bluuebunny/crossref_metadata_2025 huggingface dataset:
Naturally occurring fire coral clones demonstrate a genetic and environmental basis of microbiome composition
Authors: Dubé C. E. , Ziegler M. , Mercière A. , Boissin E. , Planes S. , Bourmaud C. A. -F. , Voolstra C. R.
Published: November 2021

Coral microbiomes are critical to holobiont functioning, but much remains to be understood about how prevailing environment and host genotype affect microbial communities in ecosystems. Resembling human identical twin studies, we examined bacterial community differences of naturally occurring fire coral clones within and between contrasting reef habitats to assess the relative contribution of host genotype and environment to microbiome structure. Bacterial community composition of coral clones differed between reef habitats, highlighting the contribution of the environment. Similarly, but to a lesser extent, microbiomes varied across different genotypes in identical habitats, denoting the influence of host genotype. Predictions of genomic function based on taxonomic profiles suggest that environmentally determined taxa supported a functional restructuring of the microbial metabolic network. In contrast, bacteria determined by host genotype seemed to be functionally redundant. Our study suggests microbiome flexibility as a mechanism of environmental adaptation with association of different bacterial taxa partially dependent on host genotype.
Slow oxidation of magnetite nanoparticles elucidates the limits of the Verwey transition
Authors: Kim Taehun , Sim Sangwoo , Lim Sumin , Patino Midori Amano , Hong Jaeyoung , Lee Jisoo , Hyeon Taeghwan , Shimakawa Yuichi , Lee Soonchil , Attfield J. Paul , Park Je-Geun
Published: November 2021

Magnetite (Fe3O4) is of fundamental importance for the Verwey transition near TV = 125 K, below which a complex lattice distortion and electron orders occur. The Verwey transition is suppressed by chemical doping effects giving rise to well-documented first and second-order regimes, but the origin of the order change is unclear. Here, we show that slow oxidation of monodisperse Fe3O4 nanoparticles leads to an intriguing variation of the Verwey transition: an initial drop of TV to a minimum at 70 K after 75 days and a followed recovery to 95 K after 160 days. A physical model based on both doping and doping-gradient effects accounts quantitatively for this evolution between inhomogeneous to homogeneous doping regimes. This work demonstrates that slow oxidation of nanoparticles can give exquisite control and separation of homogeneous and inhomogeneous doping effects on the Verwey transition and offers opportunities for similar insights into complex electronic and magnetic phase transitions in other materials.
SPINDOC binds PARP1 to facilitate PARylation
Authors: Yang Fen , Chen Jianji , Liu Bin , Gao Guozhen , Sebastian Manu , Jeter Collene , Shen Jianjun , Person Maria D. , Bedford Mark T.
Published: November 2021

SPINDOC is tightly associated with the histone H3K4me3 effector protein SPIN1. To gain a better understanding of the biological roles of SPINDOC, we identified its interacting proteins. Unexpectedly, SPINDOC forms two mutually exclusive protein complexes, one with SPIN1 and the other with PARP1. Consistent with its ability to directly interact with PARP1, SPINDOC expression is induced by DNA damage, likely by KLF4, and recruited to DNA lesions with dynamics that follows PARP1. In SPINDOC knockout cells, the levels of PARylation are reduced, in both the absence and presence of DNA damage. The SPINDOC/PARP1 interaction promotes the clearance of PARP1 from damaged DNA, and also impacts the expression of known transcriptional targets of PARP1. To address the in vivo roles of SPINDOC in PARP1 regulation, we generate SPINDOC knockout mice, which are viable, but slightly smaller than their wildtype counterparts. The KO mice display reduced levels of PARylation and, like PARP1 KO mice, are hypersensitive to IR-induced DNA damage. The findings identify a SPIN1-independent role for SPINDOC in the regulation of PARP1-mediated PARylation and the DNA damage response.
Genome-wide profiling in colorectal cancer identifies PHF19 and TBC1D16 as oncogenic super enhancers
Authors: Li Qing-Lan , Lin Xiang , Yu Ya-Li , Chen Lin , Hu Qi-Xin , Chen Meng , Cao Nan , Zhao Chen , Wang Chen-Yu , Huang Cheng-Wei , Li Lian-Yun , Ye Mei , Wu Min
Published: November 2021

Colorectal cancer is one of the most common cancers in the world. Although genomic mutations and single nucleotide polymorphisms have been extensively studied, the epigenomic status in colorectal cancer patient tissues remains elusive. Here, together with genomic and transcriptomic analysis, we use ChIP-Seq to profile active enhancers at the genome wide level in colorectal cancer paired patient tissues (tumor and adjacent tissues from the same patients). In total, we sequence 73 pairs of colorectal cancer tissues and generate 147 H3K27ac ChIP-Seq, 144 RNA-Seq, 147 whole genome sequencing and 86 H3K4me3 ChIP-Seq samples. Our analysis identifies 5590 gain and 1100 lost variant enhancer loci in colorectal cancer, and 334 gain and 121 lost variant super enhancer loci. Multiple key transcription factors in colorectal cancer are predicted with motif analysis and core regulatory circuitry analysis. Further experiments verify the function of the super enhancers governing PHF19 and TBC1D16 in regulating colorectal cancer tumorigenesis, and KLF3 is identified as an oncogenic transcription factor in colorectal cancer. Taken together, our work provides an important epigenomic resource and functional factors for epigenetic studies in colorectal cancer.
Temporal inhibition of chromatin looping and enhancer accessibility during neuronal remodeling
Authors: Chen Dahong , McManus Catherine E. , Radmanesh Behram , Matzat Leah H. , Lei Elissa P.
Published: November 2021

During development, looping of an enhancer to a promoter is frequently observed in conjunction with temporal and tissue-specific transcriptional activation. The chromatin insulator-associated protein Alan Shepard (Shep) promotes Drosophila post-mitotic neuronal remodeling by repressing transcription of master developmental regulators, such as brain tumor (brat), specifically in maturing neurons. Since insulator proteins can promote looping, we hypothesized that Shep antagonizes brat promoter interaction with an as yet unidentified enhancer. Using chromatin conformation capture and reporter assays, we identified two enhancer regions that increase in looping frequency with the brat promoter specifically in pupal brains after Shep depletion. The brat promoters and enhancers function independently of Shep, ruling out direct repression of these elements. Moreover, ATAC-seq in isolated neurons demonstrates that Shep restricts chromatin accessibility of a key brat enhancer as well as other enhancers genome-wide in remodeling pupal but not larval neurons. These enhancers are enriched for chromatin targets of Shep and are located at Shep-inhibited genes, suggesting direct Shep inhibition of enhancer accessibility and gene expression during neuronal remodeling. Our results provide evidence for temporal regulation of chromatin looping and enhancer accessibility during neuronal maturation.
Cancer immune therapy with PD-1-dependent CD137 co-stimulation provides localized tumour killing without systemic toxicity
Authors: Qiao Yunqian , Qiu Yangmin , Ding Jie , Luo Nana , Wang Hao , Ling Xiaomin , Sun Jiya , Wu Zhihai , Wang Yisen , Liu Yanpeng , Guo Feifei , Sun Ta , Shen Wanwan , Zhang Min , Wu Dongdong , Chen Bingliang , Xu Wei , Wang Xuan
Published: November 2021

Expression of the cell surface receptor CD137 has been shown to enhance anti-cancer T cell function via engagement with its natural ligand 4-1BBL. CD137 ligation with engineered ligands has emerged as a cancer immunotherapy strategy, yet clinical development of agonists has been hindered by either toxicity or limited efficacy. Here we show that a CD137/PD-1 bispecific antibody, IBI319, is able to overcome these limitations by coupling CD137 activation to PD-1-crosslinking. In CT26 and MC38 syngeneic mouse tumour models, IBI319 restricts T cell co-stimulation to PD-1-rich microenvironments, such as tumours and tumour-draining lymph nodes, hence systemic (liver) toxicity arising from generalised T cell activation is reduced. Besides limiting systemic T cell co-stimulation, the anti-PD-1 arm of IBI319 also exhibits checkpoint blockade functions, with an overall result of T and NK cell infiltration into tumours. Toxicology profiling in non-human primates shows that IBI319 is a well-tolerated molecule with IgG-like pharmacokinetic properties, thus a suitable candidate for further clinical development.
Focusing the electromagnetic field to 10−6λ for ultra-high enhancement of field-matter interaction
Authors: Chen Xiang-Dong , Wang En-Hui , Shan Long-Kun , Feng Ce , Zheng Yu , Dong Yang , Guo Guang-Can , Sun Fang-Wen
Published: November 2021

Focusing electromagnetic field to enhance the interaction with matter has been promoting researches and applications of nano electronics and photonics. Usually, the evanescent-wave coupling is adopted in various nano structures and materials to confine the electromagnetic field into a subwavelength space. Here, based on the direct coupling with confined electron oscillations in a nanowire, we demonstrate a tight localization of microwave field down to 10−6λ. A hybrid nanowire-bowtie antenna is further designed to focus the free-space microwave to this deep-subwavelength space. Detected by the nitrogen vacancy center in diamond, the field intensity and microwave-spin interaction strength are enhanced by 2.0 × 108 and 1.4 × 104 times, respectively. Such a high concentration of microwave field will further promote integrated quantum information processing, sensing and microwave photonics in a nanoscale system.
Correlation of SARS-CoV-2-breakthrough infections to time-from-vaccine
Authors: Mizrahi Barak , Lotan Roni , Kalkstein Nir , Peretz Asaf , Perez Galit , Ben-Tov Amir , Chodick Gabriel , Gazit Sivan , Patalon Tal
Published: November 2021

The short-term effectiveness of a two-dose regimen of the BioNTech/Pfizer mRNA BNT162b2 severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) vaccine was widely demonstrated. However, long term effectiveness is still unknown. Leveraging the centralized computerized database of Maccabi Healthcare Services (MHS), we assessed the correlation between time-from-vaccine and incidence of breakthrough infection between June 1 and July 27, the date of analysis. After controlling for potential confounders as age and comorbidities, we found a significant 1.51 fold (95% CI, 1.38–1.66) increased risk for infection for early vaccinees compared to those vaccinated later that was similar across all ages groups. The increased risk reached 2.26- fold (95% CI, 1.80–3.01) when comparing those who were vaccinated in January to those vaccinated in April. This preliminary finding of vaccine waning as a factor of time from vaccince should prompt further investigations into long-term protection against different strains.
Electron shelving of a superconducting artificial atom
Authors: Cottet Nathanaël , Xiong Haonan , Nguyen Long B. , Lin Yen-Hsiang , Manucharyan Vladimir E.
Published: November 2021

Interfacing long-lived qubits with propagating photons is a fundamental challenge in quantum technology. Cavity and circuit quantum electrodynamics (cQED) architectures rely on an off-resonant cavity, which blocks the qubit emission and enables a quantum non-demolition (QND) dispersive readout. However, no such buffer mode is necessary for controlling a large class of three-level systems that combine a metastable qubit transition with a bright cycling transition, using the electron shelving effect. Here we demonstrate shelving of a circuit atom, fluxonium, placed inside a microwave waveguide. With no cavity modes in the setup, the qubit coherence time exceeds 50 μs, and the cycling transition’s radiative lifetime is under 100 ns. By detecting a homodyne fluorescence signal from the cycling transition, we implement a QND readout of the qubit and account for readout errors using a minimal optical pumping model. Our result establishes a resource-efficient (cavityless) alternative to cQED for controlling superconducting qubits.
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

The 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

The 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

The 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

Quantitative 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

Autism 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

Distributed 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

Vaccine 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

Here 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

Imaging 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

Describing 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

As 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

Here, 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

With 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

Foodborne 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

L-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.
Lactate activates hypothalamic POMC neurons by intercellular signaling
Authors: Órdenes P. , Villar P. S. , Tarifeño-Saldivia E. , Salgado M. , Elizondo-Vega R. , Araneda Ricardo C. , García-Robles María A.
Published: November 2021

Previous studies indicate that the activity of hypothalamic POMC neurons can be regulated by glucose via intracellular mechanisms, but its regulation by lactate is poorly understood. In addition to its energetic role, lactate acts as a signaling molecule. In this study, we evaluated the function and location of the lactate receptor, hydroxycarboxylic acid receptor 1 (HCAR1). We used a conditional genetic approach to label POMC neurons and evaluated their sensitivity to lactate using patch-clamp recordings. l-Lactate and 3-chloro-5-hydroxybenzoic acid (3Cl-HBA), HCAR1 specific agonist depolarized POMC neurons and the increase in excitability was abolished by pertussis toxin (PTX), indicating the involvement of Gαi/o-protein-coupled receptors. In addition, the depolarization of a subset of POMC neurons was sensitive to α-cyano-4-hydroxycinnamate (4-CIN), a lactate transporter blocker, suggesting that the depolarization induced by l-lactate can also occur by direct intracellular action. Surprisingly, HCAR1 was not detected in POMC neurons, but instead localized in astrocytes. These results suggest a new lactate-mediated mechanism for astrocyte-neuron intercellular communication.
Local activation of α2 adrenergic receptors is required for vagus nerve stimulation induced motor cortical plasticity
Authors: Tseng Ching-Tzu , Gaulding Solomon J. , Dancel Canice Lei E. , Thorn Catherine A.
Published: November 2021

Vagus nerve stimulation (VNS) paired with rehabilitation training is emerging as a potential treatment for improving recovery of motor function following stroke. In rats, VNS paired with skilled forelimb training results in significant reorganization of the somatotopic cortical motor map; however, the mechanisms underlying this form of VNS-dependent plasticity remain unclear. Recent studies have shown that VNS-driven cortical plasticity is dependent on noradrenergic innervation of the neocortex. In the central nervous system, noradrenergic α2 receptors (α2-ARs) are widely expressed in the motor cortex and have been critically implicated in synaptic communication and plasticity. In current study, we examined whether activation of cortical α2-ARs is necessary for VNS-driven motor cortical reorganization to occur. Consistent with previous studies, we found that VNS paired with motor training enlarges the map representation of task-relevant musculature in the motor cortex. Infusion of α2-AR antagonists into M1 blocked VNS-driven motor map reorganization from occurring. Our results suggest that local α2-AR activation is required for VNS-induced cortical reorganization to occur, providing insight into the mechanisms that may underlie the neuroplastic effects of VNS therapy.
Analysis of the effectiveness of face-coverings on the death ratio of COVID-19 using machine learning
Authors: Lafzi Ali , Boodaghi Miad , Zamani Siavash , Mohammadshafie Niyousha , Hasti Veeraraghava Raju
Published: November 2021

The recent outbreak of the COVID-19 led to death of millions of people worldwide. To stave off the spread of the virus, the authorities in the US employed different strategies, including the mask mandate order issued by the states’ governors. In the current work, we defined a parameter called average death ratio as the monthly average of the number of daily deaths to the monthly average number of daily cases. We utilized survey data to quantify people’s abidance by the mask mandate order. Additionally, we implicitly addressed the extent to which people abide by the mask mandate order, which may depend on some parameters such as population, income, and education level. Using different machine learning classification algorithms, we investigated how the decrease or increase in death ratio for the counties in the US West Coast correlates with the input parameters. The results showed that for the majority of counties, the mask mandate order decreased the death ratio, reflecting the effectiveness of such a preventive measure on the West Coast. Additionally, the changes in the death ratio demonstrated a noticeable correlation with the socio-economic condition of each county. Moreover, the results showed a promising classification accuracy score as high as 90%.
Assessing short-term risk of ischemic stroke in relation to all prescribed medications
Authors: Janszky Imre , Vardaxis Ioannis , Lindqvist Bo Henry , Horn Jens Wilhelm , Brumpton Ben Michael , Strand Linn Beate , Bakken Inger Johanne , Alsnes Ingvild Vatten , Romundstad Pål Richard , Ljung Rickard , Mukamal Kenneth Jay , Sen Abhijit
Published: November 2021

We examined the short-term risk of stroke associated with drugs prescribed in Norway or Sweden in a comprehensive, hypothesis-free manner using comprehensive nation-wide data. We identified 27,680 and 92,561 cases with a first ischemic stroke via the patient- and the cause-of-death registers in Norway (2004–2014) and Sweden (2005–2014), respectively, and linked these data to prescription databases. A case-crossover design was used that compares the drugs dispensed within 1 to 14 days before the date of ischemic stroke occurrence with those dispensed 29 to 42 days before the index event. A Bolasso approach, a version of the Lasso regression algorithm, was used to select drugs that acutely either increase or decrease the apparent risk of ischemic stroke. Application of the Bolasso regression algorithm selected 19 drugs which were associated with increased risk for ischemic stroke and 11 drugs with decreased risk in both countries. Morphine in combination with antispasmodics was associated with a particularly high risk of stroke (odds ratio 7.09, 95% confidence intervals 4.81–10.47). Several potentially intriguing associations, both within and across pharmacological classes, merit further investigation in focused, follow-up studies.
The hump-shaped effect of plant functional diversity on the biological control of a multi-species pest community
Authors: Gardarin Antoine , Pigot Justine , Valantin-Morison Muriel
Published: November 2021

Plant taxonomic and functional diversity promotes interactions at higher trophic levels, but the contribution of functional diversity effects to multitrophic interactions and ecosystem functioning remains unclear. We investigated this relationship in a factorial field experiment comparing the effect of contrasting plant communities on parasitism rates in five herbivore species. We used a mechanistic trait-matching approach between plant and parasitoids to determine the amount of nectar available and accessible to parasitoids. This trait-matching approach best explained the rates of parasitism of each herbivorous species, confirming the predominant role of mass-ratio effects. We found evidence for an effect of functional diversity only in analyses considering the ability of plant communities to support the parasitism of all herbivores simultaneously. Multi-species parasitism was maximal at intermediate levels of functional diversity. Plant specific richness had a negligible influence relative to functional metrics. Plant communities providing large amounts of accessible nectar and with intermediate levels of functional diversity were found to be the most likely to enhance the conservation biological control of diverse crop herbivores.
Tryptophan-enriched diet or 5-hydroxytryptophan supplementation given in a randomized controlled trial impacts social cognition on a neural and behavioral level
Authors: Zamoscik V. , Schmidt S. N. L. , Bravo R. , Ugartemendia L. , Plieger T. , Rodríguez A. B. , Reuter M. , Kirsch P.
Published: November 2021

Understanding of emotions and intentions are key processes in social cognition at which serotonin is an important neuromodulator. Its precursor is the essential amino acid tryptophan (TRP). Reduced TRP availability leads to weaker impulse control ability and higher aggression, while TRP supplementation promotes confidence. In a double-blind placebo-controlled fMRI study with 77 healthy adults, we investigated the influence of a 4 week TRP enriched diet and an acute 5-hydroxytryptophan (5-HTP) intake on two social-cognitive tasks, a moral evaluation and an emotion recognition task. With 5-HTP, immoral behavior without negative consequences was rated as more reprehensible. Additionally, during story reading, activation in insula and supramarginal gyrus was increased after TRP intake. No significant effects of TRP on emotion recognition were identified for the whole sample. Importantly, emotion recognition ability decreased with age which was for positive emotions compensated by TRP. Since the supramarginal gyrus is associated with empathy, pain and related information integration results could be interpreted as reflecting stricter evaluation of negative behavior due to better integration of information. Improved recognition of positive emotions with TRP in older participants supports the use of a TRP-rich diet to compensate for age related decline in social-cognitive processes.
The association of widowhood and living alone with depression among older adults in India
Authors: Srivastava Shobhit , Debnath Paramita , Shri Neha , Muhammad T.
Published: November 2021

Widowhood is a catastrophic event at any stage of life for the surviving partner particularly in old age, with serious repercussions on their physical, economic, and emotional well-being. This study investigates the association of marital status and living arrangement with depression among older adults. Additionally, the study aims to evaluate the effects of factors such as socio-economic conditions and other health problems contributing to the risk of depression among older adults in India. This study utilizes data from the nationally representative Longitudinal Ageing Study in India (LASI-2017–18). The effective sample size was 30,639 older adults aged 60 years and above. Descriptive statistics and bivariate analysis have been performed to determine the prevalence of depression. Further, binary logistic regression analysis was conducted to study the association between marital status and living arrangement on depression among older adults in India. Overall, around nine percent of the older adults suffered from depression. 10.3% of the widowed (currently married: 7.8%) and 13.6% of the older adults who were living alone suffered from depression. Further, 8.4% of the respondents who were co-residing with someone were suffering from depression. Widowed older adults were 34% more likely to be depressed than currently married counterparts [AOR: 1.34, CI 1.2–1.49]. Similarly, respondents who lived alone were 16% more likely to be depressed compared to their counterparts [AOR: 1.16; CI 1.02, 1.40]. Older adults who were widowed and living alone were 56% more likely to suffer from depression [AOR: 1.56; CI 1.28, 1.91] in reference to older adults who were currently married and co-residing. The study shows vulnerability of widowed older adults who are living alone and among those who had lack of socio-economic resources and face poor health status. The study can be used to target outreach programs and service delivery for the older adults who are living alone or widowed and suffering from depression.
Carboxyl-richness controls organic carbon preservation during coprecipitation with iron (oxyhydr)oxides in the natural environment
Authors: Curti Lisa , Moore Oliver W. , Babakhani Peyman , Xiao Ke-Qing , Woulds Clare , Bray Andrew W. , Fisher Ben J. , Kazemian Majid , Kaulich Burkhard , Peacock Caroline L.
Published: November 2021

The coprecipitation of organic carbon with iron minerals is important for its preservation in soils and sediments, but the mechanisms for carbon-iron interactions and thus the controls on organic carbon cycling are far from understood. Here we coprecipitate carboxylic acids with iron (oxyhydr)oxide ferrihydrite and use near-edge X-ray absorption fine structure spectroscopy and wet chemical treatments to determine the relationship between sequestration mechanism and organic carbon stability against its release and chemical oxidative remineralisation. We show that organic carbon sequestration, stabilisation and persistence increase with an increasing number of carboxyl functional groups. We suggest that carboxyl-richness provides an important control on organic carbon preservation in the natural environment. Our work offers a mechanistic basis for understanding the stability and persistence of organic carbon in soils and sediments, which might be used to develop an overarching relationship between organic functional group-richness, mineral interactions and organic carbon preservation in the Earth system.