bluuebunny/crossref_metadata_2025_split huggingface dataset:
Symmetry breaking of tissue mechanics in wound induced hair follicle regeneration of laboratory and spiny mice
Authors: Harn Hans I-Chen , Wang Sheng-Pei , Lai Yung-Chih , Van Handel Ben , Liang Ya-Chen , Tsai Stephanie , Schiessl Ina Maria , Sarkar Arijita , Xi Haibin , Hughes Michael , Kaemmer Stefan , Tang Ming-Jer , Peti-Peterdi Janos , Pyle April D. , Woolley Thomas E. , Evseenko Denis , Jiang Ting-Xin , Chuong Cheng-Ming 
Published: May 2021

AbstractTissue regeneration is a process that recapitulates and restores organ structure and function. Although previous studies have demonstrated wound-induced hair neogenesis (WIHN) in laboratory mice (Mus), the regeneration is limited to the center of the wound unlike those observed in African spiny (Acomys) mice. Tissue mechanics have been implicated as an integral part of tissue morphogenesis. Here, we use the WIHN model to investigate the mechanical and molecular responses of laboratory and African spiny mice, and report these models demonstrate opposing trends in spatiotemporal morphogenetic field formation with association to wound stiffness landscapes. Transcriptome analysis and K14-Cre-Twist1 transgenic mice show the Twist1 pathway acts as a mediator for both epidermal-dermal interactions and a competence factor for periodic patterning, differing from those used in development. We propose a Turing model based on tissue stiffness that supports a two-scale tissue mechanics process: (1) establishing a morphogenetic field within the wound bed (mm scale) and (2) symmetry breaking of the epidermis and forming periodically arranged hair primordia within the morphogenetic field (μm scale). Thus, we delineate distinct chemo-mechanical events in building a Turing morphogenesis-competent field during WIHN of laboratory and African spiny mice and identify its evo-devo advantages with perspectives for regenerative medicine.
Expanding the chemistry of borates with functional [BO2]− anions
Authors: Huang Chunmei , Mutailipu Miriding , Zhang Fangfang , Griffith Kent J. , Hu Cong , Yang Zhihua , Griffin John M. , Poeppelmeier Kenneth R. , Pan Shilie 
Published: May 2021

AbstractMore than 3900 crystalline borates, including borate minerals and synthetic inorganic borates, in addition to a wealth of industrially-important boron-containing glasses, have been discovered and characterized. Of these compounds, 99.9 % contain only the traditional triangular BO3 and tetrahedral BO4 units, which polymerize into superstructural motifs. Herein, a mixed metal K5Ba2(B10O17)2(BO2) with linear BO2 structural units was obtained, pushing the boundaries of structural diversity and providing a direct strategy toward the maximum thresholds of birefringence for optical materials design. 11B solid-state nuclear magnetic resonance (NMR) is a ubiquitous tool in the study of glasses and optical materials; here, density functional theory-based NMR crystallography guided the direct characterization of BO2 structural units. The full anisotropic shift and quadrupolar tensors of linear BO2 were extracted from K5Ba2(B10O17)2(BO2) containing BO2, BO3, and BO4 and serve as guides to the identification of this powerful moiety in future and, potentially, previously-characterized borate minerals, ceramics, and glasses.
Spin-polarized oxygen evolution reaction under magnetic field
Authors: Ren Xiao , Wu Tianze , Sun Yuanmiao , Li Yan , Xian Guoyu , Liu Xianhu , Shen Chengmin , Gracia Jose , Gao Hong-Jun , Yang Haitao , Xu Zhichuan J. 
Published: May 2021

AbstractThe oxygen evolution reaction (OER) is the bottleneck that limits the energy efficiency of water-splitting. The process involves four electrons’ transfer and the generation of triplet state O2 from singlet state species (OH- or H2O). Recently, explicit spin selection was described as a possible way to promote OER in alkaline conditions, but the specific spin-polarized kinetics remains unclear. Here, we report that by using ferromagnetic ordered catalysts as the spin polarizer for spin selection under a constant magnetic field, the OER can be enhanced. However, it does not applicable to non-ferromagnetic catalysts. We found that the spin polarization occurs at the first electron transfer step in OER, where coherent spin exchange happens between the ferromagnetic catalyst and the adsorbed oxygen species with fast kinetics, under the principle of spin angular momentum conservation. In the next three electron transfer steps, as the adsorbed O species adopt fixed spin direction, the OER electrons need to follow the Hund rule and Pauling exclusion principle, thus to carry out spin polarization spontaneously and finally lead to the generation of triplet state O2. Here, we showcase spin-polarized kinetics of oxygen evolution reaction, which gives references in the understanding and design of spin-dependent catalysts.
A junctional PACSIN2/EHD4/MICAL-L1 complex coordinates VE-cadherin trafficking for endothelial migration and angiogenesis
Authors: Malinova Tsveta S. , Angulo-Urarte Ana , Nüchel Julian , Tauber Marina , van der Stoel Miesje M. , Janssen Vera , de Haan Annett , Groenen Anouk G. , Tebbens Merel , Graupera Mariona , Plomann Markus , Huveneers Stephan 
Published: May 2021

AbstractAngiogenic sprouting relies on collective migration and coordinated rearrangements of endothelial leader and follower cells. VE-cadherin-based adherens junctions have emerged as key cell-cell contacts that transmit forces between cells and trigger signals during collective cell migration in angiogenesis. However, the underlying molecular mechanisms that govern these processes and their functional importance for vascular development still remain unknown. We previously showed that the F-BAR protein PACSIN2 is recruited to tensile asymmetric adherens junctions between leader and follower cells. Here we report that PACSIN2 mediates the formation of endothelial sprouts during angiogenesis by coordinating collective migration. We show that PACSIN2 recruits the trafficking regulators EHD4 and MICAL-L1 to the rear end of asymmetric adherens junctions to form a recycling endosome-like tubular structure. The junctional PACSIN2/EHD4/MICAL-L1 complex controls local VE-cadherin trafficking and thereby coordinates polarized endothelial migration and angiogenesis. Our findings reveal a molecular event at force-dependent asymmetric adherens junctions that occurs during the tug-of-war between endothelial leader and follower cells, and allows for junction-based guidance during collective migration in angiogenesis.
Semi-conducting 2D rectangles with tunable length via uniaxial living crystallization-driven self-assembly of homopolymer
Authors: Yang Sanghee , Kang Sung-Yun , Choi Tae-Lim 
Published: May 2021

AbstractSemi-conducting two-dimensional (2D) nanoobjects, prepared by self-assembly of conjugated polymers, are promising materials for optoelectronic applications. However, no examples of self-assembled semi-conducting 2D nanosheets whose lengths and aspect ratios are controlled at the same time have been reported. Herein, we successfully prepared uniform semi-conducting 2D sheets using a conjugated poly(cyclopentenylene vinylene) homopolymer and its block copolymer by blending and heating. Using these as 2D seeds, living crystallization-driven self-assembly (CDSA) was achieved by adding the homopolymer as a unimer. Interestingly, unlike typical 2D CDSA examples showing radial growth, this homopolymer assembled only in one direction. Owing to this uniaxial growth, the lengths of the 2D nanosheets could be precisely tuned from 1.5 to 8.8 μm with narrow dispersity according to the unimer-to-seed ratio. We also studied the growth kinetics of the living 2D CDSA and confirmed first-order kinetics. Subsequently, we prepared several 2D block comicelles (BCMs), including penta-BCMs in a one-shot method.
Mapping the molecular and structural specialization of the skin basement membrane for inter-tissue interactions
Authors: Tsutsui Ko , Machida Hiroki , Nakagawa Asako , Ahn Kyungmin , Morita Ritsuko , Sekiguchi Kiyotoshi , Miner Jeffrey H. , Fujiwara Hironobu 
Published: May 2021

AbstractInter-tissue interaction is fundamental to multicellularity. Although the basement membrane (BM) is located at tissue interfaces, its mode of action in inter-tissue interactions remains poorly understood, mainly because the molecular and structural details of the BM at distinct inter-tissue interfaces remain unclear. By combining quantitative transcriptomics and immunohistochemistry, we systematically identify the cellular origin, molecular identity and tissue distribution of extracellular matrix molecules in mouse hair follicles, and reveal that BM composition and architecture are exquisitely specialized for distinct inter-tissue interactions, including epithelial–fibroblast, epithelial–muscle and epithelial–nerve interactions. The epithelial–fibroblast interface, namely, hair germ–dermal papilla interface, makes asymmetrically organized side-specific heterogeneity in the BM, defined by the newly characterized interface, hook and mesh BMs. One component of these BMs, laminin α5, is required for hair cycle regulation and hair germ–dermal papilla anchoring. Our study highlights the significance of BM heterogeneity in distinct inter-tissue interactions.
Constrained crystals deep convolutional generative adversarial network for the inverse design of crystal structures
Authors: Long Teng , Fortunato Nuno M. , Opahle Ingo , Zhang Yixuan , Samathrakis Ilias , Shen Chen , Gutfleisch Oliver , Zhang Hongbin 
Published: May 2021

AbstractAutonomous materials discovery with desired properties is one of the ultimate goals for materials science, and the current studies have been focusing mostly on high-throughput screening based on density functional theory calculations and forward modeling of physical properties using machine learning. Applying the deep learning techniques, we have developed a generative model, which can predict distinct stable crystal structures by optimizing the formation energy in the latent space. It is demonstrated that the optimization of physical properties can be integrated into the generative model as on-top screening or backward propagator, both with their own advantages. Applying the generative models on the binary Bi-Se system reveals that distinct crystal structures can be obtained covering the whole composition range, and the phases on the convex hull can be reproduced after the generated structures are fully relaxed to the equilibrium. The method can be extended to multicomponent systems for multi-objective optimization, which paves the way to achieve the inverse design of materials with optimal properties.
Cutting through complexity: the Breathing, Thinking, Functioning clinical model is an educational tool that facilitates chronic breathlessness management
Authors: Spathis Anna , Burkin Julie , Moffat Catherine , Tuffnell Rachel , Barclay Stephen , Mant Jonathan , Booth Sara 
Published: May 2021

AbstractChronic breathlessness is a distressing symptom that is challenging to manage. The Breathing, Thinking, Functioning clinical model is an educational tool developed to support breathlessness management. Health professionals report that the model increases clinician and patient understanding of this complex symptom, and provides a simple and structured approach to personalised self-management.
Error suppression in adiabatic quantum computing with qubit ensembles
Authors: Mohseni Naeimeh , Narozniak Marek , Pyrkov Alexey N. , Ivannikov Valentin , Dowling Jonathan P. , Byrnes Tim 
Published: May 2021

AbstractIncorporating protection against quantum errors into adiabatic quantum computing (AQC) is an important task due to the inevitable presence of decoherence. Here, we investigate an error-protected encoding of the AQC Hamiltonian, where qubit ensembles are used in place of qubits. Our Hamiltonian only involves total spin operators of the ensembles, offering a simpler route towards error-corrected quantum computing. Our scheme is particularly suited to neutral atomic gases where it is possible to realize large ensemble sizes and produce ensemble-ensemble entanglement. We identify a critical ensemble size Nc where the nature of the first excited state becomes a single particle perturbation of the ground state, and the gap energy is predictable by mean-field theory. For ensemble sizes larger than Nc, the ground state becomes protected due to the presence of logically equivalent states and the AQC performance improves with N, as long as the decoherence rate is sufficiently low.
New freshwater mussels from two Southeast Asian genera Bineurus and Thaiconcha (Pseudodontini, Gonideinae, Unionidae)
Authors: Konopleva Ekaterina S. , Bolotov Ivan N. , Pfeiffer John M. , Vikhrev Ilya V. , Kondakov Alexander V. , Gofarov Mikhail Yu. , Tomilova Alena A. , Tanmuangpak Kitti , Tumpeesuwan Sakboworn 
Published: May 2021

AbstractThe Mekong and Chao Phraya rivers harbor a species-rich freshwater mussel assemblage containing a large radiation of the Pseudodontini species. Members of the genera Bineurus Simpson 1900 and Thaiconcha Bolotov et al., 2020 primarily inhabit small and medium-sized tributaries of these rivers. Here, we present an integrative taxonomic review of these genus-level clades. We show that Bineurus contains four species: B. mouhotii (Lea, 1863), B. exilis (Morelet, 1866) stat. rev., B. anodontinum (Rochebrune, 1882) stat. rev., and B. loeiensis sp. nov. In its turn, Thaiconcha comprises three species: T. callifera (Martens, 1860), T. munelliptica sp. nov., and T. thaiensis sp. nov. Two species, Pseudodon ovalis Morlet, 1889 and P. thomsoni Morlet, 1884, are considered here as questionable taxa. These findings further highlight that Southeast Asia represents a significant evolutionary hotspot of freshwater mussels, which requires further international collaborative research and conservation efforts.
The cytochrome P450 (CYP) superfamily in cnidarians
Authors: Pankov Kirill V. , McArthur Andrew G. , Gold David A. , Nelson David R. , Goldstone Jared V. , Wilson Joanna Y. 
Published: May 2021

AbstractThe cytochrome P450 (CYP) superfamily is a diverse and important enzyme family, playing a central role in chemical defense and in synthesis and metabolism of major biological signaling molecules. The CYPomes of four cnidarian genomes (Hydra vulgaris, Acropora digitifera, Aurelia aurita, Nematostella vectensis) were annotated; phylogenetic analyses determined the evolutionary relationships amongst the sequences and with existing metazoan CYPs. 155 functional CYPs were identified and 90 fragments. Genes were from 24 new CYP families and several new subfamilies; genes were in 9 of the 12 established metazoan CYP clans. All species had large expansions of clan 2 diversity, with H. vulgaris having reduced diversity for both clan 3 and mitochondrial clan. We identified potential candidates for xenobiotic metabolism and steroidogenesis. That each genome contained multiple, novel CYP families may reflect the large evolutionary distance within the cnidarians, unique physiology in the cnidarian classes, and/or different ecology of the individual species.
Distinctive in-planta acclimation responses to basal growth and acute heat stress were induced in Arabidopsis by cattle manure biochar
Authors: Kumar Abhay , Friedman Haya , Tsechansky Ludmila , Graber Ellen R. 
Published: May 2021

AbstractIn-planta mechanisms of biochar (BC)-mediated improved growth were evaluated by examining oxidative stress, metabolic, and hormonal changes of Arabidopsis wild-type plants under basal or acute heat stress (–HS/ + HS) conditions with or without BC (+ BC/–BC). The oxidative stress was evaluated by using Arabidopsis expressing redox-sensitive green fluorescent protein in the plastids (pla-roGFP2). Fresh biomass and inflorescence height were greater in + BC(‒HS) plants than in the –BC(‒HS) plants, despite similar leaf nutrient levels, photosystem II (PSII) maximal efficiencies and similar oxidative poise. Endogenous levels of jasmonic and abscisic acids were higher in the + BC(‒HS) treatment, suggesting their role in growth improvement. HS in ‒BC plants caused reductions in inflorescence height and PSII maximum quantum yield, as well as significant oxidative stress symptoms manifested by increased lipid peroxidation, greater chloroplast redox poise (oxidized form of roGFP), increased expression of DNAJ heat shock proteins and Zn-finger genes, and reduced expression of glutathione-S-transferase gene in addition to higher abscisic acid and salicylic acid levels. Oxidative stress symptoms were significantly reduced by BC. Results suggest that growth improvements by BC occurring under basal and HS conditions are induced by acclimation mechanisms to ‘microstresses’ associated with basal growth and to oxidative stress of HS, respectively.
Validation of a DKK1 RNAscope chromogenic in situ hybridization assay for gastric and gastroesophageal junction adenocarcinoma tumors
Authors: Caldwell Charles , Rottman James B. , Paces Will , Bueche Elizabeth , Reitsma Sofia , Gibb Joseph , Adisetiyo Vitria , Haas Michael S. , Heath Heidi , Newman Walter , Baum Jason , Gianani Roberto , Kagey Michael H. 
Published: May 2021

AbstractDickkopf-1 (DKK1) is a secreted modulator of Wnt signaling that is frequently overexpressed in tumors and associated with poor clinical outcomes. DKN-01 is a humanized monoclonal therapeutic antibody that binds DKK1 with high affinity and has demonstrated clinical activity in gastric/gastroesophageal junction (G/GEJ) patients with elevated tumoral expression of DKK1. Here we report on the validation of a DKK1 RNAscope chromogenic in situ hybridization assay to assess DKK1 expression in G/GEJ tumor tissue. To reduce pathologist time, potential pathologist variability from manual scoring and support pathologist decision making, a digital image analysis algorithm that identifies tumor cells and quantifies the DKK1 signal was developed. Following CLIA guidelines the DKK1 RNAscope chromogenic in situ hybridization assay and digital image analysis algorithm were successfully validated for sensitivity, specificity, accuracy, and precision. The DKK1 RNAscope assay in conjunction with the digital image analysis solution is acceptable for prospective screening of G/GEJ adenocarcinoma patients. The work described here will further advance the companion diagnostic development of our DKK1 RNAscope assay and could generally be used as a guide for the validation of RNAscope assays with digital image quantification.
Peering inside a cough or sneeze to explain enhanced airborne transmission under dry weather
Authors: Liu Kai , Allahyari Majid , Salinas Jorge S. , Zgheib Nadim , Balachandar S. 
Published: May 2021

AbstractHigh-fidelity simulations of coughs and sneezes that serve as virtual experiments are presented, and they offer an unprecedented opportunity to peer into the chaotic evolution of the resulting airborne droplet clouds. While larger droplets quickly fall-out of the cloud, smaller droplets evaporate rapidly. The non-volatiles remain airborne as droplet nuclei for a long time to be transported over long distances. The substantial variation observed between the different realizations has important social distancing implications, since probabilistic outlier-events do occur and may need to be taken into account when assessing the risk of contagion. Contrary to common expectations, we observe dry ambient conditions to increase by more than four times the number of airborne potentially virus-laden nuclei, as a result of reduced droplet fall-out through rapid evaporation. The simulation results are used to validate and calibrate a comprehensive multiphase theory, which is then used to predict the spread of airborne nuclei under a wide variety of ambient conditions.
Influence of survival, promotion, and growth on pattern formation in zebrafish skin
Authors: Konow Christopher , Li Ziyao , Shepherd Samantha , Bullara Domenico , Epstein Irving R. 
Published: May 2021

AbstractThe coloring of zebrafish skin is often used as a model system to study biological pattern formation. However, the small number and lack of movement of chromatophores defies traditional Turing-type pattern generating mechanisms. Recent models invoke discrete short-range competition and long-range promotion between different pigment cells as an alternative to a reaction-diffusion scheme. In this work, we propose a lattice-based “Survival model,” which is inspired by recent experimental findings on the nature of long-range chromatophore interactions. The Survival model produces stationary patterns with diffuse stripes and undergoes a Turing instability. We also examine the effect that domain growth, ubiquitous in biological systems, has on the patterns in both the Survival model and an earlier “Promotion” model. In both cases, domain growth alone is capable of orienting Turing patterns above a threshold wavelength and can reorient the stripes in ablated cells, though the wavelength for which the patterns orient is much larger for the Survival model. While the Survival model is a simplified representation of the multifaceted interactions between pigment cells, it reveals complex organizational behavior and may help to guide future studies.
Impact of histological response after neoadjuvant therapy on podocalyxin as a prognostic marker in pancreatic cancer
Authors: Eurola Annika , Ristimäki Ari , Mustonen Harri , Nurmi Anna-Maria , Hagström Jaana , Haglund Caj , Seppänen Hanna 
Published: May 2021

AbstractPodocalyxin overexpression associates with poor survival in pancreatic cancer (PDAC). We investigated whether podocalyxin expression correlates with treatment response or survival in neoadjuvant-treated PDAC. Through immunohistochemistry, we evaluated podocalyxin expression in 88 neoadjuvant and 143 upfront surgery patients using two antibodies. We developed a six-tier grading scheme for neoadjuvant responses evaluating the remaining tumor cells in surgical specimens. Strong podocalyxin immunopositivity associated with poor survival in the patients responding poorly to the neoadjuvant treatment (HR 4.16, 95% CI 1.56–11.01, p = 0.004), although neoadjuvant patients exhibited generally low podocalyxin expression (p = 0.017). Strong podocalyxin expression associated with perineural invasion (p = 0.003) and lack of radiation (p = 0.036). Two patients exhibited a complete neoadjuvant response, while a strong neoadjuvant response (≤ 5% of residual tumor cells) significantly associated with lower stage, pT-class and grade, less spread to the regional lymph nodes, less perineural invasion, and podocalyxin negativity (p < 0.05, respectively). A strong response predicted better survival (HR 0.28, 95% CI 0.09–0.94, p = 0.039). In conclusion, strong podocalyxin expression associates with poor survival among poorly responding neoadjuvant patients. A good response associates with podocalyxin negativity. A strong response associates with better outcome.