bluuebunny/crossref_metadata_2025_split huggingface dataset:
Centrifugal multimaterial 3D printing of multifunctional heterogeneous objects
Authors: Cheng Jianxiang , Wang Rong , Sun Zechu , Liu Qingjiang , He Xiangnan , Li Honggeng , Ye Haitao , Yang Xingxin , Wei Xinfeng , Li Zhenqing , Jian Bingcong , Deng Weiwei , Ge Qi 
Published: December 2022

AbstractThere are growing demands for multimaterial three-dimensional (3D) printing to manufacture 3D object where voxels with different properties and functions are precisely arranged. Digital light processing (DLP) is a high-resolution fast-speed 3D printing technology suitable for various materials. However, multimaterial 3D printing is challenging for DLP as the current multimaterial switching methods require direct contact onto the printed part to remove residual resin. Here we report a DLP-based centrifugal multimaterial (CM) 3D printing method to generate large-volume heterogeneous 3D objects where composition, property and function are programmable at voxel scale. Centrifugal force enables non-contact, high-efficiency multimaterial switching, so that the CM 3D printer can print heterogenous 3D structures in large area (up to 180 mm × 130 mm) made of materials ranging from hydrogels to functional polymers, and even ceramics. Our CM 3D printing method exhibits excellent capability of fabricating digital materials, soft robots, and ceramic devices.
Deconstructing body axis morphogenesis in zebrafish embryos using robot-assisted tissue micromanipulation
Authors: Özelçi Ece , Mailand Erik , Rüegg Matthias , Oates Andrew C. , Sakar Mahmut Selman 
Published: December 2022

AbstractClassic microsurgical techniques, such as those used in the early 1900s by Mangold and Spemann, have been instrumental in advancing our understanding of embryonic development. However, these techniques are highly specialized, leading to issues of inter-operator variability. Here we introduce a user-friendly robotic microsurgery platform that allows precise mechanical manipulation of soft tissues in zebrafish embryos. Using our platform, we reproducibly targeted precise regions of tail explants, and quantified the response in real-time by following notochord and presomitic mesoderm (PSM) morphogenesis and segmentation clock dynamics during vertebrate anteroposterior axis elongation. We find an extension force generated through the posterior notochord that is strong enough to buckle the structure. Our data suggest that this force generates a unidirectional notochord extension towards the tailbud because PSM tissue around the posterior notochord does not let it slide anteriorly. These results complement existing biomechanical models of axis elongation, revealing a critical coupling between the posterior notochord, the tailbud, and the PSM, and show that somite patterning is robust against structural perturbations.
Simultaneous profiling of histone modifications and DNA methylation via nanopore sequencing
Authors: Yue Xue , Xie Zhiyuan , Li Moran , Wang Kai , Li Xiaojing , Zhang Xiaoqing , Yan Jian , Yin Yimeng 
Published: December 2022

AbstractThe interplay between histone modifications and DNA methylation drives the establishment and maintenance of the cellular epigenomic landscape, but it remains challenging to investigate the complex relationship between these epigenetic marks across the genome. Here we describe a nanopore-sequencing-based-method, nanoHiMe-seq, for interrogating the genome-wide localization of histone modifications and DNA methylation from single DNA molecules. nanoHiMe-seq leverages a nonspecific methyltransferase to exogenously label adenine bases proximal to antibody-targeted modified nucleosomes in situ. The labelled adenines and the endogenous methylated CpG sites are simultaneously detected on individual nanopore reads using a hidden Markov model, which is implemented in the nanoHiMe software package. We demonstrate the utility, robustness and sensitivity of nanoHiMe-seq by jointly profiling DNA methylation and histone modifications at low coverage depths, concurrently determining phased patterns of DNA methylation and histone modifications, and probing the intrinsic connectivity between these epigenetic marks across the genome.
Gut microbiota as an antioxidant system in centenarians associated with high antioxidant activities of gut-resident Lactobacillus
Authors: Wu Lei , Xie Xinqiang , Li Ying , Liang Tingting , Zhong Haojie , Yang Lingshuang , Xi Yu , Zhang Jumei , Ding Yu , Wu Qingping 
Published: December 2022

AbstractThe gut microbiota plays an important role in human health and longevity, and the gut microbiota of centenarians shows unique characteristics. Nowadays, most microbial research on longevity is usually limited to the bioinformatics level, lacking validating information on culturing functional microorganisms. Here, we combined metagenomic sequencing and large-scale in vitro culture to reveal the unique gut microbial structure of the world’s longevity town—Jiaoling, China, centenarians and people of different ages. Functional strains were isolated and screened in vitro, and the possible relationship between gut microbes and longevity was explored and validated in vivo. 247 healthy Cantonese natives of different ages participated in the study, including 18 centenarians. Compared with young adults, the gut microbiota of centenarians exhibits higher microbial diversity, xenobiotics biodegradation and metabolism, oxidoreductases, and multiple species (the potential probiotics Lactobacillus, Akkermansia, the methanogenic Methanobrevibacter, gut butyrate-producing members Roseburia, and SCFA-producing species uncl Clostridiales, uncl Ruminococcaceae) known to be beneficial to host metabolism. These species are constantly changing with age. We also isolated 2055 strains from these samples by large-scale in vitro culture, most of which were detected by metagenomics, with clear complementarity between the two approaches. We also screened an age-related gut-resident Lactobacillus with independent intellectual property rights, and its metabolite (L-ascorbic acid) and itself have good antioxidant effects. Our findings underscore the existence of age-related trajectories in the human gut microbiota, and that distinct gut microbiota and gut-resident as antioxidant systems may contribute to health and longevity.
Electric-controlled tunable thermal switch based on Janus monolayer MoSSe
Authors: Wei Donghai , Zhou E , Zheng Xiong , Wang Huimin , Shen Chen , Zhang Hongbin , Qin Zhenzhen , Qin Guangzhao 
Published: December 2022

AbstractThe high-performance, wide-range tunable thermal switches play a significant role in the thermal management, high-power-density intelligent devices, energy systems, etc. However, traditional thermal switch components, such as thermal diodes, suffer from poor stability, small adjustability, low time efficiency, and difficult implementation. Herein, we propose the superior electric-controlled thermal switch (ECTS) based on Janus monolayer MoSSe. The high-effective and asymmetric regulation of the thermal conductivity driven by electric field demonstrates a wide-range adjustable thermal switch ratio, where the peak value reaches 2.09 under the electric field of 0.04 VÅ−1. The underlying mechanism is revealed by electronic structures that the interactions between electrons and phonons are renormalized due to the electric field driving charge density redistribution, which ultimately modulates the phonon anharmonicity. The high-efficiency adjustable ECTS component is expected to provide new inspiration for next-generation thermal management and information processing.
Germline genetic variation and predicting immune checkpoint inhibitor induced toxicity
Authors: Chin Ik Shin , Khan Aman , Olsson-Brown Anna , Papa Sophie , Middleton Gary , Palles Claire 
Published: December 2022

AbstractImmune checkpoint inhibitor (ICI) therapy has revolutionised the treatment of various cancer types. ICIs reinstate T-cell function to elicit an anti-cancer immune response. The resulting immune response can however have off-target effects which manifest as autoimmune type serious immune-related adverse events (irAE) in ~10–55% of patients treated. It is currently challenging to predict both who will experience irAEs and to what severity. Identification of patients at high risk of serious irAE would revolutionise patient care. While the pathogenesis driving irAE development is still unclear, host genetic factors are proposed to be key determinants of these events. This review presents current evidence supporting the role of the host genome in determining risk of irAE. We summarise the spectrum and timing of irAEs following treatment with ICIs and describe currently reported germline genetic variation associated with expression of immuno-modulatory factors within the cancer immunity cycle, development of autoimmune disease and irAE occurrence. We propose that germline genetic determinants of host immune function and autoimmune diseases could also explain risk of irAE development. We also endorse genome-wide association studies of patients being treated with ICIs to identify genetic variants that can be used in polygenic risk scores to predict risk of irAE.
Identification of microbes coexisting with Legionella spp. in bathwaters
Authors: Okunaga Masaki , Kushiro Kenta , Horie Ryohei , Kondo Akihiro , Abe Takashi 
Published: December 2022

AbstractIn Japan, bathwaters are a potential source of legionellosis; therefore, the bathwater in public facilities must be regularly tested for Legionella spp. Currently, Legionella spp. is detected using the culture method, which is time-consuming and has limited accuracy. Moreover, the reproductive environment of Legionella spp. in bathwater remains unclear. Here, we investigated the environment in which Legionella spp. reproduce by analyzing the bathwater microbiota and its relationship with Legionella spp. We identified the microbiota of 112 bathwater samples collected from bathing facilities by sequencing 16S and 18S rRNA genes. Differences in the microbiota were observed between samples that tested positive and negative for Legionella spp., according to 16S rRNA sequencing and culture methods. Methyloversatilis, Cupriavidus, Phenylobacterium, Vermamoeba, and Aspidisca were highly correlated with Legionella spp. Our results support the development of strategies against legionellosis and elucidate the relationships between Legionella spp. and the coexisting microbiota in various environments.
Immobilization of silver nanoparticles on cellulose nanofibrils incorporated into nanofiltration membrane for enhanced desalination performance
Authors: He Ming , Li Wei-Dong , Chen Jia-Chuan , Zhang Zhi-Guo , Wang Xiao-Fa , Yang Gui-Hua 
Published: December 2022

AbstractNanofiltration (NF) membranes circumventing global water scarcity with excellent separation and antibacterial performances are highly desirable for efficient water treatment but remain a great challenge. Herein, a nanofiltration membrane was fabricated by in situ immobilizing silver nanoparticles (AgNPs) on sulfated cellulose nanofibril incorporated during interfacial polymerization. AgNPs were confirmed to be uniformly distributed and in situ grown on sulfated cellulose nanofibril (SCNF) due to its abundant sulfate and hydroxyl groups by mixing them with anhydrous piperazine solution as inorganic phase and homophenyl chloride n-hexane solution as the organic phase on the surface of a polyethersulfone microporous membrane. The attributes of SCNF, excellent hydrophilicity, and highly negative charges enhanced both the rejection and water permeability. As the SCNF charge increased, the roughness of SCNF increased and the contact angle decreased, and the maximum values were 203 nm and 17.67°, respectively. Among all the composite NF membranes, H-SCNF/Ag-0.01 had better rejection of Na2SO4and NaCl, with a maximum rejection of 97.11% and 32.55%, respectively. Meanwhile, it also maintained high water permeability. Antibacterial experiments indicated that the composite NF membrane had effective inhibition againstEscherichia coliand exhibited an expected slow-release capability of Ag+, which made it have long-term antibacterial properties. It was estimated that the antibacterial effect could last for 90 days. This work demonstrated that AgNPs in situ immobilization on SCNF could be used as promising nanofillers for designing advanced functional NF membranes.
A speech corpus of Quechua Collao for automatic dimensional emotion recognition
Authors: Paccotacya-Yanque Rosa Y. G. , Huanca-Anquise Candy A. , Escalante-Calcina Judith , Ramos-Lovón Wilber R. , Cuno-Parari Álvaro E. 
Published: December 2022

AbstractAutomatic speech emotion recognition is an important research topic for human-computer interaction and affective computing. Over ten million people speak the Quechua language throughout South America, and one of the most known variants is the Quechua Collao one. However, this language can be considered a low resource for machine emotion recognition, creating a barrier for Quechua speakers who want to use this technology. Therefore, the contribution of this work is a 15 hours speech corpus in Quechua Collao, which is made publicly available to the research community. The corpus was created from a set of words and sentences explicitly collected for this task, divided into nine categorical emotions: happy, sad, bored, fear, sleepy, calm, excited, angry, and neutral. The annotation was performed on a 5-value discrete scale according to 3 dimensions: valence, arousal, and dominance. To demonstrate the usefulness of the corpus, we have performed speech emotion recognition using machine learning methods and neural networks.
Transition1x - a dataset for building generalizable reactive machine learning potentials
Authors: Schreiner Mathias , Bhowmik Arghya , Vegge Tejs , Busk Jonas , Winther Ole 
Published: December 2022

AbstractMachine Learning (ML) models have, in contrast to their usefulness in molecular dynamics studies, had limited success as surrogate potentials for reaction barrier search. This is primarily because available datasets for training ML models on small molecular systems almost exclusively contain configurations at or near equilibrium. In this work, we present the dataset Transition1x containing 9.6 million Density Functional Theory (DFT) calculations of forces and energies of molecular configurations on and around reaction pathways at the ωB97x/6–31 G(d) level of theory. The data was generated by running Nudged Elastic Band (NEB) with DFT on 10k organic reactions of various types while saving intermediate calculations. We train equivariant graph message-passing neural network models on Transition1x and cross-validate on the popular ANI1x and QM9 datasets. We show that ML models cannot learn features in transition state regions solely by training on hitherto popular benchmark datasets. Transition1x is a new challenging benchmark that will provide an important step towards developing next-generation ML force fields that also work far away from equilibrium configurations and reactive systems.
A Raman spectral reference library of potential anthropogenic and biological ocean polymers
Authors: Miller Emily A. , Yamahara Kevan M. , French Chris , Spingarn Neil , Birch James M. , Van Houtan Kyle S. 
Published: December 2022

AbstractMicroplastics have been extensively documented in marine ecosystems and food webs with devastating impacts. To solve this global crisis, identifying the polymer composition is key for resolving the material origin, geographic source, and ecosystem life cycle of ocean plastics. Visually based techniques, importantly, are not diagnostic. Raman spectroscopy is an increasingly preferred identification method for its accuracy and reduced likelihood of misinterpretation, though it can be inaccessible due to cost of paywalled spectral libraries and availability of relevant polymer spectra for comparison. Here, we provide an open-access reference library of high-quality, broad-spectrum Raman spectra of major polymer categories germane to marine environments. The library includes high-quality spectra from: (a) pristine anthropogenic polymers newly sourced from manufacturers (n = 40), (b) weathered anthropogenic polymers collected from used consumer, beachcast, agricultural, and fishery sources (n = 22), and (c) biological polymers representing diverse marine taxa, trophic levels, and tissues (n = 17). We hope this reference library can help this rapidly expanding scientific community and facilitate progress in the global plastic pollution crisis.
Chromosome-level genome assembly of the Siberian chipmunk (Tamias sibiricus)
Authors: Li Ran , Zhang Mingfei , Cha Muha , Xiang Jishan , Yi Xianfeng 
Published: December 2022

AbstractTamias sibiricus is regarded as one predominant scatter-hoarder that stores their food items both in small scattered caches and underground larder-hoards. This unique behavior, though providing essential seed dispersal services for many plant species worldwide, relies highly on accurate spatial memory and acute sense of olfaction. Here, we assembled a chromosome-scale genome of T. sibiricus using Illumina sequencing, PacBio sequencing and chromosome structure capture technique. The genome was 2.64 Gb in size with scaffold N50 length of 172.61 Mb. A total of 2.59 Gb genome data was anchored and orientated onto 19 chromosomes (ranging from 28.70 to 222.90 Mb) with a mounting rate of up to 98.03%. Meanwhile, 25,311 protein-coding genes were predicted with an average gene length of 32,936 bp, and 94.73% of these genes were functionally annotated. This reference genome will be a valuable resource for in-depth studies on basic biological possess and environmental adaptation of the Siberian chipmunk, as well as promoting comparative genomic analyses with other species within Rodentia.
Synergistic effects of defocus-incorporated multiple segments and atropine in slowing the progression of myopia
Authors: Huang Zhu , Chen Xu-Fei , He Ting , Tang Yun , Du Chi-Xin 
Published: December 2022

AbstractMyopia is a leading cause of visual impairment in young people worldwide. It sometimes increases the risk of blindness and reduces life quality. Previous reports have revealed the treatment effects of defocus-incorporated multiple segments (DIMS) and topical atropine (ATP) on myopia control. However, no study has evaluated these two interventions together. In this retrospective study, we aimed to determine whether the combination of DIMS lenses and 0.01% ATP can slow the progression of myopia compared with DIMS lenses or single vision (SV) lenses alone. We included 107 children with myopia who were treated with DIMS and 0.01% ATP combination (DIMS + ATP group), DIMS monotherapy (DIMS group), or a control group (SV group). We compared treatment effects among three groups in axial length and myopia progression. After a 1-year follow-up, the DIMS + ATP group showed a smaller change in axial length and myopia progression than the DIMS and SV groups (P < 0.05). Hence, combination treatment with DIMS and 0.01% ATP might be a better choice for children with myopia.
Quantum computing and preconditioners for hydrological linear systems
Authors: Golden John , O’Malley Daniel , Viswanathan Hari 
Published: December 2022

AbstractModeling hydrological fracture networks is a hallmark challenge in computational earth sciences. Accurately predicting critical features of fracture systems, e.g. percolation, can require solving large linear systems far beyond current or future high performance capabilities. Quantum computers can theoretically bypass the memory and speed constraints faced by classical approaches, however several technical issues must first be addressed. Chief amongst these difficulties is that such systems are often ill-conditioned, i.e. small changes in the system can produce large changes in the solution, which can slow down the performance of linear solving algorithms. We test several existing quantum techniques to improve the condition number, but find they are insufficient. We then introduce the inverse Laplacian preconditioner, which improves the scaling of the condition number of the system from O(N) to $$O(\sqrt{N})$$

O
(

N

)

and admits a quantum implementation. These results are a critical first step in developing a quantum solver for fracture systems, both advancing the state of hydrological modeling and providing a novel real-world application for quantum linear systems algorithms.
Transition in vaginal Lactobacillus species during pregnancy and prediction of preterm birth in Korean women
Authors: You Young-Ah , Park Sunwha , Kim Kwangmin , Kwon Eun Jin , Hur Young Min , Kim Soo Min , Lee Gain , Ansari AbuZar , Park Junhyung , Kim Young Ju 
Published: December 2022

AbstractThe predominance of vaginal Lactobacillus species, specifically L. crispatus, is important for pregnancy maintenance, but varies by race. The composition of the vaginal microbiome can affect susceptibility to adverse pregnancy outcomes. We performed 16S rRNA gene amplicon sequencing on vaginal swabs taken from Korean pregnant women. Here, we report the transition of Lactobacillus spp. in samples of full-term birth (FTB) collected longitudinally in the second and third trimesters of pregnancy in a cohort study (n = 23) and their association with Lactobacillus abundance and preterm birth (PTB) in a case–control study (n = 200). Lactobacillus species, which was dominant in FTB samples including those that received interventions in the second trimester, did not change until 37 weeks of gestation. However, L. crispatus was replaced by other Lactobacillus species after 37 weeks. The PTB risk showed a closer association with the Lactobacillus abundance than with community state type determined by Lactobacillus species. PTB was associated with less than 90% of Lactobacillus abundance and an increase in Ureplasma parvum in the second trimester. Thus, the vaginal microbiome may change in preparation for childbirth in response to multiple intrinsic factors after 37 weeks of gestation. Monitoring the Lactobacillus abundance may help improve the reliability of microbial PTB biomarkers.
Impairment in novelty-promoted memory via behavioral tagging and capture before apparent memory loss in a knock-in model of Alzheimer’s disease
Authors: Broadbelt Tabitha , Mutlu-Smith Menekse , Carnicero-Senabre Daniel , Saido Takaomi C. , Saito Takashi , Wang Szu-Han 
Published: December 2022

AbstractAlzheimer’s disease (AD) is associated with cognitive impairments and age-dependent memory deficits which have been studied using genetic models of AD. Whether the processes for modulating memory persistence are more vulnerable to the influence of amyloid pathology than the encoding and consolidation of the memory remains unclear. Here, we investigated whether early amyloid pathology would affect peri-learning novelty in promoting memory, through a process called behavioral tagging and capture (BTC). AppNL-G-F/NL-G-F mice and wild-type littermates were trained in an appetitive delayed matching-to-place (ADMP) task which allows for the assessment of peri-learning novelty in facilitating memory. The results show that novelty enabled intermediate-term memory in wild-type mice, but not in AppNL-G-F/NL-G-F mice in adulthood. This effect preceded spatial memory impairment in the ADMP task seen in middle age. Other memory tests in the Barnes maze, Y-maze, novel object or location recognition tasks remained intact. Together, memory modulation through BTC is impaired before apparent deficits in learning and memory. Relevant biological mechanisms underlying BTC and the implication in AD are discussed.