bluuebunny/crossref_metadata_2025_split huggingface dataset:
Tropospheric Gravity Waves Increase the Likelihood of Double Tropopauses
Authors: Shao Jia , Zhang Jian , Tian Yufang , Wang Wuke , Huang Kaiming , Zhang Shaodong 
Published: December 2023

AbstractThe tropopause region is crucial for the stratosphere‐troposphere exchange (STE) and acts as an indicator of climate change. Double tropopauses (DTs) act to increase the STE process but their driving mechanisms remain an open question. The present assessment offers for the first time the linkage between tropospheric gravity waves (GWs) and DT events by exploring a global data set of multi‐year radiosonde measurements. In the extratropics, the occurrence frequency of DT events keeps a remarkably consistent spatial‐temporal structure with GW total energy. Under the DT scenario, GW total energy has increased by 37.67% compared to single tropopause events. Based on a statistical assessment, the upward propagating GWs throughout the second tropopause region can probably raise Kelvin‐Helmholtz instability or turbulence, leading permanent irregularities in thermodynamic structure, and consequently, increasing the likelihood of DT.
Evaluating Methane Emissions From Decommissioned Unconventional Petroleum Wells in British Columbia, Canada
Authors: Cahill Aaron G. , Joukar Mohammad , Sefat Morteza , van Geloven Chelton 
Published: December 2023

AbstractHundreds of thousands of unconventional natural gas wells recently constructed across North America have transformed the global energy landscape and generated widespread concern relating to fugitive methane leakage. To date, no studies have evaluated the integrity of unconventional wells post‐abandonment. Here, we evaluated emissions at nine decommissioned unconventional wells within the Montney region of British Columbia, Canada and found two exhibited co‐emission of CH4 and CO2 from surrounding soils indicating integrity failure, releasing up to ∼2,000 kg of CO2‐eq/yr into the atmosphere. A further three wells exhibited statistically significant anomalous CO2 fluxes of ∼500 kg/year from surficial soils around the well, likely associated with minor integrity failure and derived from near total soil‐based aerobic oxidation of fugitive CH4. These findings suggest that more than half of decommissioned unconventional wells may generate emissions, however only relatively small contributions to GHG emissions result that are significantly mitigated through natural soils‐based CH4 oxidation.
Multi‐Time Scale Variations in Atlantic Niño and a Relative Atlantic Niño Index
Authors: Tan Wei , Liu Yunyun , Li Xiaofan , Johnson Nathaniel C. , Hu Zeng‐Zhen 
Published: December 2023

AbstractAtlantic Niño is a leading mode of climate variability in the tropical Atlantic Ocean with important regional impacts. Tropical Atlantic sea surface temperatures (SSTs) connected with Atlantic Niño exhibit notable multi‐time scale variations, including a quasi‐linear warming trend and sub‐annual to interdecadal variability associated with different physical processes. Contrasting the tropical Pacific SST associated with the El Niño‐Southern Oscillation (ENSO), which has a weak trend and quasi‐periodic oscillatory variability with a period of 2–7 years, the ATL3 index, the primary index for monitoring the Atlantic Niño, has no dominant time scale, that is likely responsible for its low prediction skills. Following the same spirit as the relative Niño3.4 index, we demonstrate that a relative ATL3 index, which is defined as the difference between the raw ATL3 index and the global SST anomaly, provides distinct advantages for monitoring the sub‐annual‐to‐interdecadal variations for Atlantic Niño in real time.
Organic Matrix Effect on the Molecular Light Absorption of Brown Carbon
Authors: Zhang Antai , Zeng Yaling , Yang Xin , Zhai Jinghao , Wang Yixiang , Xing Chunbo , Cai Baohua , Shi Shao , Zhang Yujie , Shen Zhenxing , Fu Tzung‐May , Zhu Lei , Shen Huizhong , Ye Jianhuai , Wang Chen 
Published: December 2023

AbstractBrown carbon (BrC) absorption impacts radiative forcing and climate change. Quantifying radiative forcing of BrC requires understanding its molecular composition and absorption characteristics. While organic molecules surrounding BrC may impact its absorption, their effects have not yet been investigated. This research determined matrix effect on BrC absorption by comparing individual BrC molecules and BrC within an organic matrix. Over 20,000 water‐soluble organic molecules constituted the water‐soluble BrC and associated organic matrix. The matrix enhanced aliphatic BrC absorption but suppressed aromatic BrC, especially with higher matrix O/C ratios indicating greater polarity and acidity. By directly measuring and modeling organic matrix effect on BrC, we can improve climate prediction precision and aerosol‐radiation interaction comprehension.
Large Methane Emissions From Tree Stems Complicate the Wetland Methane Budget
Authors: Jeffrey L. C. , Moras C. A. , Tait D. R. , Johnston S. G. , Call M. , Sippo J. Z. , Jeffrey N. C. , Laicher‐Edwards D. , Maher D. T. 
Published: December 2023

AbstractOur understanding of tree stem methane (CH4) emissions is evolving rapidly. Few studies have combined seasonal measurements of soil, water and tree stem CH4 emissions from forested wetlands, inhibiting our capacity to constrain the tree stem CH4 flux contribution to the total wetland CH4 flux. Here we present annual data from a subtropical freshwater Melaleuca quinquenervia wetland forest, spanning an elevational topo‐gradient (Lower, Transitional and Upper zones). Eight field campaigns captured an annual hydrological flood‐dry‐flood cycle, measuring stem fluxes on 30 trees, from four stem heights, and up to 30 adjacent soil or water CH4 fluxes per campaign. Tree stem CH4 fluxes ranged several orders of magnitude between hydrological seasons and topo‐gradient zones, spanning from small CH4 uptake to an emission of ∼203 mmol m−2 d−1. Soil CH4 fluxes were similarly dynamic and shifted from CH4 emission (saturated soil) to uptake (dry soil). In Lower and Transitional zones respectively, tree stem CH4 contribution to the net CH4 ecosystem flux was greatest during flooded conditions (49.9% and 70.2%) but less important during dry periods (3.1% and 28.2%). Minor tree stem emissions from the Upper elevation zone still offset the Upper zone CH4 soil sink capacity by ∼51% during dry conditions. Water table height was the strongest driver of tree stem CH4 fluxes, however tree emissions peaked once the soil was inundated and did not increase with further water depth. This study highlights the importance of quantifying the wetland tree stem CH4 emissions pathway as an important and seasonally oscillating component of wetland CH4 budgets.
Process‐Based Quantification of the Role of Wildfire in Shaping Flood Frequency
Authors: Yu Guo , Liu Tao , McGuire Luke A. , Wright Daniel B. , Hatchett Benjamin J. , Miller Julianne J. , Berli Markus , Giovando Jeremy , Bartles Michael , Floyd Ian E. 
Published: December 2023

AbstractModerate to high severity wildfire can abruptly alter watershed properties and enhance extreme hydrologic responses such as debris flows and floods. The compounding effects of wildfire on flood hazard, represented here via flood frequency analysis (FFA; e.g., 100‐year flood) are of growing importance. Standard statistical FFA approaches are ill‐suited to examining this issue because wildfire‐affected flood peak observations are limited in number and violate the assumption of independent and identically distributed events. Here, we developed a process‐based FFA framework that integrates a stochastic rainfall generator, wildfire simulation, inverse modeling, and a physics‐based hydrological model to directly simulate the impacts of wildfire on FFA. We applied this framework in the upper Arroyo Seco watershed in Southern California, which experienced Moderate to high burn during the 2009 Station Fire. An FFA analysis, performed with simulated peak flows from the first year since fire demonstrates the 100‐year flood can be three times larger than simulations that only consider peak flows in non‐fire‐affected years. On the other hand, coupling process‐based FFA with stochastically simulated wildfire events and watershed's time‐varying hydrologic recovery yields “fire continuum FFA”, a concept introduced here for the first time. Fire continuum FFA accounts for multiple wildfires within very long synthetic time series. Variability in upper tail flood peaks is substantially higher in fire continuum results as compared with pre‐wildfire FFA. This result highlights the importance of wildfire inter‐arrival time and post‐wildfire recovery processes, both of which are expected to change as a result of climatic change and evolving fire management strategies.
Parent and Adolescent Perspectives on a Novel Transdisciplinary Model of Health Care Delivery for Type 1 Diabetes
Authors: Pierce Jessica S. , Enlow Paul , Thomas Courtney , Price Julia , Wasserman Rachel , Wysocki Tim , Alderfer Melissa A. 
Published: December 2023

Objective: We aimed to obtain preadolescent/adolescent and parent input on a proposed transdisciplinary model for routine Type 1 diabetes (T1D) health care in which an advanced practice nurse, dietitian, and psychologist with expertise in T1D and extensive cross-discipline training codeliver care during quarterly T1D care visits using a family-focused approach. Method: Participants were 17 parent–youth dyads plus one additional adolescent who responded to open-ended questions about the structure and format of the proposed transdisciplinary care model via an online, private social network. A six-member coding team developed and revised a codebook, coded question responses through iterative cycles of inductive coding, and distilled major recurring themes to obtain perspectives on the transdisciplinary care model and feedback on improving the model. Results: We identified nine themes regarding reactions to our proposed transdisciplinary care model, which fell into three broad categories: (a) general perceptions of transdisciplinary care (e.g., transdisciplinary care may facilitate improved communication and collaboration among providers and result in more holistic care); (b) perceptions about transdisciplinary care providers (e.g., perspectives on the inclusion of dietitians and psychologists as members of the transdisciplinary care team were mixed); and (c) suggestions for improving the transdisciplinary care model (e.g., ensure care is patient/family-centered and holistic). Conclusions: The present findings provided important feedback to modify our transdisciplinary care model and on parent and youth preferences for T1D health care delivery. Implications for Impact Statement In this study, we aimed to obtain preadolescent/adolescent and parent input on a new model of health care for youth with Type 1 diabetes (T1D), called transdisciplinary care. In transdisciplinary care, an advanced practice nurse, dietitian, and psychologist work together with the family to deliver routine T1D care. Though qualitative analysis, we found that parents and youth identified both positive and negative perceptions of the transdisciplinary care model and offered suggestions for improving the transdisciplinary care model.
TREX1 is required for microglial cholesterol homeostasis and oligodendrocyte terminal differentiation in human neural assembloids
Authors: Goldberg Gabriela , Coelho Luisa , Mo Guoya , Adang Laura A. , Patne Meenakshi , Chen Zhoutao , Garcia-Bassets Ivan , Mesci Pinar , Muotri Alysson R. 
Published: December 2023

AbstractThree Prime Repair Exonuclease 1 (TREX1) gene mutations have been associated with Aicardi-Goutières Syndrome (AGS) – a rare, severe pediatric autoimmune disorder that primarily affects the brain and has a poorly understood etiology. Microglia are brain-resident macrophages indispensable for brain development and implicated in multiple neuroinflammatory diseases. However, the role of TREX1 – a DNase that cleaves cytosolic nucleic acids, preventing viral- and autoimmune-related inflammatory responses – in microglia biology remains to be elucidated. Here, we leverage a model of human embryonic stem cell (hESC)-derived engineered microglia-like cells, bulk, and single-cell transcriptomics, optical and transmission electron microscopy, and three-month-old assembloids composed of microglia and oligodendrocyte-containing organoids to interrogate TREX1 functions in human microglia. Our analyses suggest that TREX1 influences cholesterol metabolism, leading to an active microglial morphology with increased phagocytosis in the absence of TREX1. Notably, regulating cholesterol metabolism with an HMG-CoA reductase inhibitor, FDA-approved atorvastatin, rescues these microglial phenotypes. Functionally, TREX1 in microglia is necessary for the transition from gliogenic intermediate progenitors known as pre-oligodendrocyte precursor cells (pre-OPCs) to precursors of the oligodendrocyte lineage known as OPCs, impairing oligodendrogenesis in favor of astrogliogenesis in human assembloids. Together, these results suggest routes for therapeutic intervention in pathologies such as AGS based on microglia-specific molecular and cellular mechanisms.
What happens to regulatory T cells in multiple myeloma
Authors: Chen Huixian , Wang Xueling , Wang Yan , Chang Xiaotian 
Published: December 2023

AbstractAbnormal tumor microenvironment and immune escape in multiple myeloma (MM) are associated with regulatory T cells (Tregs), which play an important role in maintaining self-tolerance and regulating the overall immune response to infection or tumor cells. In patients with MM, there are abnormalities in the number, function and distribution of Tregs, and these abnormalities may be related to the disease stage, risk grade and prognosis of patients. During the treatment, Tregs have different responses to various treatment regiments, thus affecting the therapeutic effect of MM. It is also possible to predict the therapeutic response by observing the changes of Tregs. In addition to the above, we reviewed the application of Tregs in the treatment of MM. In conclusion, there is still much room for research on the mechanism and application of Tregs in MM.
ChillsDB 2.0: Individual Differences in Aesthetic Chills Among 2,900+ Southern California Participants
Authors: Schoeller Felix , Christov Moore Leo , Lynch Caite , Reggente Nicco 
Published: December 2023

AbstractWe significantly enriched ChillsDB, a dataset of audiovisual stimuli validated to elicit aesthetic chills. A total of 2,937 participants from Southern California were exposed to 40 stimuli, consisting of 20 stimuli (10 from ChillsDB and 10 new) presented either in audiovisual or audio-only formats. Questionnaires were administered assessing demographics, personality traits, state affect, and political orientation. Detailed data on chills responses is captured alongside participants’ ratings of the stimuli. The dataset combines controlled elicitation of chills using previously validated materials with individual difference measures to enable investigation of predictors and correlates of aesthetic chills phenomena. It aims to support continued research on the mechanisms and therapeutic potential of aesthetic chills responses.
A global database of bird nest traits
Authors: Chia Stephanie Yuan , Fang Yi-Ting , Su Yi-Ting , Tsai Pei-Yu , Hsieh Chia , Tsao Shu-Han , Juang Jia-Yang , Hung Chih-Ming , Tuanmu Mao-Ning 
Published: December 2023

AbstractThe reproductive success of birds is closely tied to the characteristics of their nests. It is crucial to understand the distribution of nest traits across phylogenetic and geographic dimensions to gain insight into bird evolution and adaptation. Despite the extensive historical documentation on breeding behavior, a structured dataset describing bird nest characteristics has been lacking. To address this gap, we have compiled a comprehensive dataset that characterizes three ecologically and evolutionarily significant nest traits—site, structure, and attachment—for 9,248 bird species, representing all 36 orders and 241 out of the 244 families. By defining seven sites, seven structures, and four attachment types, we have systematically classified the nests of each species using information from text descriptions, photos, and videos sourced from online databases and literature. This nest traits dataset serves as a valuable addition to the existing body of morphological and ecological trait data for bird species, providing a useful resource for a wide range of avian macroecological and macroevolutionary research.
MarFERReT, an open-source, version-controlled reference library of marine microbial eukaryote functional genes
Authors: Groussman R. D. , Blaskowski S. , Coesel S. N. , Armbrust E. V. 
Published: December 2023

AbstractMetatranscriptomics generates large volumes of sequence data about transcribed genes in natural environments. Taxonomic annotation of these datasets depends on availability of curated reference sequences. For marine microbial eukaryotes, current reference libraries are limited by gaps in sequenced organism diversity and barriers to updating libraries with new sequence data, resulting in taxonomic annotation of about half of eukaryotic environmental transcripts. Here, we introduce Marine Functional EukaRyotic Reference Taxa (MarFERReT), a marine microbial eukaryotic sequence library designed for use with taxonomic annotation of eukaryotic metatranscriptomes. We gathered 902 publicly accessible marine eukaryote genomes and transcriptomes and assessed their sequence quality and cross-contamination issues, selecting 800 validated entries for inclusion in MarFERReT. Version 1.1 of MarFERReT contains reference sequences from 800 marine eukaryotic genomes and transcriptomes, covering 453 species- and strain-level taxa, totaling nearly 28 million protein sequences with associated NCBI and PR2 Taxonomy identifiers and Pfam functional annotations. The MarFERReT project repository hosts containerized build scripts, documentation on installation and use case examples, and information on new versions of MarFERReT.
Chromosomal-level assembly of Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki genomes
Authors: Okuno Miki , Mochimaru Yuta , Matsuoka Kentaro , Yamabe Takahiro , Matiz-Ceron Luisa , Jogahara Takamichi , Toyoda Atsushi , Kuroiwa Asato , Itoh Takehiko 
Published: December 2023

AbstractHerein, we present the first high-quality long-read-based chromosome-level genome assemblies and gene annotations of the genomes of three endangered Tokudaia species: Tokudaia osimensis, Tokudaia tokunoshimensis, and Tokudaia muenninki. These species, which are endemic to different islands of the Ryukyu Islands, Japan, exhibited unique karyotypes and sex chromosomal characteristics. The genome assemblies generated using PacBio, Illumina, and Hi-C sequence data consisted of 13 (corresponded to 12 autosomes and one X chromosome), 23 (corresponded to 22 autosomes and one X chromosome), and 23 (corresponded to 21 autosomes and the neo- and ancestral X regions) chromosome-level scaffolds that contained 2,445, 2,477, and 2,661 Mbp of sequence data, respectively. Annotations of protein-coding genes were performed using RNA-Seq-based, homology-based, and Ab initio methods. BUSCO completeness values for every species exceeded 96% for genomes and 98% for genes. These data can be an important resource for contributing to our understanding of species genomes resulting from allopatric speciation and provide insights into mammalian sex-determination mechanisms and sex chromosome evolution.
Study on reasonable anchorage length based on failure mechanism of the bolt anchorage system
Authors: Wang Meng , Shang Liyou , Zhang Baoan , Li Yatao , Su Jinshuai , Wang Shuai 
Published: December 2023

AbstractIn addition to analysing the mechanism of failure of the prestressed rock anchor anchor system and investigating the appropriate depth for fixing the rock anchors, theoretical equations were derived to calculate the rock anchors' axial force, ultimate capacity, and the interfacial shear force in the elastic phase. These equations are then used to analyse the pressure distribution within the rock bolt anchorage section and to investigate the effect of interfacial shear strength, shear stiffness, and anchorage length on interface failure. Drawing on the findings from both field-based rock bolt pull-out tests and numerical simulations, analyzed the failure mechanism of the anchor system, and proposed a reasonable anchor length design method for rock bolt. The results show that there is a strong dependence between ultimate load carrying capability of rock bolts and interfacial shear stress and shear rigidity, and that increasing the anchorage length and reducing the interface shear stiffness can avoid the stress concentration phenomenon. The primary factor leading to the anchor system failure is secondary interface failure. The evolution law of interface damage is that the damage occurs first at the initial position. As the interface damage location changes, the peak shearing stress moves towards the bottom of the anchored section. The engineering application results verified the feasibility of a reasonable anchorage length calculation method and rock bolt design process. The findings of this paper can be used as a basic reference for determining rock bolt anchorage support parameters during the design and construction of underground engineering projects.
Communities in C. elegans connectome through the prism of non-backtracking walks
Authors: Onuchin Arsenii A. , Chernizova Alina V. , Lebedev Mikhail A. , Polovnikov Kirill E. 
Published: December 2023

AbstractThe fundamental relationship between the mesoscopic structure of neuronal circuits and organismic functions they subserve is one of the major challenges in contemporary neuroscience. Formation of structurally connected modules of neurons enacts the conversion from single-cell firing to large-scale behaviour of an organism, highlighting the importance of their accurate profiling in the data. While connectomes are typically characterized by significant sparsity of neuronal connections, recent advances in network theory and machine learning have revealed fundamental limitations of traditionally used community detection approaches in cases where the network is sparse. Here we studied the optimal community structure in the structural connectome of Caenorhabditis elegans, for which we exploited a non-conventional approach that is based on non-backtracking random walks, virtually eliminating the sparsity issue. In full agreement with the previous asymptotic results, we demonstrated that non-backtracking walks resolve the ground truth annotation into clusters on stochastic block models (SBM) with the size and density of the connectome better than the spectral methods related to simple random walks. Based on the cluster detectability threshold, we determined that the optimal number of modules in a recently mapped connectome of C. elegans is 10, which precisely corresponds to the number of isolated eigenvalues in the spectrum of the non-backtracking flow matrix. The discovered communities have a clear interpretation in terms of their functional role, which allows one to discern three structural compartments in the worm: the Worm Brain (WB), the Worm Movement Controller (WMC), and the Worm Information Flow Connector (WIFC). Broadly, our work provides a robust network-based framework to reveal mesoscopic structures in sparse connectomic datasets, paving way to further investigation of connectome mechanisms for different functions.