bluuebunny/crossref_metadata_2025_split huggingface dataset:
Transitions between phyllotactic lattice states in curved geometries
Authors: Ansell H. S. , Tomlinson A. A. , Wilkin N. K. 
Published: October 2020

AbstractPhyllotaxis, the regular arrangement of leaves or other lateral organs in plants including pineapples, sunflowers and some cacti, has attracted scientific interest for centuries. More recently there has been interest in phyllotaxis within physical systems, especially for cylindrical geometry. In this letter, we expand from a cylindrical geometry and investigate transitions between phyllotactic states of soft vortex matter confined to a conical frustum. We show that the ground states of this system are consistent with previous results for cylindrical confinement and discuss the resulting defect structures at the transitions. We then eliminate these defects from the system by introducing a density gradient to create a configuration in a single state. The nature of the density gradient limits this approach to a small parameter range on the conical system. We therefore seek a new surface, the horn, for which a defect-free state can be maintained for a larger range of parameters.
Numerical model of hybrid mode-locked Tm-doped all-fibre laser
Authors: Donodin Aleksandr , Voropaev Vasilii , Batov Daniil , Vlasov Dmitrii , Lazarev Vladimir , Tarabrin Mikhail , Khegai Aleksandr , Likhachev Mikhail 
Published: October 2020

AbstractUltrafast Tm-doped fibre lasers have been actively studied for the last decade due to their potential applications in precise mid-IR spectroscopy, LIDARs, material processing and more. The majority of research papers is devoted to the comparison between a numerical modelling and experimental results; however, little attention is being paid to the comprehensive description of the mathematical models and parameters of the active and passive components forming cavities of Tm-doped all-fibre lasers. Thus, here we report a numerical model of a stretched-pulsed Tm-doped fibre laser with hybrid mode-locking and compare it with experimental results. The key feature of the developed numerical model is employment of the experimentally measured dispersion coefficients and optimisation of some model parameters, such as the bandwidth of the spectral filter spectral filtering and the saturation power of the active fibre, for a conformity with the experiment. The developed laser emits 331.7 fs pulses with a 23.8 MHz repetition rate, 6 mW of average power, 0.25 nJ of pulse energy, and a 21.66 nm spectral bandwidth at a peak wavelength of 1899.5 nm. The numerical model characteristics coincide with experimentally achieved spectral width, pulse duration, and average power with inaccuracy of 4.7%, 5.4%, and 22.9%, respectively. Moreover, in the discussion of the work the main possible reasons influencing this inaccuracy are highlighted. Elimination of those factors might allow to increase accuracy even more. We show that numerical model has a good agreement with the experiment and can be used for development of ultrafast Tm-doped fibre laser systems.
A neuroimaging marker for predicting longitudinal changes in pain intensity of subacute back pain based on large-scale brain network interactions
Authors: Park Bo-yong , Lee Jae-Joong , Kim Hong Ji , Woo Choong-Wan , Park Hyunjin 
Published: October 2020

AbstractIdentification of predictive neuroimaging markers of pain intensity changes is a crucial issue to better understand macroscopic neural mechanisms of pain. Although a single connection between the medial prefrontal cortex and nucleus accumbens has been suggested as a powerful marker, how the complex interactions on a large-scale brain network can serve as the markers is underexplored. Here, we aimed to identify a set of functional connections predictive of longitudinal changes in pain intensity using large-scale brain networks. We re-analyzed previously published resting-state functional magnetic resonance imaging data of 49 subacute back pain (SBP) patients. We built a network-level model that predicts changes in pain intensity over one year by combining independent component analysis and a penalized regression framework. Connections involving top-down pain modulation, multisensory integration, and mesocorticolimbic circuits were identified as predictive markers for pain intensity changes. Pearson’s correlations between actual and predicted pain scores were r = 0.33–0.72, and group classification results between SBP patients with persisting pain and recovering patients, in terms of area under the curve (AUC), were 0.89/0.75/0.75 for visits four/three/two, thus outperforming the previous work (AUC 0.83/0.73/0.67). This study identified functional connections important for longitudinal changes in pain intensity in SBP patients, providing provisional markers to predict future pain using large-scale brain networks.
Evolutionary motor biases and cognition in children with and without autism
Authors: Forrester Gillian S. , Davis Rachael , Malatesta Gianluca , Todd Brenda K. 
Published: October 2020

AbstractEvolution has endowed vertebrates with a divided brain that allows for processing of critical survival behaviours in parallel. Most humans possess astandardfunctional brain organisation for these ancient sensory-motor behaviours, favouring the right hemisphere for fight-or-flight processes and the left hemisphere for performing structured motor sequences. However, a significant minority of the population possess an organisational phenotype that represents crowding of function in one hemisphere, or a reversal of the standard functional organisation. Using behavioural biases as a proxy for brain organisation, results indicate that reversed brain organisation phenotype increases in populations with autism and is associated with weaker cognitive abilities. Moreover, this study revealed that left-handedness, alone, is not associated with decreased cognitive ability or autism. Rather, left-handedness acts as a marker for decreased cognitive performance when paired with the reversed brain phenotype. The results contribute to comparative research suggesting that modern human abilities are supported by evolutionarily old, lateralised sensory-motor processes. Systematic, longitudinal investigations, capturing genetic measures and brain correlates, are essential to reveal how cognition emerges from these foundational processes. Importantly, strength and direction of biases can act as early markers of brain organisation and cognitive development, leading to promising, novel practices for diagnoses and interventions.
Theoretical study of the impact of adaptation on cell-fate heterogeneity and fractional killing
Authors: Hurbain Julien , Labavić Darka , Thommen Quentin , Pfeuty Benjamin 
Published: October 2020

AbstractFractional killing illustrates the cell propensity to display a heterogeneous fate response over a wide range of stimuli. The interplay between the nonlinear and stochastic dynamics of biochemical networks plays a fundamental role in shaping this probabilistic response and in reconciling requirements for heterogeneity and controllability of cell-fate decisions. The stress-induced fate choice between life and death depends on an early adaptation response which may contribute to fractional killing by amplifying small differences between cells. To test this hypothesis, we consider a stochastic modeling framework suited for comprehensive sensitivity analysis of dose response curve through the computation of a fractionality index. Combining bifurcation analysis and Langevin simulation, we show that adaptation dynamics enhances noise-induced cell-fate heterogeneity by shifting from a saddle-node to a saddle-collision transition scenario. The generality of this result is further assessed by a computational analysis of a detailed regulatory network model of apoptosis initiation and by a theoretical analysis of stochastic bifurcation mechanisms. Overall, the present study identifies a cooperative interplay between stochastic, adaptation and decision intracellular processes that could promote cell-fate heterogeneity in many contexts.
Effects of processing conditions on stability of immune analytes in human blood
Authors: Gottfried-Blackmore Andres , Rubin Samuel J. S. , Bai Lawrence , Aluko Sheun , Yang Yujun , Park Walter , Habtezion Aida 
Published: October 2020

AbstractMinimizing variability in collection and processing of human blood samples for research remains a challenge. Delaying plasma or serum isolation after phlebotomy (processing delay) can cause perturbations of numerous analytes. Thus, a comprehensive understanding of how processing delay affects major endpoints used in human immunology research is necessary. Therefore, we studied how processing delay affects commonly measured cytokines and immune cell populations. We hypothesized that short-term time delays inherent to human research in serum and plasma processing impact commonly studied immunological analytes. Blood from healthy donors was subjected to processing delays commonly encountered in sample collection, and then assayed by 62-plex Luminex panel, 40-parameter mass cytometry panel, and 540,000 transcript expression microarray. Variance for immunological analytes was estimated using each individual’s baseline as a control. In general, short-term processing delay led to small changes in plasma and serum cytokines (range − 10.8 to 43.5%), markers and frequencies of peripheral blood mononuclear cell phenotypes (range 0.19 to 3.54 fold), and whole blood gene expression (stable for > 20 K genes)—with several exceptions described herein. Importantly, we built an open-access web application allowing investigators to estimate the degree of variance expected from processing delay for measurements of interest based on the data reported here.
Mechanism of delayed seed germination caused by high temperature during grain filling in rice (Oryza sativa L.)
Authors: Suriyasak Chetphilin , Oyama Yui , Ishida Toshiaki , Mashiguchi Kiyoshi , Yamaguchi Shinjiro , Hamaoka Norimitsu , Iwaya-Inoue Mari , Ishibashi Yushi 
Published: October 2020

AbstractHigh temperature during grain filling considerably reduces yield and quality in rice (Oryza sativa L.); however, how high temperature affects seed germination of the next generation is not yet well understood. Here, we report that seeds from plants exposed to high temperature during the grain filling stage germinated significantly later than seeds from unstressed plants. This delay remained even after dormancy release treatments, suggesting that it was not due to primary seed dormancy determined during grain filling. In imbibed embryos of heat-stressed seeds, expression of abscisic acid (ABA) biosynthesis genes (OsNCEDs) was higher than in those of control seeds, whereas that of ABA catabolism genes (OsABA8′OHs) was lower. In the aleurone layer, despite no change in GA signaling as evidenced by no effect of heat stress on OsGAMYB gene expression, the transcripts of α-amylase genes OsAmy1C, OsAmy3B, and OsAmy3E were significantly down-regulated in heat-stressed seeds in comparison with controls. Changes in promoter methylation levels were consistent with transcriptional changes of ABA catabolism-related and α-amylase genes. These data suggest that high temperature during grain filling results in DNA methylation of ABA catabolism-related and α-amylase gene promoters, delaying germination of heat-stressed seeds.
Major explosions and paroxysms at Stromboli (Italy): a new historical catalog and temporal models of occurrence with uncertainty quantification
Authors: Bevilacqua Andrea , Bertagnini Antonella , Pompilio Massimo , Landi Patrizia , Del Carlo Paola , Di Roberto Alessio , Aspinall Willy , Neri Augusto 
Published: October 2020

AbstractStromboli volcano (Italy), always active with low energy explosive activity, is a very attractive place for visitors, scientists, and inhabitants of the island. Nevertheless, occasional more intense eruptions can present a serious danger. This study focuses on the modeling and estimation of their inter-event time and temporal rate. With this aim we constructed a new historical catalog of major explosions and paroxysms through a detailed review of scientific literature of the last ca. 140 years. The catalog includes the calendar date and phenomena descriptions for 180 explosive events, of which 36 were paroxysms. We evaluated the impact of the main sources of uncertainty affecting the historical catalog. In particular, we categorized as uncertain 45 major explosions that reportedly occurred before 1985 and tested the effect of excluding these events from our analysis. Moreover, after analyzing the entire record in the period [1879, 2020], we separately considered, as sequences, events in [1879, 1960] and in [1985, 2020] because of possible under recording issues in the period [1960, 1985]. Our new models quantify the temporal rate of major explosions and paroxysms as a function of time passed since the last event occurred. Recurrence hazard levels are found to be significantly elevated in the weeks and months following a major explosion or paroxysm, and then gradually decrease over longer periods. Computed hazard functions are also used to illustrate a methodology for estimating order-of-magnitude individual risk of fatality under certain basis conditions. This study represents a first quantitatively formal advance in determining long-term hazard levels at Stromboli.
Hepatic stem cell Numb gene is a potential target of Huang Qi Decoction against cholestatic liver fibrosis
Authors: Xu Wen , Xu Yan-nan , Zhang Xu , Xu Ying , Jian Xun , Chen Jia-mei , Chen Gao-feng , Zhang Hua , Liu Ping , Mu Yong-ping 
Published: October 2020

AbstractNumb is a negative regulator of Notch signal pathway. Previous study has demonstrated that Notch signal pathway activation is required for hepatic progenitor cell (HPC) differentiating into cholangiocytes in cholestatic liver fibrosis (CLF), and Huang Qi Decoction (HQD) could prevent CLF through inhibition of the Notch signal pathway. However, the role of Numb in HQD against CLF is yet unclear. Thus, CLF rats transplanted into rat bone marrow-derived mesenchymal stem cells with knocked down Numb gene (BMSCNumb-KD) were treated with HQD. Simultaneously, Numb gene knockdown was also performed in WB-F344 cell line and then treated with refined HQD in vitro. In vivo study revealed that liver fibrosis was inhibited by HQD plus BMSCNumb-KD treatment, while Hyp content in liver tissue, the gene and protein expression of α-SMA, gene expression of Col I, TNF-α, and TGF-β1 were increased compared to that in HQD group. Furthermore, Notch signal pathway was inhibited by HQD plus BMSCNumb-KD, while the protein expression of Numb was decreased and RBP-Jκ and Hes1 was increased compared to that in HQD group. In vitro, HQD reduced the differentiation of WB-F344 cells into cholangiocyte phenotype, while this effect was attenuated after Numb-knockdown. This study highlights that the absence of hepatic stem cell Numb gene decreases effect of HQD against CLF, which give rise the conclusion that Numb might be a potential target for HQD against CLF.
Effect of high fat diet and excessive compressive mechanical force on pathologic changes of temporomandibular joint
Authors: Du Jing , Jiang Qian , Mei Li , Yang Ren , Wen Juan , Lin Shuang , Li Huang 
Published: October 2020

AbstractThe aim of this study was to investigate the effect of high fat diet and excessive compressive mechanical force on temporomandibular joint. In vivo, a mouse model of temporomandibular joint compressive loading device was used. A high fat diet mouse model and a combined mouse model intraperitoneally treated with or without simvastatin were used in the study. The pathological changes of mandibular condylar cartilage were assessed by Safranin-O staining. The IL-1β, MMP-3, leptin expression changes in the cartilage were detected by immunohistochemistry. In vitro, the mandibular condylar chondrocytes were treated with or without L-1β and simvastatin. The mRNA expression level of matrix MMPs and leptin were assessed. Both excessive compressive mechanical force and high fat diet induced obesity caused TMJ osteoarthritis-like changes and increased expression of IL-1β, MMP-3, and leptin. These pathological changes were much more serious when the two interventions were exerted together, while simvastatin could obviously alleviate these changes. The mRNA expression of MMP-3, MMP-13, and leptin increased in the IL-1β treated chondrocytes treated with IL-1β, and decreased with simvastatin treatment. The development of temporomandibular joint pathological changes could be caused by the excessive compressive mechanical force and high fat diet induced obesity.
Crystal structure and site-directed mutagenesis of circular bacteriocin plantacyclin B21AG reveals cationic and aromatic residues important for antimicrobial activity
Authors: Gor Mian-Chee , Vezina Ben , McMahon Róisín M. , King Gordon J. , Panjikar Santosh , Rehm Bernd H. A. , Martin Jennifer L. , Smith Andrew T. 
Published: October 2020

AbstractPlantacyclin B21AG is a circular bacteriocin produced by Lactiplantibacillus plantarum B21 which displays antimicrobial activity against various Gram-positive bacteria including foodborne pathogens, Listeria monocytogenes and Clostridium perfringens. It is a 58-amino acid cyclised antimicrobial peptide, with the N and C termini covalently linked together. The circular peptide backbone contributes to remarkable stability, conferring partial proteolytic resistance and structural integrity under a wide temperature and pH range. Here, we report the first crystal structure of a circular bacteriocin from a food grade Lactobacillus. The protein was crystallised using the hanging drop vapour diffusion method and the structure solved to a resolution of 1.8 Å. Sequence alignment against 18 previously characterised circular bacteriocins revealed the presence of conserved charged and aromatic residues. Alanine substitution mutagenesis validated the importance of these residues. Minimum inhibitory concentration analysis of these Ala mutants showed that Phe8Ala and Trp45Ala mutants displayed a 48- and 32-fold reduction in activity, compared to wild type. The Lys19Ala mutant displayed the weakest activity, with a 128-fold reduction. These experiments demonstrate the relative importance of aromatic and cationic residues for the antimicrobial activity of plantacyclin B21AG and by extension, other circular bacteriocins sharing these evolutionarily conserved residues.
Submesoscale modulation of deep water formation in the Labrador Sea
Authors: Tagklis Filippos , Bracco A. , Ito T. , Castelao R. M. 
Published: October 2020

AbstractSubmesoscale structures fill the ocean surface, and recent numerical simulations and indirect observations suggest that they may extend to the ocean interior. It remains unclear, however, how far-reaching their impact may be—in both space and time, from weather to climate scales. Here transport pathways and the ultimate fate of the Irminger Current water from the continental slope to Labrador Sea interior are investigated through regional ocean simulations. Submesoscale processes modulate this transport and in turn the stratification of the Labrador Sea interior, by controlling the characteristics of the coherent vortices formed along West Greenland. Submesoscale circulations modify and control the Labrador Sea contribution to the global meridional overturning, with a linear relationship between time-averaged near surface vorticity and/or frontogenetic tendency along the west coast of Greenland, and volume of convected water. This research puts into contest the lesser role of the Labrador Sea in the overall control of the state of the MOC argued through the analysis of recent OSNAP (Overturning in the Subpolar North Atlantic Program) data with respect to estimates from climate models. It also confirms that submesoscale turbulence scales-up to climate relevance, pointing to the urgency of including its advective contribution in Earth systems models.
New insights on human IRE1 tetramer structures based on molecular modeling
Authors: Carlesso Antonio , Hörberg Johanna , Reymer Anna , Eriksson Leif A. 
Published: October 2020

AbstractInositol-Requiring Enzyme 1α (IRE1α; hereafter IRE1) is a transmembrane kinase/ribonuclease protein related with the unfolded protein response (UPR) signaling. Experimental evidence suggests that IRE1 forms several three dimensional (3D) structural variants: dimers, tetramers and higher order oligomers, where each structural variant can contain different IRE1 conformers in different arrangements. For example, studies have shown that two sets of IRE1 dimers exist; a face-to-face dimer and a back-to-back dimer, with the latter considered the important unit for UPR signaling propagation. However, the structural configuration and mechanistic details of the biologically important IRE1 tetramers are limited. Here, we combine protein–protein docking with molecular dynamics simulations to derive human IRE1 tetramer models and identify a molecular mechanism of IRE1 activation. To validate the derived models of the human IRE1 tetramer, we compare the dynamic behavior of the models with the yeast IRE1 tetramer crystallographic structure. We show that IRE1 tetramer conformational changes could be linked to the initiation of the unconventional splicing of mRNA encoding X-box binding protein-1 (XBP1), which allows for the expression of the transcription factor XBP1s (XBP1 spliced). The derived IRE1 tetrameric models bring new mechanistic insights about the IRE1 molecular activation mechanism by describing the IRE1 tetramers as active protagonists accommodating the XBP1 substrate.
The vitamin D analogue calcipotriol promotes an anti-tumorigenic phenotype of human pancreatic CAFs but reduces T cell mediated immunity
Authors: Gorchs Laia , Ahmed Sultan , Mayer Chanté , Knauf Alisa , Fernández Moro Carlos , Svensson Mattias , Heuchel Rainer , Rangelova Elena , Bergman Peter , Kaipe Helen 
Published: October 2020

AbstractThe pancreatic tumour stroma is composed of phenotypically heterogenous cancer-associated fibroblasts (CAFs) with both pro- and anti-tumorigenic functions. Here, we studied the impact of calcipotriol, a vitamin D3 analogue, on the activation of human pancreatic CAFs and T cells using 2- and 3-dimensional (2D, 3D) cell culture models. We found that calcipotriol decreased CAF proliferation and migration and reduced the release of the pro-tumorigenic factors prostaglandin E2, IL-6, periostin, and leukemia inhibitory factor. However, calcipotriol promoted PD-L1 upregulation, which could influence T cell mediated tumour immune surveillance. Calcipotriol reduced T cell proliferation and production of IFN-γ, granzyme B and IL-17, but increased IL-10 secretion. These effects were even more profound in the presence of CAFs in 2D cultures and in the presence of CAFs and pancreatic tumour cell line (PANC-1) spheroids in 3D cultures. Functional assays on tumour infiltrating lymphocytes also showed a reduction in T cell activation by calcipotriol. This suggests that calcipotriol reduces the tumour supportive activity of CAFs but at the same time reduces T cell effector functions, which could compromise the patients’ tumour immune surveillance. Thus, vitamin D3 analogues appear to have dual functions in the context of pancreatic cancer, which could have important clinical implications.