bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanism of keyhole pore formation in metal additive manufacturing
Authors: Wang Lu , Zhang Yanming , Chia Hou Yi , Yan Wentao 
Published: January 2022

AbstractDuring metal additive manufacturing, the porosity of the as-built part deteriorates the mechanical property and even hinders the further application of metal additive manufacturing. Particularly, the mechanisms of keyhole pores associated with the keyhole fluctuation are not fully understood. To reveal the mechanisms of the keyhole pores formation, we adopt a multiphysics thermal-fluid flow model incorporating heat transfer, liquid flow, metal evaporation, Marangoni effect, and Darcy’s law to simulate the keyhole pore formation process, and the results are validated with the in situ X-ray images. The simulation results present the instant bubble formation due to the keyhole instability and motion of the instant bubble pinning on the solidification front. Furthermore, comparing the keyhole pore formation under different laser scanning speeds shows that the keyhole pore is sensitive to the manufacturing parameters. Additionally, the simulation under a low ambient pressure shows the feasibility of improving the keyhole stability to reduce and even avoid the formation of keyhole pores.
Supramolecular gating of guest release from cucurbit[7]uril using de novo design
Authors: Lambert Hugues , Castillo Bonillo Alvaro , Zhu Qiang , Zhang Yong-Wei , Lee Tung-Chun 
Published: January 2022

AbstractHerein we computationally explore the modulation of the release kinetics of an encapsulated guest molecule from the cucurbit[7]uril (CB7) cavity by ligands binding to the host portal. We uncovered a correlation between the ligand-binding affinity with CB7 and the guest residence time, allowing us to rapidly predict the release kinetics through straightforward energy minimization calculations. These high-throughput predictions in turn enable a Monte-Carlo Tree Search (MCTS) to de novo design a series of cap-shaped ligand molecules with large binding affinities and boosting guest residence times by up to 7 orders of magnitude. Notably, halogenated aromatic compounds emerge as top-ranking ligands. Detailed modeling suggests the presence of halogen-bonding between the ligands and the CB7 portal. Meanwhile, the binding of top-ranked ligands is supported by 1H NMR and 2D DOSY-NMR. Our findings open up possibilities in gating of molecular transport through a nanoscale cavity with potential applications in nanopore technology and controlled drug release.
Intriguing magnetoelectric effect in two-dimensional ferromagnetic/perovskite oxide ferroelectric heterostructure
Authors: Li Ping , Zhou Xue-Song , Guo Zhi-Xin 
Published: January 2022

AbstractTwo-dimensional (2D) magnets have broad application prospects in the spintronics, but how to effectively control them with a small electric field is still an issue. Here we propose that 2D magnets can be efficiently controlled in a multiferroic heterostructure composed of 2D magnetic material and perovskite oxide ferroelectric (POF) whose dielectric polarization is easily flipped under a small electric field. We illustrate the feasibility of such strategy in the bilayer CrI3/BiFeO3(001) heterostructure by using the first-principles calculations. Different from the traditional POF multiferroic heterostructures which have strong interface interactions, we find that the interface interaction between CrI3 and BiFeO3(001) is van der Waals type. Whereas, the heterostructure has particular strong magnetoelectric coupling where the bilayer CrI3 can be efficiently switched between ferromagnetic and antiferromagnetic types by the polarized states P↑ and P↓ of BiFeO3(001). We also discover the competing effect between electron doping and the additional electric field on the interlayer exchange coupling interaction of CrI3, which is responsible to the magnetic phase transition. Our results provide a avenue for the tuning of 2D magnets with a small electric field.
A two-way photonic quantum entanglement transfer interface
Authors: Huang Yiwen , Li Yuanhua , Qi Zhantong , Feng Juan , Zheng Yuanlin , Chen Xianfeng 
Published: January 2022

AbstractA quantum interface for two-way entanglement transfer, e.g., between orbital angular momentum degree of freedom in free space and time-energy degree of freedom in optical fibers, provides a way toward establishing entanglement between remote heterogeneous quantum nodes. Here, we experimentally demonstrate this kind of transfer interface by using two interferometric cyclic gates. By using this quantum interface, we perform two-way entanglement transfer for the two degrees of freedom. The results show that the quantum entangled state can be switched back and forth between orbital angular momentum and time-energy degrees of freedom, and the fidelity of the state before and after switching is higher than 90%. Our work demonstrates the feasibility and high performance of our proposed transfer interface, and paves a route toward building a large-scale quantum communication network.
Optimal control of stimulated Raman adiabatic passage in a superconducting qudit
Authors: Zheng Wen , Zhang Yu , Dong Yuqian , Xu Jianwen , Wang Zhimin , Wang Xiaohan , Li Yong , Lan Dong , Zhao Jie , Li Shaoxiong , Tan Xinsheng , Yu Yang 
Published: January 2022

AbstractStimulated Raman adiabatic passage (STIRAP) is a widely used protocol to realize high-fidelity and robust quantum control in various quantum systems. However, further application of this protocol in superconducting qubits is limited by population leakage caused by the only weak anharmonicity. Here, we introduce an optimally controlled shortcut-to-adiabatic (STA) technique to speed-up the STIRAP protocol in a superconducting qudit. By modifying the shapes of the STIRAP pulses, we experimentally realize a fast (32 ns) and high-fidelity (0.996 ± 0.005) quantum state transfer. In addition, we demonstrate that our protocol is robust against control parameter perturbations. Our stimulated Raman shortcut-to-adiabatic passage transition provides an efficient and practical approach for quantum information processing.
Hippo-Yap/Taz signalling in zebrafish regeneration
Authors: Riley Susanna E. , Feng Yi , Hansen Carsten Gram 
Published: January 2022

AbstractThe extent of tissue regeneration varies widely between species. Mammals have a limited regenerative capacity whilst lower vertebrates such as the zebrafish (Danio rerio), a freshwater teleost, can robustly regenerate a range of tissues, including the spinal cord, heart, and fin. The molecular and cellular basis of this altered response is one of intense investigation. In this review, we summarise the current understanding of the association between zebrafish regeneration and Hippo pathway function, a phosphorylation cascade that regulates cell proliferation, mechanotransduction, stem cell fate, and tumorigenesis, amongst others. We also compare this function to Hippo pathway activity in the regenerative response of other species. We find that the Hippo pathway effectors Yap/Taz facilitate zebrafish regeneration and that this appears to be latent in mammals, suggesting that therapeutically promoting precise and temporal YAP/TAZ signalling in humans may enhance regeneration and hence reduce morbidity.
High-throughput platform for yeast morphological profiling predicts the targets of bioactive compounds
Authors: Ohnuki Shinsuke , Ogawa Itsuki , Itto-Nakama Kaori , Lu Fachuang , Ranjan Ashish , Kabbage Mehdi , Gebre Abraham Abera , Yamashita Masao , Li Sheena C. , Yashiroda Yoko , Yoshida Satoshi , Usui Takeo , Piotrowski Jeff S. , Andrews Brenda J. , Boone Charles , Brown Grant W. , Ralph John , Ohya Yoshikazu 
Published: January 2022

AbstractMorphological profiling is an omics-based approach for predicting intracellular targets of chemical compounds in which the dose-dependent morphological changes induced by the compound are systematically compared to the morphological changes in gene-deleted cells. In this study, we developed a reliable high-throughput (HT) platform for yeast morphological profiling using drug-hypersensitive strains to minimize compound use, HT microscopy to speed up data generation and analysis, and a generalized linear model to predict targets with high reliability. We first conducted a proof-of-concept study using six compounds with known targets: bortezomib, hydroxyurea, methyl methanesulfonate, benomyl, tunicamycin, and echinocandin B. Then we applied our platform to predict the mechanism of action of a novel diferulate-derived compound, poacidiene. Morphological profiling of poacidiene implied that it affects the DNA damage response, which genetic analysis confirmed. Furthermore, we found that poacidiene inhibits the growth of phytopathogenic fungi, implying applications as an effective antifungal agent. Thus, our platform is a new whole-cell target prediction tool for drug discovery.
Immune persistence and response to booster dose of Vi-DT vaccine at 27.5 months post-first dose
Authors: Capeding Maria Rosario , Tadesse Birkneh Tilahun , Sil Arijit , Alberto Edison , Kim Deok Ryun , Park Eun Lyeong , Park Ju Yeon , Yang Jae Seung , Eluru Jagadeesh Reddy , Jo Sue-Kyoung , Kim Hun , Yang Seon-Young , Ryu Ji Hwa , Park Hokeun , Shin Jong Hoon , Lee Yoonyeong , Kim Jerome H. , Mojares Zenaida Reynoso , Wartel T. Anh , Sahastrabuddhe Sushant 
Published: January 2022

AbstractVaccination with typhoid conjugate vaccines (TCV) is a major part of typhoid prevention. However, little is known about long-term immune persistence following vaccination with TCVs. In this phase-2, randomized double-blind trial (NCT03527355), 285 children aged 6–23 months were randomized to one of three groups: (1) the group that received a first dose of Vi polysaccharide conjugated to diphtheria-toxoid (Vi-DT) vaccine followed by an “early booster” at 24 weeks, (2) the group that which received a first dose of Vi-DT followed by a “late booster” at 96 or 110 weeks, and (3) comparator group. Safety and immunogenicity of anti-Vi IgG GMTs were assessed at weeks 0, 4, 24, 28, 60, 96, 110, and 114 since the first dose. Here, we describe persistence of immune responses at weeks 60, 96, 110, and 114 post first dose. The anti-Vi IgG seroconversion rate after 27.5 months of follow-up was 88.16% (95% CI: 79.00, 93.64) in late-booster and 94.76% (95% CI: 86.91, 97.88) in early booster Vi-DT groups (p = 0.081). Whereas anti-Vi IgG GMTs were significantly higher in the early booster group (11.95 [95% CI: 9.65, 14.81]) than prebooster GMTs in the late booster group (5.50 [95% CI: 4.44, 6.80], p < 0.0001). GMT in the late booster group significantly increased to 351.76 (95% CI: 265.01, 466.93) (p < 0.0001) when measured 4 weeks after they received their “late-booster” shot. In conclusion, late booster dosing with Vi-DT at 27.5 months post first dose was safe and elicited robust anti-Vi IgG immune responses. Anti-Vi IgG seroconversion rates were persistently comparable in early and late-booster Vi-DT groups.
Pre-existing antibodies directed against a tetramerizing domain enhance the immune response against artificially stabilized soluble tetrameric influenza neuraminidase
Authors: Catani João Paulo Portela , Job Emma R. , Ysenbaert Tine , Smet Anouk , Ray Satyajit , LaRue Lauren , Stegalkina Svetlana , Barro Mario , Vogel Thorsten U. , Saelens Xavier 
Published: January 2022

AbstractThe neuraminidase (NA) is an abundant antigen at the surface of influenza virions. Recent studies have highlighted the immune-protective potential of NA against influenza and defined anti-NA antibodies as an independent correlate of protection. Even though NA head domain changes at a slightly slower pace than hemagglutinin (HA), NA is still subject to antigenic drift, and therefore an NA-based influenza vaccine antigen may have to be updated regularly and thus repeatedly administered. NA is a tetrameric type II membrane protein, which readily dissociates into dimers and monomers when expressed in a soluble form. By using a tetramerizing zipper, such as the tetrabrachion (TB) fromStaphylothermus marinus, it is possible to stabilize soluble NA in its active tetrameric conformation, an imperative for the optimal induction of protective NA inhibitory antibodies. The impact of repetitive immunizations with TB-stabilized antigens on the immunogenicity of soluble TB-stabilized NA is unknown. We demonstrate that TB is immunogenic in mice. Interestingly, preexisting anti-TB antibodies enhance the anti-NA antibody response induced by immunization with TB-stabilized NA. This immune-enhancing effect was transferable by serum and operated independently of activating Fcγ receptors. We also demonstrate that priming with TB-stabilized NA antigens, enhances the NA inhibitory antibody responses against a heterosubtypic TB-stabilized NA. These findings have implications for the clinical development of oligomeric vaccine antigens that are stabilized by a heterologous oligomerizing domain.
Multi-kingdom microbiota analyses identify
bacterial–fungal interactions and biomarkers of colorectal cancer across
cohorts
Authors: Liu Ning-Ning , Jiao Na , Tan Jing-Cong , Wang Ziliang , Wu Dingfeng , Wang An-Jun , Chen Jie , Tao Liwen , Zhou Chenfen , Fang Wenjie , Cheong Io Hong , Pan Weihua , Liao Wanqing , Kozlakidis Zisis , Heeschen Christopher , Moore Geromy G. , Zhu Lixin , Chen Xingdong , Zhang Guoqing , Zhu Ruixin , Wang Hui 
Published: January 2022

AbstractDespite recent progress in our understanding of the association between
the gut microbiome and colorectal cancer (CRC), multi-kingdom gut microbiome
dysbiosis in CRC across cohorts is unexplored. We investigated four-kingdom
microbiota alterations using CRC metagenomic datasets of 1,368 samples from 8
distinct geographical cohorts. Integrated analysis identified 20 archaeal, 27
bacterial, 20 fungal and 21 viral species for each single-kingdom diagnostic model.
However, our data revealed superior diagnostic accuracy for models constructed with
multi-kingdom markers, in particular the addition of fungal species. Specifically,
16 multi-kingdom markers including 11 bacterial, 4 fungal and 1 archaeal feature,
achieved good performance in diagnosing patients with CRC (area under the receiver
operating characteristic curve (AUROC) = 0.83) and maintained
accuracy across 3 independent cohorts. Coabundance analysis of the ecological
network revealed associations between bacterial and fungal species, such as
Talaromyces islandicus and Clostridium saccharobutylicum. Using metagenome shotgun
sequencing data, the predictive power of the microbial functional potential was
explored and elevated D-amino acid metabolism and butanoate metabolism were observed
in CRC. Interestingly, the diagnostic model based on functional EggNOG genes
achieved high accuracy (AUROC = 0.86). Collectively, our findings
uncovered CRC-associated microbiota common across cohorts and demonstrate the
applicability of multi-kingdom and functional markers as CRC diagnostic tools and,
potentially, as therapeutic targets for the treatment of CRC.
p3k14c, a synthetic global database of archaeological radiocarbon dates
Authors: Bird Darcy , Miranda Lux , Vander Linden Marc , Robinson Erick , Bocinsky R. Kyle , Nicholson Chris , Capriles José M. , Finley Judson Byrd , Gayo Eugenia M. , Gil Adolfo , d’Alpoim Guedes Jade , Hoggarth Julie A. , Kay Andrea , Loftus Emma , Lombardo Umberto , Mackie Madeline , Palmisano Alessio , Solheim Steinar , Kelly Robert L. , Freeman Jacob 
Published: January 2022

AbstractArchaeologists increasingly use large radiocarbon databases to model prehistoric human demography (also termed paleo-demography). Numerous independent projects, funded over the past decade, have assembled such databases from multiple regions of the world. These data provide unprecedented potential for comparative research on human population ecology and the evolution of social-ecological systems across the Earth. However, these databases have been developed using different sample selection criteria, which has resulted in interoperability issues for global-scale, comparative paleo-demographic research and integration with paleoclimate and paleoenvironmental data. We present a synthetic, global-scale archaeological radiocarbon database composed of 180,070 radiocarbon dates that have been cleaned according to a standardized sample selection criteria. This database increases the reusability of archaeological radiocarbon data and streamlines quality control assessments for various types of paleo-demographic research. As part of an assessment of data quality, we conduct two analyses of sampling bias in the global database at multiple scales. This database is ideal for paleo-demographic research focused on dates-as-data, bayesian modeling, or summed probability distribution methodologies.
Asymmetry between right and left fundus images identified using convolutional neural networks
Authors: Kang Tae Seen , Kim Bum Jun , Nam Ki Yup , Lee Seongjin , Kim Kyonghoon , Lee Woong-sub , Kim Jinhyun , Han Yong Seop 
Published: January 2022

AbstractWe analyzed fundus images to identify whether convolutional neural networks (CNNs) can discriminate between right and left fundus images. We gathered 98,038 fundus photographs from the Gyeongsang National University Changwon Hospital, South Korea, and augmented these with the Ocular Disease Intelligent Recognition dataset. We created eight combinations of image sets to train CNNs. Class activation mapping was used to identify the discriminative image regions used by the CNNs. CNNs identified right and left fundus images with high accuracy (more than 99.3% in the Gyeongsang National University Changwon Hospital dataset and 91.1% in the Ocular Disease Intelligent Recognition dataset) regardless of whether the images were flipped horizontally. The depth and complexity of the CNN affected the accuracy (DenseNet121: 99.91%, ResNet50: 99.86%, and VGG19: 99.37%). DenseNet121 did not discriminate images composed of only left eyes (55.1%, p = 0.548). Class activation mapping identified the macula as the discriminative region used by the CNNs. Several previous studies used the flipping method to augment data in fundus photographs. However, such photographs are distinct from non-flipped images. This asymmetry could result in undesired bias in machine learning. Therefore, when developing a CNN with fundus photographs, care should be taken when applying data augmentation with flipping.
Programmable wavelength filter with double ring loaded MZI
Authors: Wang Mi , Chen Xiangfeng , Khan Umar , Bogaerts Wim 
Published: January 2022

AbstractWe propose a novel filter circuit that incorporates a double ring resonator with a balanced Mach–Zehnder interferometer (MZI). The circuit has a response equivalent to a conventional ring loaded MZI filter, but with added flexibility in terms of configurability. The second-order filter can also be cascaded to realize higher-order filters. The circuit incorporates a two-stage input and output coupler to further reduce the effect of dispersion. A combination of local and global optimization strategies to program the filter, using tailored objective functions, have been tested in simulation and experiments. To our best knowledge, this is the first time a global optimization strategy is directly used in ARMA filter synthesis and simulation without any additional requirement. We further extend the optimization strategy into experiments and demonstrated its use in practical case for programmable filter circuits.
Perception of body size and body dissatisfaction in adults
Authors: Gruszka Wojciech , Owczarek Aleksander J. , Glinianowicz Mateusz , Bąk-Sosnowska Monika , Chudek Jerzy , Olszanecka-Glinianowicz Magdalena 
Published: January 2022

AbstractSelf-perception of body size seems to be not always in line with clinical definitions of normal weight, overweight and obesity according to Word Health Organization classification. The effect of self-perception of body size disturbances and body dissatisfaction may be the development of eating disorders, such as anorexia nervosa or binge eating disorder—a major risk factor of obesity development. Therefore, the study aimed to assess separately the perception of weight status and body size as well as body dissatisfaction in adults with normal weight, overweight and obesity. The study included 744 adults (452 women; 35.9 ± 12.4 years; 21 underweight, 326 normal weight, 221 overweight, 176 obese) referred to Metabolic Management Center and volunteers. Body size perception and body dissatisfaction were assessed based on Stunkards’ Figure Rating Scale (FRS). Additionally, participants’ were asked: ‘Do you think you are: underweight/normal weight/overweight/obese?’ to assess perception of weight status. Participants’ weight and height were measured to calculate body mass index (BMI) after completing the FRS. Individuals within the overweight BMI range have rated themselves as underweight (1.4%), normal weight (30.8%) and obese (2.8%). Also individuals within the obesity BMI range have rated themselves as normal weight (2.6%), and overweight (41.6%). Compatibility of self-assessment of weight status with BMI category according to the measured values was moderate—Kappa coefficient was 0.59 (95% CI: 0.54–0.64). Underestimation of weight status was significantly more common among men than women. There were statistically significant differences in the distribution of body dissatisfaction according to the weight in both women and men. Normal-weight subjects less often than overweight and obese were dissatisfied with their own body size. The degree of body dissatisfaction was greater among women than among men. Adults subjects frequently underestimate their own weight status and body size. Women with overweight and obesity more often than men are dissatisfied with their own body size.
Noncanonical function of the Sex lethal gene controls the protogyny phenotype in Drosophila melanogaster
Authors: Seong Ki-Hyeon , Kang Siu 
Published: January 2022

AbstractDrosophila melanogaster females eclose on average 4 h faster than males owing to sexual differences in the pupal period, referred to as the protogyny phenotype. Here, to elucidate the mechanism underlying the protogyny phenotype, we used our newly developed Drosophila Individual Activity Monitoring and Detecting System (DIAMonDS) that detects the precise timing of both pupariation and eclosion in individual flies. Although sex transformation induced by tra-2, tra alteration, or msl-2 knockdown-mediated disruption of dosage compensation showed no effect on the protogyny phenotype, stage-specific whole-body knockdown and mutation of the Drosophila master sex switch gene, Sxl, was found to disrupt the protogyny phenotype. Thus, Sxl establishes the protogyny phenotype through a noncanonical pathway in D. melanogaster.