bluuebunny/crossref_metadata_2025_split huggingface dataset:
Elevated methane flux in a tropical peatland post-fire is linked to depth-dependent changes in peat microbiome assembly
Authors: Bandla Aditya , Akhtar Hasan , Lupascu Massimo , Sukri Rahayu Sukmaria , Swarup Sanjay 
Published: January 2024

AbstractFires in tropical peatlands extend to depth, transforming them from carbon sinks into methane sources and severely limit forest recovery. Peat microbiomes influence carbon transformations and forest recovery, yet our understanding of microbiome shifts post-fire is currently limited. Our previous study highlighted altered relationships between the peat surface, water table, aboveground vegetation, and methane flux after fire in a tropical peatland. Here, we link these changes to post-fire shifts in peat microbiome composition and assembly processes across depth. We report kingdom-specific and depth-dependent shifts in alpha diversity post-fire, with large differences at deeper depths. Conversely, we found shifts in microbiome composition across all depths. Compositional shifts extended to functional groups involved in methane turnover, with methanogens enriched and methanotrophs depleted at mid and deeper depths. Finally, we show that community shifts at deeper depths result from homogeneous selection associated with post-fire changes in hydrology and aboveground vegetation. Collectively, our findings provide a biological basis for previously reported methane fluxes after fire and offer new insights into depth-dependent shifts in microbiome assembly processes, which ultimately underlie ecosystem function predictability and ecosystem recovery.
Association of retinal neurodegeneration with the progression of cognitive decline in Parkinson’s disease
Authors: Murueta-Goyena Ane , Romero-Bascones David , Teijeira-Portas Sara , Urcola J. Aritz , Ruiz-Martínez Javier , Del Pino Rocío , Acera Marian , Petzold Axel , Wagner Siegfried Karl , Keane Pearse Andrew , Ayala Unai , Barrenechea Maitane , Tijero Beatriz , Gómez Esteban Juan Carlos , Gabilondo Iñigo 
Published: January 2024

AbstractRetinal thickness may serve as a biomarker in Parkinson’s disease (PD). In this prospective longitudinal study, we aimed to determine if PD patients present accelerated thinning rate in the parafoveal ganglion cell-inner plexiform layer (pfGCIPL) and peripapillary retinal nerve fiber layer (pRNFL) compared to controls. Additionally, we evaluated the relationship between retinal neurodegeneration and clinical progression in PD. A cohort of 156 PD patients and 72 controls underwent retinal optical coherence tomography, visual, and cognitive assessments between February 2015 and December 2021 in two Spanish tertiary hospitals. The pfGCIPL thinning rate was twice as high in PD (β [SE] = −0.58 [0.06]) than in controls (β [SE] = −0.29 [0.06], p < 0.001). In PD, the progression pattern of pfGCIPL atrophy depended on baseline thickness, with slower thinning rates observed in PD patients with pfGCIPL below 89.8 µm. This result was validated with an external dataset from Moorfields Eye Hospital NHS Foundation Trust (AlzEye study). Slow pfGCIPL progressors, characterized by older at baseline, longer disease duration, and worse cognitive and disease stage scores, showed a threefold increase in the rate of cognitive decline (β [SE] = −0.45 [0.19] points/year, p = 0.021) compared to faster progressors. Furthermore, temporal sector pRNFL thinning was accelerated in PD (βtime x group [SE] = −0.67 [0.26] μm/year, p = 0.009), demonstrating a close association with cognitive score changes (β [SE] = 0.11 [0.05], p = 0.052). This study suggests that a slower pattern of pfGCIPL tissue loss in PD is linked to more rapid cognitive decline, whereas changes in temporal pRNFL could track cognitive deterioration.
Discovering genetic mechanisms underlying the co-occurrence of Parkinson’s disease and non-motor traits
Authors: Gokuladhas Sreemol , Fadason Tayaza , Farrow Sophie , Cooper Antony , O’Sullivan Justin M. 
Published: January 2024

AbstractUnderstanding the biological mechanisms that underlie the non-motor symptoms of Parkinson’s disease (PD) requires comprehensive frameworks that unravel the complex interplay of genetic risk factors. Here, we used a disease-agnostic brain cortex gene regulatory network integrated with Mendelian Randomization analyses that identified 19 genes whose changes in expression were causally linked to PD. We further used the network to identify genes that are regulated by PD-associated genome-wide association study (GWAS) SNPs. Extended protein interaction networks derived from PD-risk genes and PD-associated SNPs identified convergent impacts on biological pathways and phenotypes, connecting PD with established co-occurring traits, including non-motor symptoms. These findings hold promise for therapeutic development. In conclusion, while distinct sets of genes likely influence PD risk and outcomes, the existence of genes in common and intersecting pathways associated with other traits suggests that they may contribute to both increased PD risk and symptom heterogeneity observed in people with Parkinson’s.
Topological single-photon emission from quantum emitter chains
Authors: Wang Yubin , Xu Huawen , Deng Xinyi , Liew Timothy C. H. , Ghosh Sanjib , Xiong Qihua 
Published: January 2024

AbstractWe propose a scheme for generating highly indistinguishable single photons from an active quantum Su-Schrieffer-Heeger chain composed of a collection of noisy quantum emitters. Strikingly, the single photon emission spectrum of the active quantum chain is exceedingly narrow relative to that of a single emitter or a topologically trivial chain. Furthermore, this effect is amplified dramatically in proximity to the non-trivial-to-trivial phase transition point. Exploiting this effect, we demonstrate that the single-photon linewidth of a long topological quantum chain can be arbitrarily reduced, rendering it an ideal source of indistinguishable single photons. Finally, by analyzing the most critical parameters concerning experimental realization and providing a microscopic and quantitative analysis of our model, we take concrete examples of actual quantum emitters to establish the viability of our proposal.
In vivo assembly of epitope-coated biopolymer particles that induce anti-tumor responses
Authors: Jenika Devi , Pounraj Saranya , Wibowo David , Flaxl Leonhard M. , Rehm Bernd H. A. , Mintern Justine D. 
Published: January 2024

AbstractThere is an unmet need for antigen delivery systems that elicit efficient T cell priming to prevent infectious diseases or for treatment of cancers. Here, we explored the immunogenic potential of biologically assembled biopolymer particles (BPs) that have been bioengineered to display the antigenic MHC I and MHC II epitopes of model antigen ovalbumin (OVA). Purified dendritic cells (DCs) captured BP-OVA and presented the associated antigenic epitopes to CD4+T cells and CD8+T cells. Vaccination with BP-OVA in the absence of adjuvant elicited antigen presentation to OVA-specific CD8+and CD4+T cells and cross-primed effective cytotoxic T lymphocyte (CTL) killers. BP-OVA induction of CTL killing did not require CD4+T cell help, with active CTLs generated in BP-OVA vaccinatedI-Ab−/−andCD40−/−mice. In contrast, IL-15 and type I IFN were required, with abrogated CTL activity in vaccinatedIL-15−/−andIFNAR1−/−mice. cDC1 and/or CD103+DCs were not essential for BP-OVA specific CTL with immunization eliciting responses inBatf3−/−mice. Poly I:C, but not LPS or CpG, co-administered as an adjuvant with BP-OVA boosted CTL responses. Finally, vaccination with BP-OVA protected against B16-OVA melanoma and Eμ-myc-GFP-OVA lymphoma inoculation. In summary, we have demonstrated that epitope-displaying BPs represent an antigen delivery platform exhibiting a unique mechanism to effectively engage T cell immune responses.
The hagfish genome and the evolution of vertebrates
Authors: Marlétaz Ferdinand , Timoshevskaya Nataliya , Timoshevskiy Vladimir A. , Parey Elise , Simakov Oleg , Gavriouchkina Daria , Suzuki Masakazu , Kubokawa Kaoru , Brenner Sydney , Smith Jeramiah J. , Rokhsar Daniel S. 
Published: January 2024

AbstractAs the only surviving lineages of jawless fishes, hagfishes and lampreys provide a crucial window into early vertebrate evolution1–3. Here we investigate the complex history, timing and functional role of genome-wide duplications4–7 and programmed DNA elimination8,9 in vertebrates in the light of a chromosome-scale genome sequence for the brown hagfish Eptatretus atami. Combining evidence from syntenic and phylogenetic analyses, we establish a comprehensive picture of vertebrate genome evolution, including an auto-tetraploidization (1RV) that predates the early Cambrian cyclostome–gnathostome split, followed by a mid–late Cambrian allo-tetraploidization (2RJV) in gnathostomes and a prolonged Cambrian–Ordovician hexaploidization (2RCY) in cyclostomes. Subsequently, hagfishes underwent extensive genomic changes, with chromosomal fusions accompanied by the loss of genes that are essential for organ systems (for example, genes involved in the development of eyes and in the proliferation of osteoclasts); these changes account, in part, for the simplification of the hagfish body plan1,2. Finally, we characterize programmed DNA elimination in hagfish, identifying protein-coding genes and repetitive elements that are deleted from somatic cell lineages during early development. The elimination of these germline-specific genes provides a mechanism for resolving genetic conflict between soma and germline by repressing germline and pluripotency functions, paralleling findings in lampreys10,11. Reconstruction of the early genomic history of vertebrates provides a framework for further investigations of the evolution of cyclostomes and jawed vertebrates.
Quantum computing dataset of maximum independent set problem on king lattice of over hundred Rydberg atoms
Authors: Kim Kangheun , Kim Minhyuk , Park Juyoung , Byun Andrew , Ahn Jaewook 
Published: January 2024

AbstractFinding the maximum independent set (MIS) of a large-size graph is a nondeterministic polynomial-time (NP)-complete problem not efficiently solvable with classical computations. Here, we present a set of quantum adiabatic computing data of Rydberg-atom experiments performed to solve the MIS problem of up to 141 atoms randomly arranged on the king lattice. A total of 582,916 events of Rydberg-atom measurements are collected for experimental MIS solutions of 733,853 different graphs. We provide the raw image data along with the entire binary determinations of the measured many-body ground states and the classified graph data, to offer bench-mark testing and advanced data-driven analyses for validation of the performance and system improvements of the Rydberg-atom approach.
A Time-of-Flight and Radar Dataset of a neonatal Thorax Simulator with synchronized Reference Sensor Signals for respiratory Rate Detection
Authors: Gleichauf Johanna , Herrmann Sven , Niebler Christine , Koelpin Alexander 
Published: January 2024

AbstractIn this paper we present an open-source Time-of-Flight and radar dataset of a neonatal thorax simulator for the development of respiratory rate detection algorithms. As it is very difficult to gain recordings of (preterm) neonates and there is hardly any open-source data available, we built our own neonatal thorax simulator which simulates the movement of the thorax due to respiration. We recorded Time-of-Flight (ToF) and radar data at different respiratory rates in a range of 5 to 80 breaths per minute (BPM) and with varying upstroke heights. As gold standard a laser micrometer was used. The open-source data can be used to test new algorithms for non-contact respiratory rate detection.
Australian atmospheric pressure and sea level data during the 2022 Hunga-Tonga Hunga-Ha’apai volcano tsunami
Authors: Davies Gareth , Wilson Kaya , Hague Ben , Greenslade Diana , Metters Daryl , Boswood Paul , Maddox Sam , Dakin Sarah-Kate , Palmer Karen , Galton-Fenzi Ben , French John , Kain Claire 
Published: January 2024

AbstractOn January 15, 2022, an ongoing eruption at the Hunga-Tonga Hunga-Ha’apai volcano generated a large explosion which resulted in a globally observed tsunami and atmospheric pressure wave. This paper presents time series observations of the event from Australia including 503 mean sea level pressure (MSLP) sensors and 103 tide gauges. Data is provided in its original format, which varies between data providers, and a post-processed format with consistent file structure and time zone. High-pass filtered variants of the data are also provided to facilitate study of the pressure wave and tsunami. For a minority of tide gauges the raw sea level data cannot be provided, due to licence restrictions, but high-pass filtered data is always provided. The data provides an important historical record of the volcanic pressure wave and tsunami in Australia. It will be useful for research on atmospheric and ocean waves associated with large volcanic eruptions.
Brain flexibility increases during the peri-ovulatory phase as compared to early follicular phase of the menstrual cycle
Authors: Liparoti Marianna , Cipriano Lorenzo , Troisi Lopez Emahnuel , Polverino Arianna , Minino Roberta , Sarno Laura , Sorrentino Giuseppe , Lucidi Fabio , Sorrentino Pierpaolo 
Published: January 2024

AbstractThe brain operates in a flexible dynamic regime, generating complex patterns of activity (i.e. neuronal avalanches). This study aimed at describing how brain dynamics change according to menstrual cycle (MC) phases. Brain activation patterns were estimated from resting-state magnetoencephalography (MEG) scans, acquired from women at early follicular (T1), peri-ovulatory (T2) and mid-luteal (T3) phases of the MC. We investigated the functional repertoire (number of brain configurations based on fast high-amplitude bursts of the brain signals) and the region-specific influence on large-scale dynamics across the MC. Finally, we assessed the relationship between sex hormones and changes in brain dynamics. A significantly larger number of visited configurations in T2 as compared to T1 was specifically observed in the beta frequency band. No relationship between changes in brain dynamics and sex hormones was evident. Finally, we showed that the left posterior cingulate gyrus and the right insula were recruited more often in the functional repertoire during T2 as compared to T1, while the right pallidum was more often part of the functional repertoires during T1 as compared to T2. In summary, we showed hormone-independent increased flexibility of the brain dynamics during the ovulatory phase. Moreover, we demonstrated that several specific brain regions play a key role in determining this change.
Exploring quantitative measures in metacognition of emotion
Authors: Lee Hsing-Hao , Liu Gabrielle Kaili-May , Chen Yi-Chuan , Yeh Su-Ling 
Published: January 2024

AbstractMetacognition of emotion (meta-emotion) refers to the ability to evaluate and identify one’s emotional feelings. No previous study has defined and measured this construct through objective and quantitative procedures. We established a reliable method to measure meta-emotion. With a two-interval forced-choice procedure, participants selected which of two pictures elicited stronger positive emotion; via the Law of Comparative Judgment, their responses were used to compute individual psychological distances for the emotional responses triggered by the pictures. Then, participants were asked to judge whether a pre-exposed picture induced a stronger positive emotion than the median of that elicited by the whole picture set, followed by a confidence rating. By utilizing each individual’s psychological distance, the correctness of a participant’s emotional experience was quantified by dʹ, and meta-emotion was quantified using meta-dʹ, M-ratio, and M-diff as indices of metacognitive sensitivity and efficiency based on Signal-Detection Theory. Test–retest reliabilities, validated by Spearman correlation, were observed in meta-dʹ, M-ratio, and marginally with M-diff, suggesting the stability of meta-emotion in the current design. This study unveils a validated procedure to quantify meta-emotion, extendable for assessing metacognition of other subjective feelings. Nevertheless, caution is warranted in interpretation, as the measured processes may be influenced by non-metacognitive factors.
Hyperoxia prevents the dynamic neonatal increases in lung mesenchymal cell diversity
Authors: Zanini Fabio , Che Xibing , Suresh Nina E. , Knutsen Carsten , Klavina Paula , Xie Yike , Domingo-Gonzalez Racquel , Liu Min , Kum Alexander , Jones Robert C. , Quake Stephen R. , Alvira Cristina M. , Cornfield David N. 
Published: January 2024

AbstractRapid expansion of the pulmonary microvasculature through angiogenesis drives alveolarization, the final stage of lung development that occurs postnatally and dramatically increases lung gas-exchange surface area. Disruption of pulmonary angiogenesis induces long-term structural and physiologic lung abnormalities, including bronchopulmonary dysplasia, a disease characterized by compromised alveolarization. Although endothelial cells are primary determinants of pulmonary angiogenesis, mesenchymal cells (MC) play a critical and dual role in angiogenesis and alveolarization. Therefore, we performed single cell transcriptomics and in-situ imaging of the developing lung to profile mesenchymal cells during alveolarization and in the context of lung injury. Specific mesenchymal cell subtypes were present at birth with increasing diversity during alveolarization even while expressing a distinct transcriptomic profile from more mature correlates. Hyperoxia arrested the transcriptomic progression of the MC, revealed differential cell subtype vulnerability with pericytes and myofibroblasts most affected, altered cell to cell communication, and led to the emergence of Acta1 expressing cells. These insights hold the promise of targeted treatment for neonatal lung disease, which remains a major cause of infant morbidity and mortality across the world.
On computational models of theory of mind and the imitative reinforcement learning in spiking neural networks
Authors: Gorgan Mohammadi Ashena , Ganjtabesh Mohammad 
Published: January 2024

AbstractTheory of Mind is referred to the ability of inferring other’s mental states, and it plays a crucial role in social cognition and learning. Biological evidences indicate that complex circuits are involved in this ability, including the mirror neuron system. The mirror neuron system influences imitation abilities and action understanding, leading to learn through observing others. To simulate this imitative learning behavior, a Theory-of-Mind-based Imitative Reinforcement Learning (ToM-based ImRL) framework is proposed. Employing the bio-inspired spiking neural networks and the mechanisms of the mirror neuron system, ToM-based ImRL is a bio-inspired computational model which enables an agent to effectively learn how to act in an interactive environment through observing an expert, inferring its goals, and imitating its behaviors. The aim of this paper is to review some computational attempts in modeling ToM and to explain the proposed ToM-based ImRL framework which is tested in the environment of River Raid game from Atari 2600 series.
Investigation and analysis of maker education curriculum from the perspective of artificial intelligence
Authors: Ou Qizhong , Chen Xinglin 
Published: January 2024

AbstractAs an education model that focuses on the cultivation of students’ creativity and practical ability, the integration of maker education and the development of artificial intelligence is of great significance. In order to analyze and study the application effect of artificial intelligence in maker education, based on this, this study adopts the method of questionnaire and case analysis to investigate and analyze students from three dimensions: learning experience, learning attitude and learning emotion, learning effect and transfer. The survey results show that, on the whole, the integration of artificial intelligence technology into maker education can significantly improve students’ learning feelings and attitudes, and enhance the enthusiasm of learning emotions. The research also finds that it has a positive impact on students’ learning effect and transfer ability. Learning experience, learning attitude and learning emotion, learning effect and learning transfer are related to gender, teaching time, teaching subjects or majors. Therefore, the article will suggest creating a maker cultural atmosphere, creating a maker resource space, and improving the maker education system. This provides a valuable reference for further promoting the development of maker education courses in the field of artificial intelligence.
Sensitivity and quality factor improvement of photonic crystal sensors by geometrical optimization of waveguides and micro-ring resonators combination
Authors: Fallahi Vahid , Kordrostami Zoheir , Hosseini Mehdi 
Published: January 2024

AbstractIn this work, the process of designing and simulating optical sensors based on photonic crystal (PC) micro-ring resonators (MRRs) has been investigated. According to the PC type, different waveguides and resonators can be designed, and various topologies can be proposed from their combination, for optical sensor applications. Here, the investigated MRR is of the symmetrical micro-hexagonal ring resonator (MHRR) type. Different arrays of MHRR arrangement have been designed to investigate their effects on the output spectrum. The results of the design and simulation of different topologies have been analyzed and compared with other numerical researches. Considering all the necessary aspects of PC optical sensors, a detailed and comprehensive algorithm has been presented for designing these devices and choosing the optimal structure. In a more complementary process, the effects of reflector rods have been investigated, which indicates the existence of similarity and compatibility in the design between the distance of reflector rods and the length of MHRRs to obtain the optimal structure. Finally, the effect of different values of lattice constant and radius of dielectric rods on FWHM, transmission (TR) and resonant wavelength is studied, and the most optimal mode is presented. In order to measure the performance of the proposed optimal sensor, its application for gas detection has been analyzed. TR, FWHM, quality factor (QF), sensitivity (S) and figure of merit (FOM) of the proposed sensor were equal to 96%, 0.31 nm, 2636, 6451 nm/RIU and 2960 RIU−1 respectively. An examination of results from similar research indicates a rational and effective approach for generating diverse topologies, aiming to attain the most optimal configuration for optical sensors employing MRRs. Furthermore, employing a systematic design process based on established principles and the proposed algorithm helps prevent arbitrary parameter variations, facilitating the attainment of desired outcomes in a more streamlined and efficient manner. Given the comprehensive nature of this research, it presents a viable solution for designing optical devices based on MRRs for use in optical integrated circuits (OICs) applications.