bluuebunny/crossref_metadata_2025_split huggingface dataset:
The contributions of mitochondrial and nuclear mitochondrial genetic variation to neuroticism
Authors: Xia Charley , Pickett Sarah J. , Liewald David C. M. , Weiss Alexander , Hudson Gavin , Hill W. David 
Published: May 2023

AbstractNeuroticism is a heritable trait composed of separate facets, each conferring different levels of protection or risk, to health. By examining mitochondrial DNA in 269,506 individuals, we show mitochondrial haplogroups explain 0.07-0.01% of variance in neuroticism and identify five haplogroup and 15 mitochondria-marker associations across a general factor of neuroticism, and two special factors of anxiety/tension, and worry/vulnerability with effect sizes of the same magnitude as autosomal variants. Within-haplogroup genome-wide association studies identified H-haplogroup-specific autosomal effects explaining 1.4% variance of worry/vulnerability. These H-haplogroup-specific autosomal effects show a pleiotropic relationship with cognitive, physical and mental health that differs from that found when assessing autosomal effects across haplogroups. We identify interactions between chromosome 9 regions and mitochondrial haplogroups at P < 5 × 10−8, revealing associations between general neuroticism and anxiety/tension with brain-specific gene co-expression networks. These results indicate that the mitochondrial genome contributes toward neuroticism and the autosomal links between neuroticism and health.
A cryo-EM structure of KTF1-bound polymerase V transcription elongation complex
Authors: Zhang Hong-Wei , Huang Kun , Gu Zhan-Xi , Wu Xiao-Xian , Wang Jia-Wei , Zhang Yu 
Published: May 2023

AbstractDe novo DNA methylation in plants relies on transcription of RNA polymerase V (Pol V) along with KTF1, which produce long non-coding RNAs for recruitment and assembly of the DNA methylation machinery. Here, we report a cryo-EM structure of the Pol V transcription elongation complex bound to KTF1. The structure reveals the conformation of the structural motifs in the active site of Pol V that accounts for its inferior RNA-extension ability. The structure also reveals structural features of Pol V that prevent it from interacting with the transcription factors of Pol II and Pol IV. The KOW5 domain of KTF1 binds near the RNA exit channel of Pol V providing a scaffold for the proposed recruitment of Argonaute proteins to initiate the assembly of the DNA methylation machinery. The structure provides insight into the Pol V transcription elongation process and the role of KTF1 during Pol V transcription-coupled DNA methylation.
Afferent convergence to a shared population of interneuron AMPA receptors
Authors: Pennock Reagan L. , Coddington Luke T. , Yan Xiaohui , Overstreet-Wadiche Linda , Wadiche Jacques I. 
Published: May 2023

AbstractPrecise alignment of pre- and postsynaptic elements optimizes the activation of glutamate receptors at excitatory synapses. Nonetheless, glutamate that diffuses out of the synaptic cleft can have actions at distant receptors, a mode of transmission called spillover. To uncover the extrasynaptic actions of glutamate, we localized AMPA receptors (AMPARs) mediating spillover transmission between climbing fibers and molecular layer interneurons in the cerebellar cortex. We found that climbing fiber spillover generates calcium transients mediated by Ca2+-permeable AMPARs at parallel fiber synapses. Spillover occludes parallel fiber synaptic currents, indicating that separate, independently regulated afferent pathways converge onto a common pool of AMPARs. Together these findings demonstrate a circuit motif wherein glutamate ‘spill-in’ from an unconnected afferent pathway co-opts synaptic receptors, allowing activation of postsynaptic AMPARs even when canonical glutamate release is suppressed.
Soil organic carbon is a key determinant of CH4 sink in global forest soils
Authors: Lee Jaehyun , Oh Youmi , Lee Sang Tae , Seo Yeon Ok , Yun Jeongeun , Yang Yerang , Kim Jinhyun , Zhuang Qianlai , Kang Hojeong 
Published: May 2023

AbstractSoil organic carbon (SOC) is a primary regulator of the forest–climate feedback. However, its indicative capability for the soil CH4 sink is poorly understood due to the incomplete knowledge of the underlying mechanisms. Therefore, SOC is not explicitly included in the current model estimation of the global forest CH4 sink. Here, using in-situ observations, global meta-analysis, and process-based modeling, we provide evidence that SOC constitutes an important variable that governs the forest CH4 sink. We find that a CH4 sink is enhanced with increasing SOC content on regional and global scales. The revised model with SOC function better reproduces the field observation and estimates a 39% larger global forest CH4 sink (24.27 Tg CH4 yr−1) than the model without considering SOC effects (17.46 Tg CH4 yr−1). This study highlights the role of SOC in the forest CH4 sink, which shall be factored into future global CH4 budget quantification.
Enabling rapid X-ray CT characterisation for additive manufacturing using CAD models and deep learning-based reconstruction
Authors: Ziabari Amirkoushyar , Venkatakrishnan S. V. , Snow Zackary , Lisovich Aleksander , Sprayberry Michael , Brackman Paul , Frederick Curtis , Bhattad Pradeep , Graham Sarah , Bingham Philip , Dehoff Ryan , Plotkowski Alex , Paquit Vincent 
Published: May 2023

AbstractMetal additive manufacturing (AM) offers flexibility and cost-effectiveness for printing complex parts but is limited to few alloys. Qualifying new alloys requires process parameter optimisation to produce consistent, high-quality components. High-resolution X-ray computed tomography (XCT) has not been effective for this task due to artifacts, slow scan speed, and costs. We propose a deep learning-based approach for rapid XCT acquisition and reconstruction of metal AM parts, leveraging computer-aided design models and physics-based simulations of nonlinear interactions between X-ray radiation and metals. This significantly reduces beam hardening and common XCT artifacts. We demonstrate high-throughput characterisation of over a hundred AlCe alloy components, quantifying improvements in characterisation time and quality compared to high-resolution microscopy and pycnometry. Our approach facilitates investigating the impact of process parameters and their geometry dependence in metal AM.
Polymer graph neural networks for multitask property learning
Authors: Queen Owen , McCarver Gavin A. , Thatigotla Saitheeraj , Abolins Brendan P. , Brown Cameron L. , Maroulas Vasileios , Vogiatzis Konstantinos D. 
Published: May 2023

AbstractThe prediction of a variety of polymer properties from their monomer composition has been a challenge for material informatics, and their development can lead to a more effective exploration of the material space. In this work, PolymerGNN, a multitask machine learning architecture that relies on polymeric features and graph neural networks has been developed towards this goal. PolymerGNN provides accurate estimates for polymer properties based on a database of complex and heterogeneous polyesters (linear/branched, homopolymers/copolymers) with experimentally refined properties. In PolymerGNN, each polyester is represented as a set of monomer units, which are introduced as molecular graphs. A virtual screening of a large, computationally generated database with materials of variable composition was performed, a task that demonstrates the applicability of the PolymerGNN on future studies that target the exploration of the polymer space. Finally, a discussion on the explainability of the models is provided.
Inverse orbital Hall effect and orbitronic terahertz emission observed in the materials with weak spin-orbit coupling
Authors: Wang Ping , Feng Zheng , Yang Yuhe , Zhang Delin , Liu Quancheng , Xu Zedong , Jia Zhiyan , Wu Yong , Yu Guoqiang , Xu Xiaoguang , Jiang Yong 
Published: May 2023

AbstractThe Orbital Hall effect, which originates from materials with weak spin-orbit coupling, has attracted considerable interest for spin-orbitronic applications. Here, we demonstrate the inverse effect of the orbital Hall effect and observe orbitronic terahertz emission in the Ti and Mn materials. Through spin-orbit transition in the ferromagnetic layer, the generated orbital current can be converted to charge current in the Ti and Mn layers via the inverse orbital Hall effect. Furthermore, the inserted W layer provides an additional conversion of the orbital-charge current in the Ti and Mn layers, significantly enhancing the orbitronic terahertz emission. Moreover, the orbitronic terahertz emission can be manipulated by cooperating with the inverse orbital Hall effect and the inverse spin Hall effect in the different sample configurations. Our results not only discover the physical mechanism of condensed matter physics but also pave the way for designing promising spin-orbitronic devices and terahertz emitters.
Characterization of lab-based swarms of Anopheles gambiae mosquitoes using 3D-video tracking
Authors: Cavagna Andrea , Giardina Irene , Gucciardino Michela Anna , Iacomelli Gloria , Lombardi Max , Melillo Stefania , Monacchia Giulia , Parisi Leonardo , Peirce Matthew J. , Spaccapelo Roberta 
Published: May 2023

AbstractMosquito copulation is a crucial determinant of its capacity to transmit malaria-causing Plasmodium parasites as well as underpinning several highly-anticipated vector control methodologies such as gene drive and sterile insect technique. For the anopheline mosquitoes responsible for African malaria transmission, mating takes place within crepuscular male swarms which females enter solely to mate. However, the mechanisms that regulate swarm structure or that govern mate choice remain opaque. We used 3D-video tracking approaches and computer vision algorithms developed for the study of other complex biological systems to document swarming behavior of a lab-adapted Anopheles gambiae line in a lab-based setting. By reconstructing trajectories of individual mosquitoes lasting up to 15.88 s, in swarms containing upwards of 200 participants, we documented swarm-like behavior in both males and females. In single sex swarms, encounters between individuals were fleeting (< 0.75 s). By contrast, in mixed swarms, we were able to detect 79 ‘brief encounters’ (> 0.75 s; < 2.5 s) and 17 longer-lived encounters (> 2.5 s). We also documented several examples of apparent male-male mating competition. These findings represent the first steps towards a more detailed and quantitative description of swarming and courtship behavior in one of the most important vectors of malaria.
Cosmic coding and transfer storage (COSMOCATS) for invincible key storage
Authors: Tanaka Hiroyuki K. M. 
Published: May 2023

AbstractThus far, a perfectly secure encryption key storage system doesn’t exist. As long as key storage is connected to a network system, there is always a chance that it can be cracked. Even if storage is not continually connected to a network system; it is repeatedly necessary for an individual to access storage to upload and download the data; hence there is always a loophole with every conventional encryption key storage system. By utilizing the penetrative nature of cosmic-ray muons, the COSMOCAT (Cosmic coding and transfer) technique may tackle this problem by eliminating the requirement for any network connection to data storage. COSMOCAT was invented as a post quantum key generation and distribution technique for wireless near field communication. However, in its first stage of development, COSMOCAT relied on standard comparators and Global Positioning System (GPS) or other Global Navigation Satellite Systems (GNSS) for key generation. Temporal jitters of the signals outputted from comparators and frequency fluctuations in GPS-disciplined oscillators degraded the key strength and the efficiency of both the key generation and distribution. New strategies are tested in this paper to improve these factors. As a result, the key strength and the key authenticating rate limit are respectively improved by 4 orders of magnitude and more than 5 orders of magnitude. As a consequence, it has become possible to propose a practical methodology for a new key storage and authentication strategy which has the potential to be an impregnable defense against any kind of cyber/physical attack to data storage. Practical applications of COSMOCATS-based symmetric-key cryptosystems to an electronic digital signing system, communication, and cloud storage are also discussed.
Forecasting COVID-19 activity in Australia to support pandemic response: May to October 2020
Authors: Moss Robert , Price David J. , Golding Nick , Dawson Peter , McVernon Jodie , Hyndman Rob J. , Shearer Freya M. , McCaw James M. 
Published: May 2023

AbstractAs of January 2021, Australia had effectively controlled local transmission of COVID-19 despite a steady influx of imported cases and several local, but contained, outbreaks in 2020. Throughout 2020, state and territory public health responses were informed by weekly situational reports that included an ensemble forecast of daily COVID-19 cases for each jurisdiction. We present here an analysis of one forecasting model included in this ensemble across the variety of scenarios experienced by each jurisdiction from May to October 2020. We examine how successfully the forecasts characterised future case incidence, subject to variations in data timeliness and completeness, showcase how we adapted these forecasts to support decisions of public health priority in rapidly-evolving situations, evaluate the impact of key model features on forecast skill, and demonstrate how to assess forecast skill in real-time before the ground truth is known. Conditioning the model on the most recent, but incomplete, data improved the forecast skill, emphasising the importance of developing strong quantitative models of surveillance system characteristics, such as ascertainment delay distributions. Forecast skill was highest when there were at least 10 reported cases per day, the circumstances in which authorities were most in need of forecasts to aid in planning and response.
Impact of repeated morning bright white light exposures on attention in a simulated office environment
Authors: Canazei Markus , Dick Maximilian , Pohl Wilfried , Weninger Johannes , Hubel Niclas , Staggl Siegmund , Weiss Elisabeth M. 
Published: May 2023

AbstractAttention is essential to the work. This study investigated the effects of two different light pulses on a simple attention task. In addition, the effects of subsequent exposure to constant but different illuminance levels on the continuation of the simple attention task and a subsequent complex attention task were examined. A total of 56 subjects were assigned in random order to two white light interventions that were repeated five times during the morning. Each light intervention consisted of a brief light pulse followed by constant light exposure and differed in temporal dimming dynamics and corneal illuminance. Subjective and psychometric parameters were recorded several times during light exposure. Heart rate variability (HRV) was derived from continuous electrocardiograms. Subjects showed improved reaction speed in the simple attention task, accompanied by higher HRV under a brighter light pulse without habituation by repetition. This difference in simple attention performance disappeared when light exposure remained the same after the light pulse. In addition, higher reaction speed and HRV were observed in the complex attention task under constant bright light exposure. Intermittent bright light seems promising to acutely improve attentional performance in office workplaces. Future research is needed to investigate daytime light effects on other work-related cognitive functions.
Surface protein profiling of milk and serum extracellular vesicles unveils body fluid-specific signatures
Authors: Giovanazzi Alberta , van Herwijnen Martijn J. C. , Kleinjan Marije , van der Meulen Gerbrich N. , Wauben Marca H. M. 
Published: May 2023

AbstractCell-derived extracellular vesicles (EVs) are currently in the limelight as potential disease biomarkers. The promise of EV-based liquid biopsy resides in the identification of specific disease-associated EV signatures. Knowing the reference EV profile of a body fluid can facilitate the identification of such disease-associated EV-biomarkers. With this aim, we purified EVs from paired human milk and serum samples and used the MACSPlex bead-based flow-cytometry assay to capture EVs on bead-bound antibodies specific for a certain surface protein, followed by EV detection by the tetraspanins CD9, CD63, and CD81. Using this approach we identified body fluid-specific EV signatures, e.g. breast epithelial cell signatures in milk EVs and platelet signatures in serum EVs, as well as body fluid-specific markers associated to immune cells and stem cells. Interestingly, comparison of pan-tetraspanin detection (simultaneous CD9, CD63 and CD81 detection) and single tetraspanin detection (detection by CD9, CD63 or CD81) also unveiled body fluid-specific tetraspanin distributions on EVs. Moreover, certain EV surface proteins were associated with a specific tetraspanin distribution, which could be indicative of the biogenesis route of this EV subset. Altogether, the identified body fluid-specific EV profiles can contribute to study EV profile deviations in these fluids during disease processes.
Effects of snow cover on urban light climate environment in the high latitudes of northeast China
Authors: Zhang Fan , Wang Nan , Zhang Lijuan , Chu Yue , Wang Shiwen , Huang Yutao 
Published: May 2023

AbstractLight climate environment (LCE) has a significant impact on human health, behavioral characteristics, and the safety of life and property due to the high albedo of snow on the ground cover type, which in turn affects the regional climate and socio-economic development, but less relevant studies have been found. In this study, the effect of snow on daytime and nighttime light levels was quantified using comparative field observations and controlled experiments in artificial climate chambers, combined with analysis of variance and model fitting. The results of the study found that there was a significant difference between the presence and absence of snow on both daytime and nighttime light levels. During daytime, the ambient light level on the ground with snow is 5.68 times higher than without snow, an improvement of 12,711.06 Lux. At night, with moonlight, the nighttime illuminance with and without snow is 0.213 Lux and 0.01 Lux, respectively. When there is no moonlight, the snow has no significant effect on the light level. In addition, significant differences in LCE intensity with different snow depths, snow densities and black carbon (BC) pollution. At the same background light intensity, the LCE intensity varies significantly with increasing snow depth, snow density and BC pollution. The results reveals the quantitative impact of snow on LCE, providing scientific support for regional natural light energy use, human health and safety, urban environmental management and economic development.
Deep learning model accurately classifies metastatic tumors from primary tumors based on mutational signatures
Authors: Zheng Weisheng , Pu Mengchen , Li Xiaorong , Du Zhaolan , Jin Sutong , Li Xingshuai , Zhou Jielong , Zhang Yingsheng 
Published: May 2023

AbstractMetastatic propagation is the leading cause of death for most cancers. Prediction and elucidation of metastatic process is crucial for the treatment of cancer. Even though somatic mutations have been linked to tumorigenesis and metastasis, it is less explored whether metastatic events can be identified through genomic mutational signatures, which are concise descriptions of the mutational processes. Here, we developed MetaWise, a Deep Neural Network (DNN) model, by applying mutational signatures as input features calculated from Whole-Exome Sequencing (WES) data of TCGA and other metastatic cohorts. This model can accurately classify metastatic tumors from primary tumors and outperform traditional machine learning (ML) models and a deep learning (DL) model, DiaDeL. Signatures of non-coding mutations also have a major impact on the model’s performance. SHapley Additive exPlanations (SHAP) and Local Surrogate (LIME) analyses identify several mutational signatures which are directly correlated to metastatic spread in cancers, including APOBEC-mutagenesis, UV-induced signatures, and DNA damage response deficiency signatures.
Comparative genomic analysis uncovers candidate genes related with milk production and adaptive traits in goat breeds
Authors: Amiri Ghanatsaman Zeinab , Ayatolahi Mehrgardi Ahmad , Asadollahpour Nanaei Hojjat , Esmailizadeh Ali 
Published: May 2023

AbstractDuring the process of animal domestication, both natural and artificial selection cause variation in allele frequencies among populations. Identifying genomic areas of selection in domestic animals may aid in the detection of genomic areas linked to ecological and economic traits. We studied genomic variation in 140 worldwide goat individuals, including 75 Asian, 30 African and 35 European goats. We further carried out comparative population genomics to detect genomic regions under selection for adaptability to harsh conditions in local Asian ecotypes and also milk production traits in European commercial breeds. In addition, we estimated the genetic distances among 140 goat individuals. The results showed that among all studied goat groups, local breeds from West and South Asia emerged as an independent group. Our search for selection signatures in local goats from West and South Asia revealed candidate genes related to adaptation to hot climate (HSPB6, HSF4, VPS13A and NBEA genes) and immune response (IL7, IL5, IL23A and LRFN5) traits. Furthermore, selection signatures in European commercial goats involved several milk production related genes, such as VPS13C, NCAM2, TMPRSS15, CSN3 and ABCG2. The identified candidate genes could be the fundamental genetic resource for enhancement of goat production and environmental-adaptive traits, and as such they should be used in goat breeding programs to select more efficient breeds.