bluuebunny/crossref_metadata_2025_split huggingface dataset:
smiFISH and embryo segmentation for single-cell multi-gene RNA quantification in arthropods
Authors: Calvo Llilians , Ronshaugen Matthew , Pettini Tom 
Published: March 2021

AbstractRecently, advances in fluorescent in-situ hybridization techniques and in imaging technology have enabled visualization and counting of individual RNA molecules in single cells. This has greatly enhanced the resolution in our understanding of transcriptional processes. Here, we adapt a recently published smiFISH protocol (single-molecule inexpensive fluorescent in-situ hybridization) to whole embryos across a range of arthropod model species, and also to non-embryonic tissues. Using multiple fluorophores with distinct spectra and white light laser confocal imaging, we simultaneously detect and separate single RNAs from up to eight different genes in a whole embryo. We also combine smiFISH with cell membrane immunofluorescence, and present an imaging and analysis pipeline for 3D cell segmentation and single-cell RNA counting in whole blastoderm embryos. Finally, using whole embryo single-cell RNA count data, we propose two alternative single-cell variability measures to the commonly used Fano factor, and compare the capacity of these three measures to address different aspects of single-cell expression variability.
Pol α-primase dependent nuclear localization of the mammalian CST complex
Authors: Kelich Joseph M. , Papaioannou Harry , Skordalakes Emmanuel 
Published: March 2021

AbstractThe human CST complex composed of CTC1, STN1, and TEN1 is critically involved in telomere maintenance and homeostasis. Specifically, CST terminates telomere extension by inhibiting telomerase access to the telomeric overhang and facilitates lagging strand fill in by recruiting DNA Polymerase alpha primase (Pol α-primase) to the telomeric C-strand. Here we reveal that CST has a dynamic intracellular localization that is cell cycle dependent. We report an increase in nuclear CST several hours after the initiation of DNA replication, followed by exit from the nucleus prior to mitosis. We identify amino acids of CTC1 involved in Pol α-primase binding and nuclear localization. We conclude, the CST complex does not contain a nuclear localization signal (NLS) and suggest that its nuclear localization is reliant on Pol α-primase. Hypomorphic mutations affecting CST nuclear import are associated with telomere syndromes and cancer, emphasizing the important role of this process in health.
Structural basis of the dynamic human CEACAM1 monomer-dimer equilibrium
Authors: Gandhi Amit K. , Sun Zhen-Yu J. , Kim Walter M. , Huang Yu-Hwa , Kondo Yasuyuki , Bonsor Daniel A. , Sundberg Eric J. , Wagner Gerhard , Kuchroo Vijay K. , Petsko Gregory A. , Blumberg Richard S. 
Published: March 2021

AbstractHuman (h) carcinoembryonic antigen-related cell adhesion molecule 1 (CEACAM1) function depends upon IgV-mediated homodimerization or heterodimerization with host ligands, including hCEACAM5, hTIM-3, PD-1, and a variety of microbial pathogens. However, there is little structural information available on how hCEACAM1 transitions between monomeric and dimeric states which in the latter case is critical for initiating hCEACAM1 activities. We therefore mutated residues within the hCEACAM1 IgV GFCC′ face including V39, I91, N97, and E99 and examined hCEACAM1 IgV monomer-homodimer exchange using differential scanning fluorimetry, multi-angle light scattering, X-ray crystallography and/or nuclear magnetic resonance. From these studies, we describe hCEACAM1 homodimeric, monomeric and transition states at atomic resolution and its conformational behavior in solution through NMR assignment of the wildtype (WT) hCEACAM1 IgV dimer and N97A mutant monomer. These studies reveal the flexibility of the GFCC’ face and its important role in governing the formation of hCEACAM1 dimers and selective heterodimers.
CAP2 is a regulator of actin pointed end dynamics and myofibrillogenesis in cardiac muscle
Authors: Colpan Mert , Iwanski Jessika , Gregorio Carol C. 
Published: March 2021

AbstractThe precise assembly of actin-based thin filaments is crucial for muscle contraction. Dysregulation of actin dynamics at thin filament pointed ends results in skeletal and cardiac myopathies. Here, we discovered adenylyl cyclase-associated protein 2 (CAP2) as a unique component of thin filament pointed ends in cardiac muscle. CAP2 has critical functions in cardiomyocytes as it depolymerizes and inhibits actin incorporation into thin filaments. Strikingly distinct from other pointed-end proteins, CAP2’s function is not enhanced but inhibited by tropomyosin and it does not directly control thin filament lengths. Furthermore, CAP2 plays an essential role in cardiomyocyte maturation by modulating pre-sarcomeric actin assembly and regulating α-actin composition in mature thin filaments. Identification of CAP2’s multifunctional roles provides missing links in our understanding of how thin filament architecture is regulated in striated muscle and it reveals there are additional factors, beyond Tmod1 and Lmod2, that modulate actin dynamics at thin filament pointed ends.
Inside-out chicken enteroids with leukocyte component as a model to study host–pathogen interactions
Authors: Nash Tessa J. , Morris Katrina M. , Mabbott Neil A. , Vervelde Lonneke 
Published: March 2021

AbstractMammalian three-dimensional (3D) enteroids mirror in vivo intestinal organisation and are powerful tools to investigate intestinal cell biology and host–pathogen interactions. We have developed complex multilobulated 3D chicken enteroids from intestinal embryonic villi and adult crypts. These avian enteroids develop optimally in suspension without the structural support required to produce mammalian enteroids, resulting in an inside-out enteroid conformation with media-facing apical brush borders. Histological and transcriptional analyses show these enteroids comprise of differentiated intestinal epithelial cells bound by cell-cell junctions, and notably, include intraepithelial leukocytes and an inner core of lamina propria leukocytes. The advantageous polarisation of these enteroids has enabled infection of the epithelial apical surface withSalmonellaTyphimurium, influenza A virus andEimeria tenellawithout the need for micro-injection. We have created a comprehensive model of the chicken intestine which has the potential to explore epithelial and leukocyte interactions and responses in host–pathogen, food science and pharmaceutical research.
The structure of a major surface antigen SAG19 from Eimeria tenella unifies the Eimeria SAG family
Authors: Ramly Nur Zazarina , Dix Samuel R. , Ruzheinikov Sergey N. , Sedelnikova Svetlana E. , Baker Patrick J. , Chow Yock-Ping , Tomley Fiona M. , Blake Damer P. , Wan Kiew-Lian , Nathan Sheila , Rice David W. 
Published: March 2021

AbstractIn infections by apicomplexan parasites includingPlasmodium,Toxoplasma gondii, andEimeria, host interactions are mediated by proteins including families of membrane-anchored cysteine-rich surface antigens (SAGs) and SAG-related sequences (SRS).Eimeria tenellacauses caecal coccidiosis in chickens and has a SAG family with over 80 members making up 1% of the proteome. We have solved the structure of a representativeE. tenellaSAG, EtSAG19, revealing that, despite a low level of sequence similarity, the entireEimeriaSAG family is unified by its three-layer αβα fold which is related to that of the CAP superfamily. Furthermore, sequence comparisons show that theEimeriaSAG fold is conserved in surface antigens of the human coccidial parasiteCyclospora cayetanensisbut this fold is unrelated to that of the SAGs/SRS proteins expressed in other apicomplexans includingPlasmodiumspecies and the cyst-forming coccidiaToxoplasma gondii,Neospora caninumandBesnoitia besnoiti. However, despite having very different structures, Consurf analysis showed thatEimeriaSAG andToxoplasmaSRS families each exhibit marked hotspots of sequence hypervariability that map to their surfaces distal to the membrane anchor. This suggests that the primary and convergent purpose of the different structures is to provide a platform onto which sequence variability can be imposed.
Evolutionary histories and antimicrobial resistance in Shigella flexneri and Shigella sonnei in Southeast Asia
Authors: Chung The Hao , Bodhidatta Ladaporn , Pham Duy Thanh , Mason Carl J. , Ha Thanh Tuyen , Voong Vinh Phat , Turner Paul , Hem Sopheak , Dance David A. B. , Newton Paul N. , Phetsouvanh Rattanaphone , Davong Viengmon , Thwaites Guy E. , Thomson Nicholas R. , Baker Stephen , Rabaa Maia A. 
Published: March 2021

AbstractConventional disease surveillance for shigellosis in developing country settings relies on serotyping and low-resolution molecular typing, which fails to contextualise the evolutionary history of the genus. Here, we interrogated a collection of 1,804 Shigella whole genome sequences from organisms isolated in four continental Southeast Asian countries (Thailand, Vietnam, Laos, and Cambodia) over three decades to characterise the evolution of both S. flexneri and S. sonnei. We show that S. sonnei and each major S. flexneri serotype are comprised of genetically diverse populations, the majority of which were likely introduced into Southeast Asia in the 1970s–1990s. Intranational and regional dissemination allowed widespread propagation of both species across the region. Our data indicate that the epidemiology of S. sonnei and the major S. flexneri serotypes were characterised by frequent clonal replacement events, coinciding with changing susceptibility patterns against contemporaneous antimicrobials. We conclude that adaptation to antimicrobial pressure was pivotal to the recent evolutionary trajectory of Shigella in Southeast Asia.
Oncolytic adeno-immunotherapy modulates the immune system enabling CAR T-cells to cure pancreatic tumors
Authors: Rosewell Shaw Amanda , Porter Caroline E. , Yip Tiffany , Mah Way-Champ , McKenna Mary K. , Dysthe Matthew , Jung Youngrock , Parihar Robin , Brenner Malcolm K. , Suzuki Masataka 
Published: March 2021

AbstractHigh expression levels of human epidermal growth factor receptor 2 (HER2) have been associated with poor prognosis in patients with pancreatic adenocarcinoma (PDAC). However, HER2-targeting immunotherapies have been unsuccessful to date. Here we increase the breadth, potency, and duration of anti-PDAC HER2-specific CAR T-cell (HER2.CART) activity with an oncolytic adeno-immunotherapy that produces cytokine, immune checkpoint blockade, and a safety switch (CAdTrio). Combination treatment with CAdTrio and HER2.CARTs cured tumors in two PDAC xenograft models and produced durable tumor responses in humanized mice. Modifications to the tumor immune microenvironment contributed to the antitumor activity of our combination immunotherapy, as intratumoral CAdTrio treatment induced chemotaxis to enable HER2.CART migration to the tumor site. Using an advanced PDAC model in humanized mice, we found that local CAdTrio treatment of primary tumor stimulated systemic host immune responses that repolarized distant tumor microenvironments, improving HER2.CART anti-tumor activity. Overall, our data demonstrate that CAdTrio and HER2.CARTs provide complementary activities to eradicate metastatic PDAC and may represent a promising co-operative therapy for PDAC patients.
Long-term stability in γ-CsPbI3 perovskite via an ultraviolet-curable polymer network
Authors: Cho Nam-Kwang , Na Hyun-Jae , Yoo Jeeyoung , Kim Youn Sang 
Published: March 2021

AbstractBlack-colored (α, γ-phase) CsPbI3perovskites have a small bandgap and excellent absorption properties in the visible light regime, making them attractive for solar cells. However, their long-term stability in ambient conditions is limited. Here, we demonstrate a strategy to improve structural and electrical long-term stability in γ-CsPbI3by the use of an ultraviolet-curable polyethylene glycol dimethacrylate (PEGDMA) polymer network. Oxygen lone pair electrons from the PEGDMA are found to capture Cs+and Pb2+cations, improving crystal growth of γ-CsPbI3around PEGDMA. In addition, the PEGDMA polymer network strongly contributes to maintaining the black phase of γ-CsPbI3for more than 35 days in air, and an optimized perovskite film retained ~90% of its initial electrical properties under red, green, and blue light irradiation.
Black Sea hydroclimate and coupled hydrology was strongly controlled by high-latitude glacial climate dynamics
Authors: Wegwerth Antje , Plessen Birgit , Kleinhanns Ilka C. , Arz Helge W. 
Published: March 2021

AbstractThe Black Sea experienced pronounced millennial-scale changes in temperature and rainfall during the last glacial coinciding with Dansgaard-Oeschger cycles. However, little is known regarding the amount and sources of freshwater reaching this inland basin. Here, we present detailed ostracod δ18O data from the glacial Black Sea showing subdued Dansgaard-Oeschger cyclicity and four prominent longer-term saw-tooth shaped Bond-like cycles. We propose that the δ18Oostracods signature primarily reflects changes in the atmospheric circulation in response to the waxing and waning Eurasian Ice Sheet. The millennial-scale ice sheet variations likely resulted not only in latitudinal migrations of atmospheric frontal systems but also in shifts of dominant moisture sources for the Black Sea. Heavier isotopic precipitation arrived from the North Atlantic-Mediterranean realm during the warmer interstadials and lighter isotopic precipitation from the Eurasian continental interior during the colder stadials. The subdued Dansgaard-Oeschger variability likely reflects an integrated precipitation signal additionally affected by the long mixing times of the large Black Sea volume up to 1,500 years as suggested from hydrologic-isotope-balance modelling.
Lanthanide-based bis-(3,5-dicarboxy-phenyl)terephthalamide metal–organic frameworks: slow relaxation of magnetization and detection of trace Fe2+ and Fe3+
Authors: Lin Qingfang , Xie Wen , Zong Zhihui , Liu Zicheng , Sun Yuqing , Liang Lili 
Published: March 2021

{[Dy2(BDPT)1.5(DMF)4]·H2O}n (1) and [Sm2(BDPT)1.5(DMF)4]n (2) were prepared with highly sensitive fluorescent detection of trace Fe2+ and Fe3+. 1 exhibits weak antiferromagnetic interactions with signature of SMM behavior.
High expression of COL5A2, a member of COL5 family, indicates the poor survival and facilitates cell migration in gastric cancer
Authors: Tan Yuen , Chen Qingchuan , Xing Yao , Zhang Chao , Pan Siwei , An Wen , Xu Huimian 
Published: March 2021

Abstract
Background: Gastric cancer (GC) metastasis determines the prognosis of patients, and exploring the molecular mechanism of GC metastasis is expected to provide a theoretical basis for clinical treatment. Recent studies have shown that extracellular matrix protein is closely related to GC metastasis. The present study aimed to explore the expression profile and role of COL5A2, as an extracellular matrix protein, in GC.
Methods: The expression, overall survival, and progression-free survival data of COL5 family members were extracted from The Cancer Genome Atlas (TCGA) database, respectively. Weighted gene co-expression network analysis of the GSE62229 database was performed out to identify modules and associated genes.
Results: COL5A2 was selected as our research target in the TCGA database, and was also verified in the GSE62229 and GSE15459 datasets. COL5A2 was up-regulated in GC tissues by paraffin immunohistochemistry and RT-qPCR. The prognosis of patients with low COL5A2 expression was better than that of patients with high COL5A2 expression. Scratch and migration experiments showed that knockdown of COL5A2 decreased the migration ability of gastric cancer cells compared with the control group. In vivo, mice with tail vein injection COL5A2 knockdown had fewer and smaller metastatic nodules in liver. GSEA results showed that the TCGA and GSE62229 samples were significantly enriched in several well-known cancer-related pathways, such as the TGF-β, MAPK, and JAK2 signaling pathways.
Conclusion: COL5A2 was most closely related to advanced GC among COL5 family members. High COL5A2 expression is associated with a poor prognosis, and may be a novel therapeutic target for GC.
A spatial attentive and temporal dilated (SATD) GCN for skeleton‐based action recognition
Authors: Zhang Jiaxu , Ye Gaoxiang , Tu Zhigang , Qin Yongtao , Qin Qianqing , Zhang Jinlu , Liu Jun 
Published: March 2021

AbstractCurrent studies have shown that the spatial‐temporal graph convolutional network (ST‐GCN) is effective for skeleton‐based action recognition. However, for the existing ST‐GCN‐based methods, their temporal kernel size is usually fixed over all layers, which makes them cannot fully exploit the temporal dependency between discontinuous frames and different sequence lengths. Besides, most of these methods use average pooling to obtain global graph feature from vertex features, resulting in losing much fine‐grained information for action classification. To address these issues, in this work, the authors propose a novel spatial attentive and temporal dilated graph convolutional network (SATD‐GCN). It contains two important components, that is, a spatial attention pooling module (SAP) and a temporal dilated graph convolution module (TDGC). Specifically, the SAP module can select the human body joints which are beneficial for action recognition by a self‐attention mechanism and alleviates the influence of data redundancy and noise. The TDGC module can effectively extract the temporal features at different time scales, which is useful to improve the temporal perception field and enhance the robustness of the model to different motion speed and sequence length. Importantly, both the SAP module and the TDGC module can be easily integrated into the ST‐GCN‐based models, and significantly improve their performance. Extensive experiments on two large‐scale benchmark datasets, that is, NTU‐RGB + D and Kinetics‐Skeleton, demonstrate that the authors’ method achieves the state‐of‐the‐art performance for skeleton‐based action recognition.
Design and voice‐based control of a nasal endoscopic surgical robot
Authors: He Yucheng , Deng Zhen , Zhang Jianwei 
Published: March 2021

AbstractIn traditional nasal surgery, surgeons are prone to fatigue and jitter by holding the endoscope for a long‐time. Some complex operations require assistant surgeon to assist with holding the endoscope. To address the above problems, the authors design a remote centre of motion based nasal robot, and propose a voice‐based robot control method. First, through the operation space analysis of nasal surgery, the design scheme of the robot based on RCM mechanism is proposed. On this basis, the design parameters of the robot are analysed to complete the entire design of robot. Then, considering that the surgeon's hands are occupied by surgical instruments during complex surgical operations, a voice‐based robot control method is proposed. This method obtains direction instructions from surgeons by analysing the movement of the endoscopic image. Afterward, a commercial speech recognition interface is used to realise the offline grammar controlwords lib compatible with both Chinese and English, and the overall strategy of robot control is proposed. Finally, an experimental platform for virtual robot control is established, and the voice‐based robot control experiment is performed. The results show that the proposed voice‐based control method is feasible, and it provides guidance for the subsequent development and control of the actual robot system.
Robust design and evaluation of phase codes for radar performance optimization with a finite alphabet constraint
Authors: Lu Jianhua , Fan Tao , Yu Xianxiang , Li Yunpeng , Cui Wei , Tang Bin 
Published: March 2021

AbstractThis letter considers the robust design of radar waveform with discrete phase codes under constant modulus constraint to enhance target detectability. To solve the resultant max‐min non‐convex optimization problem, a robust discrete phase coding algorithm via iterative technology (R‐DPCA‐IT) is developed which monotonically improves the worst‐case SNR and has an upper bound ensuring to converge a finite value. At each iteration, the original multidimensional quadratic optimization problem is turned into multiple one‐dimensional optimization problems solved globally via line search. Finally, the computational time and objective value of the proposed algorithm are assessed in comparison with the existing methods.
Corner reflector tag with RCS frequency coding by dielectric resonators
Authors: Alhaj Abbas Ali , El‐Absi Mohammed , Abuelhaija Ashraf , Solbach Klaus , Kaiser Thomas 
Published: March 2021

AbstractFor a novel indoor‐localization system, chipless tags with high retro‐directive radar cross‐section (RCS) under wide‐angle incidence are required as fixed landmarks. Tags based on dielectric resonators (DRs) were proposed to provide identification by resonance frequency coding. To achieve a satisfactory read range for the localization system, the low RCS levels of these tags require a major boost. A solution was found by adopting the metallic corner reflector which is known for high RCS levels over a wide bandwidth and over a wide angle of incidence. The study presents a novel corner reflector design where notches in the RCS spectral signature are created by the attachment of arrays of dielectric resonators to the metallic surfaces of corner reflectors. It is shown that notches appear due to the increased scattering of the resonators at resonance and by the power loss due to grating lobes formed in addition to the specular reflection from the arrays and from the metallic surfaces. Results from electromagnetic simulations are verified by measurements of an example dihedral corner reflector of 100 × 100 mm2 plate size with two arrays of 3 × 3 DRs producing a notch signature at about 7 GHz.
Permutation test and bootstrap methods for unsupervised detection and estimation of behind‐the‐meter photovoltaic generation
Authors: Liu Chao , Shi Jing , Chen Hongkun , Chen Lei , Li Guocheng 
Published: March 2021

AbstractThe penetration of unmonitored behind‐the‐meter photovoltaic systems has increased rapidly over the past decade. While unsupervised methods have been proposed to estimate behind‐the‐meter photovoltaic generation, their performance is significantly affected by hyperparameters. Existing methods for choosing hyperparameters require labelled data, which are unavailable to system operators. In this paper, a data‐driven method is proposed to generate labelled data to optimize the hyperparameters for unsupervised estimation of behind‐the‐meter photovoltaic generation. First, a permutation‐test based method is developed to detect photovoltaic installation in an unsupervised way. Second, consumers without PV are combined with limited monitored photovoltaic sites to simulate the original system through the bootstrap method. The simulated system provides labelled data for hyperparameter optimization. Finally, the near‐optimal hyperparameters are searched on the simulated system and applied to the original system's estimation. Through experiments on a smart meter dataset, the effectiveness of the proposed methodology is verified.