bluuebunny/crossref_metadata_2025_split huggingface dataset:
Using secondary cases to characterize the severity of an emerging or re-emerging infection
Authors: Tsang Tim K. , Wang Can , Yang Bingyi , Cauchemez Simon , Cowling Benjamin J. 
Published: November 2021

AbstractThe methods to ascertain cases of an emerging infectious disease are typically biased toward cases with more severe disease, which can bias the average infection-severity profile. Here, we conducted a systematic review to extract information on disease severity among index cases and secondary cases identified by contact tracing of index cases for COVID-19. We identified 38 studies to extract information on measures of clinical severity. The proportion of index cases with fever was 43% higher than for secondary cases. The proportion of symptomatic, hospitalized, and fatal illnesses among index cases were 12%, 126%, and 179% higher than for secondary cases, respectively. We developed a statistical model to utilize the severity difference, and estimate 55% of index cases were missed in Wuhan, China. Information on disease severity in secondary cases should be less susceptible to ascertainment bias and could inform estimates of disease severity and the proportion of missed index cases.
Dynamic Europa ocean shows transient Taylor columns and convection driven by ice melting and salinity
Authors: Ashkenazy Yosef , Tziperman Eli 
Published: November 2021

AbstractThe deep (~100 km) ocean of Europa, Jupiter’s moon, covered by a thick icy shell, is one of the most probable places in the solar system to find extraterrestrial life. Yet, its ocean dynamics and its interaction with the ice cover have received little attention. Previous studies suggested that Europa’s ocean is turbulent using a global model and taking into account non-hydrostatic effects and the full Coriolis force. Here we add critical elements, including consistent top and bottom heating boundary conditions and the effects of icy shell melting and freezing on ocean salinity. We find weak stratification that is dominated by salinity variations. The ocean exhibits strong transient convection, eddies, and zonal jets. Transient motions organize in Taylor columns parallel to Europa’s axis of rotation, are static inside of the tangent cylinder and propagate equatorward outside the cylinder. The meridional oceanic heat transport is intense enough to result in a nearly uniform ice thickness, that is expected to be observable in future missions.
Tracking Brownian motion in three dimensions and characterization of individual nanoparticles using a fiber-based high-finesse microcavity
Authors: Kohler Larissa , Mader Matthias , Kern Christian , Wegener Martin , Hunger David 
Published: November 2021

AbstractThe dynamics of nanosystems in solution contain a wealth of information with relevance for diverse fields ranging from materials science to biology and biomedical applications. When nanosystems are marked with fluorophores or strong scatterers, it is possible to track their position and reveal internal motion with high spatial and temporal resolution. However, markers can be toxic, expensive, or change the object’s intrinsic properties. Here, we simultaneously measure dispersive frequency shifts of three transverse modes of a high-finesse microcavity to obtain the three-dimensional path of unlabeled SiO2 nanospheres with 300 μs temporal and down to 8 nm spatial resolution. This allows us to quantitatively determine properties such as the polarizability, hydrodynamic radius, and effective refractive index. The fiber-based cavity is integrated in a direct-laser-written microfluidic device that enables the precise control of the fluid with ultra-small sample volumes. Our approach enables quantitative nanomaterial characterization and the analysis of biomolecular motion at high bandwidth.
Computational optical sectioning with an incoherent multiscale scattering model for light-field microscopy
Authors: Zhang Yi , Lu Zhi , Wu Jiamin , Lin Xing , Jiang Dong , Cai Yeyi , Xie Jiachen , Wang Yuling , Zhu Tianyi , Ji Xiangyang , Dai Qionghai 
Published: November 2021

AbstractQuantitative volumetric fluorescence imaging at high speed across a long term is vital to understand various cellular and subcellular behaviors in living organisms. Light-field microscopy provides a compact computational solution by imaging the entire volume in a tomographic way, while facing severe degradation in scattering tissue or densely-labelled samples. To address this problem, we propose an incoherent multiscale scattering model in a complete space for quantitative 3D reconstruction in complicated environments, which is called computational optical sectioning. Without the requirement of any hardware modifications, our method can be generally applied to different light-field schemes with reduction in background fluorescence, reconstruction artifacts, and computational costs, facilitating more practical applications of LFM in a broad community. We validate the superior performance by imaging various biological dynamics in Drosophila embryos, zebrafish larvae, and mice.
A recurrent SHANK3 frameshift variant in Autism Spectrum Disorder
Authors: Loureiro Livia O. , Howe Jennifer L. , Reuter Miriam S. , Iaboni Alana , Calli Kristina , Roshandel Delnaz , Pritišanac Iva , Moses Alan , Forman-Kay Julie D. , Trost Brett , Zarrei Mehdi , Rennie Olivia , Lau Lynette Y. S. , Marshall Christian R. , Srivastava Siddharth , Godlewski Brianna , Buttermore Elizabeth D. , Sahin Mustafa , Hartley Dean , Frazier Thomas , Vorstman Jacob , Georgiades Stelios , Lewis Suzanne M. E. , Szatmari Peter , Bradley Clarrisa A. , Tabet Anne-Claude , Willems Marjolaine , Lumbroso Serge , Piton Amélie , Lespinasse James , Delorme Richard , Bourgeron Thomas , Anagnostou Evdokia , Scherer Stephen W. 
Published: November 2021

AbstractAutism Spectrum Disorder (ASD) is genetically complex with ~100 copy number variants and genes involved. To try to establish more definitive genotype and phenotype correlations in ASD, we searched genome sequence data, and the literature, for recurrent predicted damaging sequence-level variants affecting single genes. We identified 18 individuals from 16 unrelated families carrying a heterozygous guanine duplication (c.3679dup; p.Ala1227Glyfs*69) occurring within a string of 8 guanines (genomic location [hg38]g.50,721,512dup) affecting SHANK3, a prototypical ASD gene (0.08% of ASD-affected individuals carried the predicted p.Ala1227Glyfs*69 frameshift variant). Most probands carried de novo mutations, but five individuals in three families inherited it through somatic mosaicism. We scrutinized the phenotype of p.Ala1227Glyfs*69 carriers, and while everyone (17/17) formally tested for ASD carried a diagnosis, there was the variable expression of core ASD features both within and between families. Defining such recurrent mutational mechanisms underlying an ASD outcome is important for genetic counseling and early intervention.
Practical distributed quantum information processing with LOCCNet
Authors: Zhao Xuanqiang , Zhao Benchi , Wang Zihe , Song Zhixin , Wang Xin 
Published: November 2021

AbstractDistributed quantum information processing is essential for building quantum networks and enabling more extensive quantum computations. In this regime, several spatially separated parties share a multipartite quantum system, and the most natural set of operations is Local Operations and Classical Communication (LOCC). As a pivotal part in quantum information theory and practice, LOCC has led to many vital protocols such as quantum teleportation. However, designing practical LOCC protocols is challenging due to LOCC’s intractable structure and limitations set by near-term quantum devices. Here we introduce LOCCNet, a machine learning framework facilitating protocol design and optimization for distributed quantum information processing tasks. As applications, we explore various quantum information tasks such as entanglement distillation, quantum state discrimination, and quantum channel simulation. We discover protocols with evident improvements, in particular, for entanglement distillation with quantum states of interest in quantum information. Our approach opens up new opportunities for exploring entanglement and its applications with machine learning, which will potentially sharpen our understanding of the power and limitations of LOCC. An implementation of LOCCNet is available in Paddle Quantum, a quantum machine learning Python package based on PaddlePaddle deep learning platform.
A method to estimate probability of disease and vaccine efficacy from clinical trial immunogenicity data
Authors: Dudášová Julie , Laube Regina , Valiathan Chandni , Wiener Matthew C. , Gheyas Ferdous , Fišer Pavel , Ivanauskaite Justina , Liu Frank , Sachs Jeffrey R. 
Published: November 2021

AbstractVaccine efficacy is often assessed by counting disease cases in a clinical trial. A new quantitative framework proposed here (“PoDBAY,” Probability of Disease Bayesian Analysis), estimates vaccine efficacy (and confidence interval) using immune response biomarker data collected shortly after vaccination. Given a biomarker associated with protection, PoDBAY describes the relationship between biomarker and probability of disease as a sigmoid probability of disease (“PoD”) curve. The PoDBAY framework is illustrated using clinical trial simulations and with data for influenza, zoster, and dengue virus vaccines. The simulations demonstrate that PoDBAY efficacy estimation (which integrates the PoD and biomarker data), can be accurate and more precise than the standard (case-count) estimation, contributing to more sensitive and specific decisions than threshold-based correlate of protection or case-count-based methods. For all three vaccine examples, the PoD fit indicates a substantial association between the biomarkers and protection, and efficacy estimated by PoDBAY from relatively little immunogenicity data is predictive of the standard estimate of efficacy, demonstrating how PoDBAY can provide early assessments of vaccine efficacy. Methods like PoDBAY can help accelerate and economize vaccine development using an immunological predictor of protection. For example, in the current effort against the COVID-19 pandemic it might provide information to help prioritize (rank) candidates both earlier in a trial and earlier in development.
Strong immunogenicity of heterologous prime-boost immunizations with the experimental vaccine GRAd-COV2 and BNT162b2 or ChAdOx1-nCOV19
Authors: Agrati Chiara , Capone Stefania , Castilletti Concetta , Cimini Eleonora , Matusali Giulia , Meschi Silvia , Tartaglia Eleonora , Camerini Roberto , Lanini Simone , Milleri Stefano , Colloca Stefano , Vitelli Alessandra , Folgori Antonella 
Published: November 2021

AbstractHere we report on the humoral and cellular immune response in eight volunteers who autonomously chose to adhere to the Italian national COVID-19 vaccination campaign more than 3 months after receiving a single-administration GRAd-COV2 vaccine candidate in the context of the phase-1 clinical trial. We observed a clear boost of both binding/neutralizing antibodies as well as T-cell responses upon receipt of the heterologous BNT162b2 or ChAdOx1-nCOV19 vaccines. These results, despite the limitation of the small sample size, support the concept that a single dose of an adenoviral vaccine may represent an ideal tool to effectively prime a balanced immune response, which can be boosted to high levels by a single dose of a different vaccine platform.
Imaging intact human organs with local resolution of cellular structures using hierarchical phase-contrast tomography
Authors: Walsh C. L. , Tafforeau P. , Wagner W. L. , Jafree D. J. , Bellier A. , Werlein C. , Kühnel M. P. , Boller E. , Walker-Samuel S. , Robertus J. L. , Long D. A. , Jacob J. , Marussi S. , Brown E. , Holroyd N. , Jonigk D. D. , Ackermann M. , Lee P. D. 
Published: November 2021

AbstractImaging intact human organs from the organ to the cellular scale in three dimensions is a goal of biomedical imaging. To meet this challenge, we developed hierarchical phase-contrast tomography (HiP-CT), an X-ray phase propagation technique using the European Synchrotron Radiation Facility (ESRF)’s Extremely Brilliant Source (EBS). The spatial coherence of the ESRF-EBS combined with our beamline equipment, sample preparation and scanning developments enabled us to perform non-destructive, three-dimensional (3D) scans with hierarchically increasing resolution at any location in whole human organs. We applied HiP-CT to image five intact human organ types: brain, lung, heart, kidney and spleen. HiP-CT provided a structural overview of each whole organ followed by multiple higher-resolution volumes of interest, capturing organotypic functional units and certain individual specialized cells within intact human organs. We demonstrate the potential applications of HiP-CT through quantification and morphometry of glomeruli in an intact human kidney and identification of regional changes in the tissue architecture in a lung from a deceased donor with coronavirus disease 2019 (COVID-19).
Associations between carabid beetles and fungi in the light of 200 years of published literature
Authors: Pozsgai Gábor , Ben Fekih Ibtissem , Kohnen Markus V. , Amrani Said , Bérces Sándor , Fülöp Dávid , Jaber Mohammed Y. M. , Meyling Nicolai Vitt , Ruszkiewicz-Michalska Malgorzata , Pfliegler Walter P. , Sánchez-García Francisco Javier , Zhang Jie , Rensing Christopher , Lövei Gábor L. , You Minsheng 
Published: November 2021

AbstractDescribing and conserving ecological interactions woven into ecosystems is one of the great challenges of the 21st century. Here, we present a unique dataset compiling the biotic interactions between two ecologically and economically important taxa: ground beetles (Coleoptera: Carabidae) and fungi. The resulting dataset contains the carabid-fungus associations collected from 392 scientific publications, 129 countries, mostly from the Palearctic region, published over a period of 200 years. With an updated taxonomy to match the currently accepted nomenclature, 3,378 unique associations among 5,564 records were identified between 1,776 carabid and 676 fungal taxa. Ectoparasitic Laboulbeniales were the most frequent fungal group associated with carabids, especially with Trechinae. The proportion of entomopathogens was low. Three different formats of the data have been provided along with an interactive data digest platform for analytical purposes. Our database summarizes the current knowledge on biotic interactions between insects and fungi, while offering a valuable resource to test large-scale hypotheses on those interactions.
Development of a fully automatic deep learning system for L3 selection and body composition assessment on computed tomography
Authors: Ha Jiyeon , Park Taeyong , Kim Hong-Kyu , Shin Youngbin , Ko Yousun , Kim Dong Wook , Sung Yu Sub , Lee Jiwoo , Ham Su Jung , Khang Seungwoo , Jeong Heeryeol , Koo Kyoyeong , Lee Jeongjin , Kim Kyung Won 
Published: November 2021

AbstractAs sarcopenia research has been gaining emphasis, the need for quantification of abdominal muscle on computed tomography (CT) is increasing. Thus, a fully automated system to select L3 slice and segment muscle in an end-to-end manner is demanded. We aimed to develop a deep learning model (DLM) to select the L3 slice with consideration of anatomic variations and to segment cross-sectional areas (CSAs) of abdominal muscle and fat. Our DLM, named L3SEG-net, was composed of a YOLOv3-based algorithm for selecting the L3 slice and a fully convolutional network (FCN)-based algorithm for segmentation. The YOLOv3-based algorithm was developed via supervised learning using a training dataset (n = 922), and the FCN-based algorithm was transferred from prior work. Our L3SEG-net was validated with internal (n = 496) and external validation (n = 586) datasets. Ground truth L3 level CT slice and anatomic variation were identified by a board-certified radiologist. L3 slice selection accuracy was evaluated by the distance difference between ground truths and DLM-derived results. Technical success for L3 slice selection was defined when the distance difference was < 10 mm. Overall segmentation accuracy was evaluated by CSA error and DSC value. The influence of anatomic variations on DLM performance was evaluated. In the internal and external validation datasets, the accuracy of automatic L3 slice selection was high, with mean distance differences of 3.7 ± 8.4 mm and 4.1 ± 8.3 mm, respectively, and with technical success rates of 93.1% and 92.3%, respectively. However, in the subgroup analysis of anatomic variations, the L3 slice selection accuracy decreased, with distance differences of 12.4 ± 15.4 mm and 12.1 ± 14.6 mm, respectively, and with technical success rates of 67.2% and 67.9%, respectively. The overall segmentation accuracy of abdominal muscle areas was excellent regardless of anatomic variation, with CSA errors of 1.38–3.10 cm2. A fully automatic system was developed for the selection of an exact axial CT slice at the L3 vertebral level and the segmentation of abdominal muscle areas.
Selenium-enriched Bacillus subtilis yb-114246 improved growth and immunity of broiler chickens through modified ileal bacterial composition
Authors: Yang Jiajun , Wang Jing , Huang Kehe , Liu Qingxin , GuofangLiu  , Xu Xiaozhou , Zhang Hao , Zhu Mengling 
Published: November 2021

AbstractHere, a Selenium-enriched Bacillus subtilis (SEBS) strain was generated and supplemented to broiler chickens’ diet, and the impact in ileum bacterial microbiome, immunity and body weight were assessed. In a nutshell, five hundred 1-old old chicken were randomly divided into five groups: control, inorganic Se, Bacillus subtilis (B. subtilis), SEBS, and antibiotic, and colonization with B. subtilis and SEBS in the gastrointestinal tract (GIT) were measured by fluorescence in situ hybridization (FISH) assay and quantitative real-time polymerase chain reaction (qPCR). In summary, Chicks fed SEBS or B. subtilis had higher body weight than the control chicks or those given inorganic Se. SEBS colonized in distal segments of the ileum improved bacterial diversity, reduced the endogenous pathogen burden and increased the number of Lactobacillus sp. in the ileal mucous membrane. Species of unclassified Lachnospiraceae, uncultured Anaerosporobacter, Peptococcus, Lactobacillus salivarius, and Ruminococcaceae_UCG-014, and unclassified Butyricicoccus in the ileal mucous membrane played a key role in promoting immunity. Inorganic Se supplementation also improved bacterial composition of ileal mucous membranes, but to a less extent. In conclusion, SEBS improved performance and immunity of broiler chickens through colonization and modulation of the ileal mucous membrane microbiome.
Intelligent energy optimization in park-wide farming considering user’s preferences
Authors: Jiangzhou Cheng , Zhiyou Niu 
Published: November 2021

AbstractWith the development of park-level agricultural, agricultural production and household electricity fusion, it is of great significance to promote users to actively respond to power consumption plan based on their own habits. In this paper, a multi-objective household intelligent power consumption optimization model is proposed from two aspects of economy and comfort. Firstly, the operating constraints of interruptible loads and non-interruptible loads were established based on the working characteristics of various household appliances. Then, the expenditure model was constructed to take into account the electricity sales situation of surplus electricity generated by photovoltaic, and a three-layer index system quantifying the influence of user preference on comfort level was constructed. The preference coefficient was determined by analytic hierarchy process, which was used to construct the users’ comfort level model. Finally, the multi-objective particle swarm optimization algorithm was applied to obtain optimization results. Considering the seasonal difference, the simulation showed that this model minimized the expenditure and increased the comfort level during summer and winter by 26.0% and 27.5% respectively.
Crowdsourcing and machine learning approaches for extracting entities indicating potential foodborne outbreaks from social media
Authors: Tao Dandan , Zhang Dongyu , Hu Ruofan , Rundensteiner Elke , Feng Hao 
Published: November 2021

AbstractFoodborne outbreaks are a serious but preventable threat to public health that often lead to illness, loss of life, significant economic loss, and the erosion of consumer confidence. Understanding how consumers respond when interacting with foods, as well as extracting information from posts on social media may provide new means of reducing the risks and curtailing the outbreaks. In recent years, Twitter has been employed as a new tool for identifying unreported foodborne illnesses. However, there is a huge gap between the identification of sporadic illnesses and the early detection of a potential outbreak. In this work, the dual-task BERTweet model was developed to identify unreported foodborne illnesses and extract foodborne-illness-related entities from Twitter. Unlike previous methods, our model leveraged the mutually beneficial relationships between the two tasks. The results showed that the F1-score of relevance prediction was 0.87, and the F1-score of entity extraction was 0.61. Key elements such as time, location, and food detected from sentences indicating foodborne illnesses were used to analyze potential foodborne outbreaks in massive historical tweets. A case study on tweets indicating foodborne illnesses showed that the discovered trend is consistent with the true outbreaks that occurred during the same period.
Expression of L-type amino acid transporter 1 is a poor prognostic factor for Non-Hodgkin’s lymphoma
Authors: Jigjidkhorloo Narangerel , Kanekura Kohsuke , Matsubayashi Jun , Akahane Daigo , Fujita Koji , Oikawa Keiki , Kurata Atsushi , Takanashi Masakatsu , Endou Hitoshi , Nagao Toshitaka , Gotoh Akihiko , Norov Oyundelger , Kuroda Masahiko 
Published: November 2021

AbstractL-type neutral amino acid transporter 1 (LAT1) is a heterodimeric membrane transport protein involved in neutral amino acid transport. LAT1 is highly expressed in various malignant solid tumors and plays an essential role in cell proliferation. However, its role in malignant lymphoma remains unknown. Here, we evaluated LAT1 expression level in tissues from 138 patients with Non-Hodgkin lymphoma (NHL). Overexpression of LAT1 was confirmed in all types of NHL and we found that there is a significant correlation between the level of LAT1 expression and lymphoma grade. The LAT1 expression was higher in aggressive types of lymphomas when compared with static types of lymphomas, suggesting that active tumor proliferation requires nutrient uptake via LAT1. The expression level of LAT1 was inversely correlated with patients’ survival span. Furthermore, pharmacological inhibition of LAT1 by a specific inhibitor JPH203 inhibits lymphoma cell growth. In conclusion, our study demonstrated that LAT1 expression can be used as a prognostic marker for patients with NHL and targeting LAT1 by JPH203 can be a novel therapeutic modality for NHL.