dimensional matrix product state. Using tensor network techniques, we develop and implement an efficient optimization algorithm that approaches the optimal implementation, requiring a polynomial number of iterations. We, next, consider the implementation of the proposed optimization algorithm directly on a quantum computer and overcome inherent barren plateaus by employing a local cost function. Our work offers a universal method to prepare target states using local gates and represents a significant improvement over known strategies.
Experimental error suppression in Cross-Resonance gates via multi-derivative pulse shaping
Authors: Li Boxi , Calarco Tommaso , Motzoi Felix 
Published: July 2024

AbstractWhile quantum circuits are reaching impressive widths in the hundreds of qubits, their depths have not been able to keep pace. In particular, cloud computing gates on multi-qubit, fixed-frequency superconducting chips continue to hover around the 1% error range, contrasting with the progress seen on carefully designed two-qubit chips, where error rates have been pushed towards 0.1%. Despite the strong impetus and a plethora of research, experimental demonstration of error suppression on these multi-qubit devices remains challenging, primarily due to the wide distribution of qubit parameters and the demanding calibration process required for advanced control methods. Here, we achieve this goal, using a simple control method based on multi-derivative, multi-constraint pulse shaping, which acts simultaneously against multiple error sources. Our approach establishes a two to fourfold improvement on the default calibration scheme, demonstrated on four qubits on the IBM Quantum Platform with limited and intermittent access, enabling these large-scale fixed-frequency systems to fully take advantage of their superior coherence times. The achieved CNOT fidelities of 99.7(1)% on those publically available qubits come from both coherent control error suppression and accelerated gate time.
Using static magnetic field to recover ammonia efficiently by DNRA process
Authors: Xie Yuyang , Wang Zhibin , Ni Shou-Qing 
Published: July 2024

AbstractDissimilatory nitrate reduction to ammonium (DNRA) has garnered attention due to its ability to recover ammonia and reduce greenhouse gas emissions simultaneously. In this study, the potential of using static magnetic field (SMF) to improve DNRA process was explored from the sight of molecular biology. Functional genes, microbial community structure, and metabolism pathways were discussed. SMF of 40 mT shortened the start-up time of DNRA from 75 days to 41 days, while 80 mT SMF delayed it to 103 days. On day 80, DNRA potential rate under 40 mT SMF, reached 174 ± 11 μmol kg−1 h−1, significantly surpassing 0 mT (88 ± 6 μmol kg−1 h−1) and 80 mT SMF (52 ± 4 μmol kg−1 h−1). SMF of 40 mT also accelerated community succession and the enrichment of functional bacteria like Geobacter (from 15.71% to 32.11%). qPCR results suggested that 40 mT SMF promoted the rapid enrichment of DNRA functional gene nrfA and 80 mT SMF promoted the enrichment of nirS gene on day 40. Dynamic responses of Thauera sp. RT1901, Stutzerimonas stutzeri, Shewanella oneidensis MR-1, and Shewanella loihica PV-4 to SMF at transcriptional levels confirmed SMF could improve the nitrogen removal and electron transfer of DNRA and denitrification bacteria. Consequently, this work validated the possibility of using SMF to improve DNRA process for ammonia recovery and investigated the underlying mechanisms, which could promote the application of DNRA in full-scale.
Electrically tunable giant Nernst effect in two-dimensional van der Waals heterostructures
Authors: Pasquale Gabriele , Sun Zhe , Migliato Marega Guilherme , Watanabe Kenji , Taniguchi Takashi , Kis Andras 
Published: July 2024

AbstractThe Nernst effect, a transverse thermoelectric phenomenon, has attracted significant attention for its potential in energy conversion, thermoelectrics and spintronics. However, achieving high performance and versatility at low temperatures remains elusive. Here we demonstrate a large and electrically tunable Nernst effect by combining the electrical properties of graphene with the semiconducting characteristics of indium selenide in a field-effect geometry. Our results establish a new platform for exploring and manipulating this thermoelectric effect, showcasing the first electrical tunability with an on/off ratio of 103. Moreover, photovoltage measurements reveal a stronger photo-Nernst signal in the graphene/indium selenide heterostructure compared with individual components. Remarkably, we observe a record-high Nernst coefficient of 66.4 μV K−1 T−1 at ultralow temperatures and low magnetic fields, an important step towards applications in quantum information and low-temperature emergent phenomena.
Chromosome-level genome assembly of Korean holoparasitic plants, Orobanche coerulescens
Authors: Kim Bongsang , Jhang So Yun , Koh Bomin , Kim Soonok , Chi Won-Jae , Park Jeong-Mi , Lim Chae Eun , Hong Yoonjee , Kim Heebal , Yu Jaewoong , Cho Seoae 
Published: July 2024

AbstractOrobanche coerulescens is a parasitic plant that cannot complete its life cycle without a host and is incapable of photosynthesis. The habitats of O. coerulescens span the coasts of Korea and its volcanic islands, Ulleungdo and Dokdo. Those on the volcanic islands exhibit morphological differences and have distinct hosts compared to those on the peninsula. The family of Orobanchaceae, encompassing both autotrophic and parasitic species, serves as a model for evolutionary studies of parasitic states. However, there are limited genome assemblies for the Orobanche genus. In our study, we produced approximately 100x ONT long reads to construct a chromosome-level genome of O. coerulescens. The resulting assembly has a total size of 3,648 Mb with an N50 value of 195 Mb, and 82.0% of BUSCO genes were identified as complete. Results of the repeat annotation revealed that 86.3% of the genome consisted of repeat elements, and 29,395 protein-coding genes were annotated. This chromosome-level genome will be an important biological resource for conserving biodiversity and further understanding parasitic plants.
HVSMR-2.0: A 3D cardiovascular MR dataset for whole-heart segmentation in congenital heart disease
Authors: Pace Danielle F. , Contreras Hannah T. M. , Romanowicz Jennifer , Ghelani Shruti , Rahaman Imon , Zhang Yue , Gao Patricia , Jubair Mohammad Imrul , Yeh Tom , Golland Polina , Geva Tal , Ghelani Sunil , Powell Andrew J. , Moghari Mehdi Hedjazi 
Published: July 2024

AbstractPatients with congenital heart disease often have cardiac anatomy that deviates significantly from normal, frequently requiring multiple heart surgeries. Image segmentation from a preoperative cardiovascular magnetic resonance (CMR) scan would enable creation of patient-specific 3D surface models of the heart, which have potential to improve surgical planning, enable surgical simulation, and allow automatic computation of quantitative metrics of heart function. However, there is no publicly available CMR dataset for whole-heart segmentation in patients with congenital heart disease. Here, we release the HVSMR-2.0 dataset, comprising 60 CMR scans alongside manual segmentation masks of the 4 cardiac chambers and 4 great vessels. The images showcase a wide range of heart defects and prior surgical interventions. The dataset also includes masks of required and optional extents of the great vessels, enabling fairer comparisons across algorithms. Detailed diagnoses for each subject are also provided. By releasing HVSMR-2.0, we aim to encourage development of robust segmentation algorithms and clinically relevant tools for congenital heart disease.
Unique algorithm for the evaluation of embryo photon emission and viability
Authors: Berke József , Gulyás István , Bognár Zoltán , Berke Dávid , Enyedi Attila , Kozma-Bognár Veronika , Mauchart Péter , Nagy Bernadett , Várnagy Ákos , Kovács Kálmán , Bódis József 
Published: July 2024

AbstractLiving cells have spontaneous ultraweak photon emission derived from metabolic reactions associated with physiological conditions. The ORCA-Quest CMOS camera (Hamamatsu Photonics, Japan) is a highly sensitive and essential tool for photon detection; its use with a microscope incubator (Olympus) enables the detection of photons emitted by embryos with the exclusion of harmful visible light. With the application of the second law of thermodynamics, the low-entropy energy absorbed and used by embryos can be distinguished from the higher-entropy energy released and detectable in their environment. To evaluate higher-entropy energy data from embryos, we developed a unique algorithm for the calculation of the entropy-weighted spectral fractal dimension, which demonstrates the self-similar structure of the energy (photons) released by embryos. Analyses based on this structure enabled the distinction of living and degenerated mouse embryos, and of frozen and fresh embryos and the background. This novel detection of ultra-weak photon emission from mouse embryos can provide the basis for the development of a photon emission embryo control system. The ultraweak photon emission fingerprints of embryos may be used for the selection of viable specimens in an ideal dark environment.
Superluminal light propagation in a three-level ladder system
Authors: Gładysz Piotr , Pustelny Szymon , Słowik Karolina 
Published: July 2024

AbstractSuperluminal light propagation is typically accompanied by significant absorption that might prevent its observation in realistic samples. We propose an all-optical implementation exploiting the two-photon resonance in three-level media to overcome this problem. With several computational methods, we analyze three possible configurations of optically-dressed systems and identify an optimal configuration for superluminal propagation. Due to the far-detuned operating regime with low absorption, this scenario avoids the usual need for population inversion, gain assistance or nonlinear optical response. Our analysis covers a broad parameter space and aims for the identification of conditions where significant pulse advancement can be achieved at high transmission levels. In this context, a figure of merit is introduced accounting for a trade-off between the desired group-index values and transmission level. This quantity helps to identify the optimal characteristics of the dressing beam.