bluuebunny/crossref_metadata_2025_split huggingface dataset:
A high-throughput single-particle imaging platform for antibody characterization and a novel competition assay for therapeutic antibodies
Authors: Seymour Elif , Ünlü M. Selim , Connor John H. 
Published: January 2023

AbstractMonoclonal antibodies (mAbs) play an important role in diagnostics and therapy of infectious diseases. Here we utilize a single-particle interferometric reflectance imaging sensor (SP-IRIS) for screening 30 mAbs against Ebola, Sudan, and Lassa viruses (EBOV, SUDV, and LASV) to find out the ideal capture antibodies for whole virus detection using recombinant vesicular stomatitis virus (rVSV) models expressing surface glycoproteins (GPs) of EBOV, SUDV, and LASV. We also make use of the binding properties on SP-IRIS to develop a model for mapping the antibody epitopes on the GP structure. mAbs that bind to mucin-like domain or glycan cap of the EBOV surface GP show the highest signal on SP-IRIS, followed by mAbs that target the GP1-GP2 interface at the base domain. These antibodies were shown to be highly efficacious against EBOV infection in non-human primates in previous studies. For LASV detection, 8.9F antibody showed the best performance on SP-IRIS. This antibody binds to a unique region on the surface GP compared to other 15 mAbs tested. In addition, we demonstrate a novel antibody competition assay using SP-IRIS and rVSV-EBOV models to reveal the competition between mAbs in three successful therapeutic mAb cocktails against EBOV infection. We provide an explanation as to why ZMapp cocktail has higher efficacy compared to the other two cocktails by showing that three mAbs in this cocktail (13C6, 2G4, 4G7) do not compete with each other for binding to EBOV GP. In fact, the binding of 13C6 enhances the binding of 2G4 and 4G7 antibodies. Our results establish SP-IRIS as a versatile tool that can provide high-throughput screening of mAbs, multiplexed and sensitive detection of viruses, and evaluation of therapeutic antibody cocktails.
P-TarPmiR accurately predicts plant-specific miRNA targets
Authors: Ajila Victoria , Colley Laura , Ste-Croix Dave T. , Nissan Nour , Golshani Ashkan , Cober Elroy R. , Mimee Benjamin , Samanfar Bahram , Green James R. 
Published: January 2023

AbstractmicroRNAs (miRNAs) are small non-coding ribonucleic acids that post-transcriptionally regulate gene expression through the targeting of messenger RNA (mRNAs). Most miRNA target predictors have focused on animal species and prediction performance drops substantially when applied to plant species. Several rule-based miRNA target predictors have been developed in plant species, but they often fail to discover new miRNA targets with non-canonical miRNA–mRNA binding. Here, the recently published TarDB database of plant miRNA–mRNA data is leveraged to retrain the TarPmiR miRNA target predictor for application on plant species. Rigorous experiment design across four plant test species demonstrates that animal-trained predictors fail to sustain performance on plant species, and that the use of plant-specific training data improves accuracy depending on the quantity of plant training data used. Surprisingly, our results indicate that the complete exclusion of animal training data leads to the most accurate plant-specific miRNA target predictor indicating that animal-based data may detract from miRNA target prediction in plants. Our final plant-specific miRNA prediction method, dubbed P-TarPmiR, is freely available for use at http://ptarpmir.cu-bic.ca. The final P-TarPmiR method is used to predict targets for all miRNA within the soybean genome. Those ranked predictions, together with GO term enrichment, are shared with the research community.
Generation of V-point polarization singularity using single phase encoding with a spatial light modulator
Authors: Kumar Praveen , Rao A. Srinivasa , Omatsu Takashige 
Published: January 2023

AbstractA liquid crystal Spatial Light Modulator (SLM) can be used in various ways to produce vector-vortices. Superposition of scalar vortices with orthogonal polarization is a common approach, while a more recent technique is to use dual-phase modulation. These approaches require modulation of at least two phase patterns with a SLM or multiple SLMs. In this paper, we propose a novel technique to produce vector-vortices by modulating orthogonal light components through a single phase pattern with a SLM. It does not require interferometric setups, and simplifies the generation of light beams with V-point polarization singularities. Because of compact and robustness of our experimental setup, it can be easily integrated to any device for applications of vector-vortices.
Unique insertion/deletion polymorphisms within histidine-rich region of histidine-rich glycoprotein in Thoroughbred horses
Authors: Muko Ryo , Sunouchi Tomoya , Urayama Shuntaro , Toishi Yuko , Kusano Kanichi , Sato Hiroaki , Muranaka Masanori , Shin Taekyun , Oikawa Masa-aki , Ojima Yoshinobu , Ali Mohammad , Nomura Yoshihiro , Matsuda Hiroshi , Tanaka Akane 
Published: January 2023

AbstractHistidine-rich glycoprotein (HRG) is abundant plasma protein with various effects on angiogenesis, coagulation, and immune responses. Previously, we identified the base and amino acid sequences of equine HRG (eHRG) and revealed that eHRG regulates neutrophil functions. In this study, we first conducted a large-scale gene analysis with DNA samples extracted from 1700 Thoroughbred horses and identified unique insertion/deletion polymorphisms in the histidine-rich region (HRR) of eHRG. Here we report two types of polymorphisms (deletion type 1 [D1] and deletion type 2 [D2]) containing either a 45 bp or 90 bp deletion in the HRR of eHRG, and five genotypes of eHRG (insertion/insertion [II], ID1, ID2, D1D1, and D1D2) in Thoroughbred horses. Allele frequency of I, D1, and D2, was 0.483, 0.480, and 0.037 and the incidence of each genotype was II: 23.4%, ID1: 46.2%, ID2: 3.6%, D1D1: 23.1%, and D1D2: 3.7%, respectively. The molecular weights of each plasma eHRG protein collected from horses with each genotype was detected as bands of different molecular size, which corresponded to the estimated amino acid sequence. The nickel-binding affinity of the D1 or D2 deletion eHRG was reduced, indicating a loss of function at the site. eHRG proteins show a variety of biological and immunological activities in vivo, and HRR is its active center, suggesting that genetic polymorphisms in eHRG may be involved in the performance in athletic ability, productivity, and susceptibility to infectious diseases in Thoroughbred horses.
Direct observation of Cu in high-silica chabazite zeolite by electron ptychography using Wigner distribution deconvolution
Authors: Mitsuishi Kazutaka , Nakazawa Katsuaki , Sagawa Ryusuke , Shimizu Masahiko , Matsumoto Hajime , Shima Hisashi , Takewaki Takahiko 
Published: January 2023

AbstractDirect observation of Cu in Cu-chabazite (CHA) zeolite has been achieved by electron ptychography using the Wigner distribution deconvolution. The imaging properties of ptychographically reconstructed images were evaluated by comparing the intensities of six-membered-ring columns of the zeolite with and without Cu using simulated ptychography images. It was concluded that although false contrast may appear at Cu-free columns for some acquisition conditions, ptychography can discriminate columns with and without Cu. Experimental observation of CHA with and without Cu was performed. Images obtained from the Cu-containing sample showed contrast at the six-membered-rings, while no contrast was observed for the Cu-free sample. The results show that ptychography is a promising technique for visualizing the atomic structures of beam-sensitive materials.
Time-lapse mechanical imaging of neural tube closure in live embryo using Brillouin microscopy
Authors: Handler Chenchen , Scarcelli Giuliano , Zhang Jitao 
Published: January 2023

AbstractNeural tube closure (NTC) is a complex process of embryonic development involving molecular, cellular, and biomechanical mechanisms. While the genetic factors and biochemical signaling have been extensively investigated, the role of tissue biomechanics remains mostly unexplored due to the lack of tools. Here, we developed an optical modality that can conduct time-lapse mechanical imaging of neural plate tissue as the embryo is experiencing neurulation. This technique is based on the combination of a confocal Brillouin microscope and a modified ex ovo culturing of chick embryo with an on-stage incubator. With this technique, for the first time, we captured the mechanical evolution of the neural plate tissue with live embryos. Specifically, we observed the continuous increase in tissue modulus of the neural plate during NTC for ex ovo cultured embryos, which is consistent with the data of in ovo culture as well as previous studies. Beyond that, we found that the increase in tissue modulus was highly correlated with the tissue thickening and bending. We foresee this non-contact and label-free technique opening new opportunities to understand the biomechanical mechanisms in embryonic development.
Double-branch feature fusion transformer for hyperspectral image classification
Authors: Dang Lanxue , Weng Libo , Hou Yane , Zuo Xianyu , Liu Yang 
Published: January 2023

AbstractDeep learning methods, particularly Convolutional Neural Network (CNN), have been widely used in hyperspectral image (HSI) classification. CNN can achieve outstanding performance in the field of HSI classification due to its advantages of fully extracting local contextual features of HSI. However, CNN is not good at learning the long-distance dependency relation and dealing with the sequence properties of HSI. Thus, it is difficult to continuously improve the performance of CNN-based models because they cannot take full advantage of the rich and continuous spectral information of HSI. This paper proposes a new Double-Branch Feature Fusion Transformer model for HSI classification. We introduce Transformer into the process of HSI on account of HSI with sequence characteristics. The two branches of the model extract the global spectral features and global spatial features of HSI respectively, and fuse both spectral and spatial features through a feature fusion layer. Furthermore, we design two attention modules to adaptively adjust the importance of spectral bands and pixels for classification in HSI. Experiments and comparisons are carried out on four public datasets, and the results demonstrate that our model outperforms any compared CNN-Based models in terms of accuracy.
Effects of the long-term influence of bisphenol A and bisphenol S on the population of nitrergic neurons in the enteric nervous system of the mouse stomach
Authors: Makowska Krystyna , Całka Jarosław , Gonkowski Sławomir 
Published: January 2023

AbstractBisphenol A (BPA) is an endocrine disruptor commonly used in the production of plastics. Due to its relatively well-known harmful effects on living organisms, BPA is often replaced by its various analogues. One of them is bisphenol S (BPS), widely used in the plastics industry. Until recently, BPS was considered completely safe, but currently, it is known that it is not safe for various internal organs. However, knowledge about the influence of BPS on the nervous system is scarce. Therefore, the aim of this study was to investigate the influence of two doses of BPA and BPS on the enteric nitrergic neurons in the CD1 strain mouse stomach using the double-immunofluorescence technique. The study found that both substances studied increased the number of nitrergic neurons, although changes under the impact of BPS were less visible than those induced by BPA. Therefore, the obtained results, for the first time, clearly indicate that BPS is not safe for the innervation of the gastrointestinal tract.
A theory of unusual anisotropic magnetoresistance in bilayer heterostructures
Authors: Wang X. R. , Wang C. , Wang X. S. 
Published: January 2023

AbstractThe observation of magnetoresistance (MR) varying with the rotation of magnetization in the plane perpendicular to the electric current is an important discovery in spintronics in recent years. The famous conventional anisotropic MR (AMR) says that the resistance of a polycrystalline magnetic material must depend on magnetization component along the current direction only, thus cannot account for this newly observed unusual AMR (UAMR). This UAMR leads to the notion of the spin-Hall MR (SMR) in the famous SMR theory. However, the SMR theory may only explain UAMR observed in heavy-metal/magnetic-insulator bilayers, not other types of bilayers. Here, we present a two-vector theory that can explain not only all existing experiments on the unusual angular dependence of longitudinal and transverse resistivity when the magnetization rotates in three mutually perpendicular planes, but also how three amplitudes of MR angular oscillation are related to each other. The theory is very general and its correctness depends only on the assumption that the magnetization and interfacial field are the only vectors affecting electron transport besides of other scalar variables such as the temperatures and impurities. Experiments that can test this theory against the SMR theory are also proposed.
Proteomics analysis in myocardium of spontaneously hypertensive rats
Authors: Wang Tingjun , Cai Xiaoqi , Li Jinze , Xie Liangdi 
Published: January 2023

AbstractHypertension-related left ventricular hypertrophy is recognized as a good predictor of adverse cardiovascular events. However, the underlying mechanism of left ventricular hypertrophy is still not fully understood. This study employed liquid chromatography coupled with tandem mass spectrometry to investigate global changes in protein profile in myocardium of spontaneously hypertensive rat, a classical animal model of essential hypertension. There were 369 differentially expressed proteins in myocardium between spontaneously hypertensive rats and normotensive rats. Xenobiotic catabolic process, cholesterol binding and mitochondrial proton-transporting ATP synthase were found to be the most significantly enriched biological process, molecular function and cellular component terms of Gene Ontology, respectively. Drug metabolism-cytochrome P450 was revealed to be the most significantly enriched Kyoto Encyclopedia of Genes and Genomes pathways. FYN proto-oncogene, Src family tyrosine kinase was found to have the most interactions with other proteins. Differentially expressed proteins involved in xenobiotic catabolic process, lipid transport and metabolism, mitochondrial function might be targets for further study of hypertension-related left ventricular hypertrophy.
Combining controlled-release urea with potassium chloride to reduce soil N/K leaching and promote growth of Italian ryegrass
Authors: Geng Jibiao , Yang Xiuyi , Lei Shutong , Zhang Qingping , Li Hui , Lang Ying , Huo Xianqi , Liu Qianjin 
Published: January 2023

AbstractNitrogen (N) and potassium (K) are essential nutrients for Italian ryegrass (Lolium multiflorum L.) growth. A 2-year field experiment with a split-plot design was conducted to study the effect of N fertilizer type combined with different K fertilizer rates on the soil mineral N and K availability, and growth characteristics of Italian ryegrass. The main plots were assigned to two N fertilizer types, controlled-release urea (CRU) and common urea. While low, moderate and high potassium chloride (KCl) rates (150, 300 and 450 kg ha−1, respectively) were assigned to the subplots. Compared with the common urea treatments, the CRU significantly increased the SPAD value, plant height, leaf area, and photosynthetic index of Italian ryegrass, which significantly prolonged the green stage of Italian ryegrass and prevented premature senescence. Moreover, the dry yields of the CRU increased by 4.5–12.5% in 2019 and 10.9–25.3% in 2020 compared with the urea, respectively. At the same time, compared with the KCl150 and KCl450 treatments, the KCl300 treatment resulted in better plant growth. Overall, the CRU × KCl300 maximized the soil inorganic N and different soil K forms, and reduced the soil N/K leaching. The root length, volume, surface area, average diameter, tips and branches were also improved, and there was a significant N × K interaction effect on the tips. The CRU combined with 300 kg ha−1 KCl fertilization enhanced crop growth by improving leaf photosynthesis, soil fertility, and yield and should be recommended as the best fertilizer ratio for Italian ryegrass production.
Highly concentrated trehalose induces prohealing senescence-like state in fibroblasts via CDKN1A/p21
Authors: Muto Jun , Fukuda Shinji , Watanabe Kenji , Dai Xiuju , Tsuda Teruko , Kiyoi Takeshi , Kameda Kenji , Kawakami Ryosuke , Mori Hideki , Shiraishi Ken , Murakami Masamoto , Imamura Takeshi , Higashiyama Shigeki , Fujisawa Yasuhiro , Mizukami Yoichi , Sayama Koji 
Published: January 2023

AbstractTrehalose is the nonreducing disaccharide of glucose, evolutionarily conserved in invertebrates. The living skin equivalent (LSE) is an organotypic coculture containing keratinocytes cultivated on fibroblast-populated dermal substitutes. We demonstrated that human primary fibroblasts treated with highly concentrated trehalose promote significantly extensive spread of the epidermal layer of LSE without any deleterious effects. The RNA-seq analysis of trehalose-treated 2D and 3D fibroblasts at early time points revealed the involvement of the CDKN1A pathway, the knockdown of which significantly suppressed the upregulation ofDPT,ANGPT2,VEGFA,EREG, andFGF2. The trehalose-treated fibroblasts were positive for senescence-associated β-galactosidase. Finally, transplantation of the dermal substitute with trehalose-treated fibroblasts accelerated wound closure and increased capillary formation significantly in the experimental mouse wounds in vivo, which was canceled by the CDKN1A knockdown. These data indicate that high-concentration trehalose can induce the senescence-like state in fibroblasts via CDKN1A/p21, which may be therapeutically useful for optimal wound repair.
Underrated past herbivore densities could lead to misoriented sustainability policies
Authors: Manzano Pablo , Pardo Guillermo , Itani Moustapha A. , del Prado Agustín 
Published: January 2023

AbstractKnowing the carrying capacity of the Earth’s grazed ecosystems, and the relevance of herbivory, is important for many scientific disciplines, as well as for policy. Current herbivore levels are estimated to be four to five times larger than at the Pleistocene–Holocene transition or the start of the industrial revolution. While this estimate can lead the general public and the scientific community to predict severe, widespread environmental impacts by livestock in terms of deforestation, biodiversity loss, and climate change, it ignores the inherent uncertainty of such calculations. We revise the evidence published during the last decade regarding Late Pleistocene herbivore abundance, along with contemporary and some pre-industrial data on herbivore density in grazed ecosystems. Both Late Pleistocene and pre-industrial herbivore levels are likely to be consistently higher than what has generally been assumed, confirming increasing awareness on the importance of herbivory as a widespread ecological process. We therefore call for more refined research in this field to have the reliable baselines currently demanded by society and policy. These baselines should orient sound action toward policies on biodiversity conservation, ecosystem restoration, food systems, and climate change.
Reduced predation pressure as a potential driver of prey diversity and abundance in complex habitats
Authors: Chang Chia-chen , Todd Peter A. 
Published: January 2023

AbstractHabitat complexity is positively associated with biodiversity and abundance and is often a focus of habitat restoration programmes, however, the mechanisms underlying these relationships are not yet resolved. In this Perspective, we postulate that reduced predation pressure in complex habitats could contribute to increased prey diversity and abundance. Based on a systematic review and meta-analysis of experimental studies, reduced predation pressure in complex habitats is consistent across freshwater and marine ecosystems, field and laboratory experiments, different hunting modes of predators, and different numbers of prey species. However, the effects are less clear in terrestrial ecosystems. Easing predation pressure, in conjunction with increased resources for prey, could help explain the high biodiversity and abundance found in complex habitats. This knowledge can be used in restoration and ecological engineering projects to maximise species diversity and abundance gains.
Establishment of a gut-on-a-chip device with controllable oxygen gradients to study the contribution of Bifidobacterium bifidum to inflammatory bowel disease
Authors: Liu Jun , Lu Ronghao , Zheng Xiaolin , Hou Wensheng , Wu Xiaoying , Zhao Hezhao , Wang Guixue , Tian Tian 
Published: January 2023

Numerical simulations were applied to guide the design of a gut-on-a-chip device with controllable oxygen gradients. Bifidobacterium bifidum was demonstrated to increase the stability of the intestinal epithelial barrier on the disease model.
Guest Editorial: Grid‐forming converters placement and utilisation to enhance transmission and distribution performances under high penetration of inverter‐based resources
Authors: Babak Badrzadeh , Julia Matevosyan , Zia Emin , Chao Lu 
Published: January 2023

AbstractPower systems around the world are rapidly transitioning to much higher shares of inverter‐based resources (IBRs) with few synchronous generators remaining online. IBRs and synchronous generators have fundamentally different dynamic performance characteristics resulting in a difference in the overall power system dynamic performance. IBRs are generally more flexible and controllable than synchronous generators; however, at the same time they exhibit significantly more complex control systems. Furthermore, new and emerging capabilities are being developed progressively and in particular the so‐called grid‐forming inverters (GFM). GFM offer several new capabilities not previously possible with conventional grid‐following inverters (GFL). However, they are not well understood currently when applied in a mega scale and moving forward when they will likely take over the role synchronous generators have been performing for several decades as the workhorse of system security support. Key questions currently in the technical community include the extent to which GFM shall be similar or different to each of the synchronous machines and conventional GFL, and how various control strategies can assist in maximising the grid support capabilities sought and minimise or ideally eliminate any adverse impacts. The objective of this special issue is to provide insights into some of these unknowns.