bluuebunny/crossref_metadata_2025_split huggingface dataset:
Missing self triggers NK cell-mediated chronic vascular rejection of solid organ transplants
Authors: Koenig Alice , Chen Chien-Chia , Marçais Antoine , Barba Thomas , Mathias Virginie , Sicard Antoine , Rabeyrin Maud , Racapé Maud , Duong-Van-Huyen Jean-Paul , Bruneval Patrick , Loupy Alexandre , Dussurgey Sébastien , Ducreux Stéphanie , Meas-Yedid Vannary , Olivo-Marin Jean-Christophe , Paidassi Héléna , Guillemain Romain , Taupin Jean-Luc , Callemeyn Jasper , Morelon Emmanuel , Nicoletti Antonino , Charreau Béatrice , Dubois Valérie , Naesens Maarten , Walzer Thierry , Defrance Thierry , Thaunat Olivier 
Published: November 2019

AbstractCurrent doctrine is that microvascular inflammation (MVI) triggered by a transplant -recipient antibody response against alloantigens (antibody-mediated rejection) is the main cause of graft failure. Here, we show that histological lesions are not mediated by antibodies in approximately half the participants in a cohort of 129 renal recipients with MVI on graft biopsy. Genetic analysis of these patients shows a higher prevalence of mismatches between donor HLA I and recipient inhibitory killer cell immunoglobulin-like receptors (KIRs). Human in vitro models and transplantation of β2-microglobulin-deficient hearts into wild-type mice demonstrates that the inability of graft endothelial cells to provide HLA I-mediated inhibitory signals to recipient circulating NK cells triggers their activation, which in turn promotes endothelial damage. Missing self-induced NK cell activation is mTORC1-dependent and the mTOR inhibitor rapamycin can prevent the development of this type of chronic vascular rejection.
The importance of relativistic effects on two-photon absorption spectra in metal halide perovskites
Authors: Wei Zimu , Guo Dengyang , Thieme Jos , Katan Claudine , Caselli Valentina M. , Even Jacky , Savenije Tom J. 
Published: November 2019

AbstractDespite intense research into the optoelectronic properties of metal halide perovskites (MHPs), sub-bandgap absorption in MHPs remains largely unexplored. Here we recorded two-photon absorption spectra of MHPs using the time-resolved microwave conductivity technique. A two-step upward trend is observed in the two-photon absorption spectrum for methylammonium lead iodide, and some analogues, which implies that the commonly used scaling law is not applicable to MHPs. This aspect is further confirmed by temperature-dependent conductivity measurements. Using an empirical multiband tight binding model, spectra for methylammonium lead iodide were calculated by integration over the entire Brillouin zone, showing compelling similarity with experimental results. We conclude that the second upward trend in the two-photon absorption spectrum originates from additional optical transitions to the heavy and light electron bands formed by the strong spin-orbit coupling. Hence, valuable insight can be obtained in the opto-electronic properties of MHPs by sub-bandgap spectroscopy, complemented by modelling.
Heritability of skewed X-inactivation in female twins is tissue-specific and associated with age
Authors: Zito Antonino , Davies Matthew N. , Tsai Pei-Chien , Roberts Susanna , Andres-Ejarque Rosa , Nardone Stefano , Bell Jordana T. , Wong Chloe C. Y. , Small Kerrin S. 
Published: November 2019

AbstractFemale somatic X-chromosome inactivation (XCI) balances the X-linked transcriptional dosages between the sexes. Skewed XCI toward one parental X has been observed in several complex human traits, but the extent to which genetics and environment influence skewed XCI is largely unexplored. To address this, we quantify XCI-skew in multiple tissues and immune cell types in a twin cohort. Within an individual, XCI-skew differs between blood, fat and skin tissue, but is shared across immune cell types. XCI skew increases with age in blood, but not other tissues, and is associated with smoking. XCI-skew is increased in twins with Rheumatoid Arthritis compared to unaffected identical co-twins. XCI-skew is heritable in blood of females >55 years old (h2 = 0.34), but not in younger individuals or other tissues. This results in a Gene x Age interaction that shifts the functional dosage of all X-linked heterozygous loci in a tissue-restricted manner.
Birds repurpose the role of drag and lift to take off and land
Authors: Chin Diana D. , Lentink David 
Published: November 2019

AbstractThe lift that animal wings generate to fly is typically considered a vertical force that supports weight, while drag is considered a horizontal force that opposes thrust. To determine how birds use lift and drag, here we report aerodynamic forces and kinematics of Pacific parrotlets (Forpus coelestis) during short, foraging flights. At takeoff they incline their wing stroke plane, which orients lift forward to accelerate and drag upward to support nearly half of their bodyweight. Upon landing, lift is oriented backward to contribute a quarter of the braking force, which reduces the aerodynamic power required to land. Wingbeat power requirements are dominated by downstrokes, while relatively inactive upstrokes cost almost no aerodynamic power. The parrotlets repurpose lift and drag during these flights with lift-to-drag ratios below two. Such low ratios are within range of proto-wings, showing how avian precursors may have relied on drag to take off with flapping wings.
Global chromatin conformation differences in the Drosophila dosage compensated chromosome X
Authors: Pal Koustav , Forcato Mattia , Jost Daniel , Sexton Thomas , Vaillant Cédric , Salviato Elisa , Mazza Emilia Maria Cristina , Lugli Enrico , Cavalli Giacomo , Ferrari Francesco 
Published: November 2019

AbstractIn Drosophila melanogaster the single male chromosome X undergoes an average twofold transcriptional upregulation for balancing the transcriptional output between sexes. Previous literature hypothesised that a global change in chromosome structure may accompany this process. However, recent studies based on Hi-C failed to detect these differences. Here we show that global conformational differences are specifically present in the male chromosome X and detectable using Hi-C data on sex-sorted embryos, as well as male and female cell lines, by leveraging custom data analysis solutions. We find the male chromosome X has more mid-/long-range interactions. We also identify differences at structural domain boundaries containing BEAF-32 in conjunction with CP190 or Chromator. Weakening of these domain boundaries in male chromosome X co-localizes with the binding of the dosage compensation complex and its co-factor CLAMP, reported to enhance chromatin accessibility. Together, our data strongly indicate that chromosome X dosage compensation affects global chromosome structure.
Identification of the periplasmic DNA receptor for natural transformation of Helicobacter pylori
Authors: Damke Prashant P. , Di Guilmi Anne Marie , Varela Paloma Fernández , Velours Christophe , Marsin Stéphanie , Veaute Xavier , Machouri Mérick , Gunjal Gaurav V. , Rao Desirazu N. , Charbonnier Jean-Baptiste , Radicella J. Pablo 
Published: November 2019

AbstractHorizontal gene transfer through natural transformation is a major driver of antibiotic resistance spreading in many pathogenic bacterial species. In the case of Gram-negative bacteria, and in particular of Helicobacter pylori, the mechanisms underlying the handling of the incoming DNA within the periplasm are poorly understood. Here we identify the protein ComH as the periplasmic receptor for the transforming DNA during natural transformation in H. pylori. ComH is a DNA-binding protein required for the import of DNA into the periplasm. Its C-terminal domain displays strong affinity for double-stranded DNA and is sufficient for the accumulation of DNA in the periplasm, but not for DNA internalisation into the cytoplasm. The N-terminal region of the protein allows the interaction of ComH with a periplasmic domain of the inner-membrane channel ComEC, which is known to mediate the translocation of DNA into the cytoplasm. Our results indicate that ComH is involved in the import of DNA into the periplasm and its delivery to the inner membrane translocator ComEC.
Assembly of chromosome-scale contigs by efficiently resolving repetitive sequences with long reads
Authors: Du Huilong , Liang Chengzhi 
Published: November 2019

AbstractThe abundant repetitive sequences in complex eukaryotic genomes cause fragmented assemblies, which lose value as reference genomes, often due to incomplete gene sequences and unanchored or mispositioned contigs on chromosomes. Here we report a genome assembly method HERA, which resolves repeats efficiently by constructing a connection graph from an overlap graph. We test HERA on the genomes of rice, maize, human, and Tartary buckwheat with single-molecule sequencing and mapping data. HERA correctly assembles most of the previously unassembled regions, resulting in dramatically improved, highly contiguous genome assemblies with newly assembled gene sequences. For example, the maize contig N50 size reaches 61.2 Mb and the Tartary buckwheat genome comprises only 20 contigs. HERA can also be used to fill gaps and fix errors in reference genomes. The application of HERA will greatly improve the quality of new or existing assemblies of complex genomes.
Simultaneous multi-signal quantification for highly precise serodiagnosis utilizing a rationally constructed platform
Authors: Liu Yuxin , Wei Zheng , Zhou Jing , Ma Zhanfang 
Published: November 2019

AbstractSerodiagnosis with a single quantification method suffers from high false positive/negative rates. In this study, a three-channel platform with an accessional instrumented system was constructed for simultaneous electrochemical, luminescent, and photothermal quantification of H2S, a bio-indicator for acute pancreatitis (AP) diagnosis. Utilizing the specific reaction between platform and H2S, the three-channel platform showed high sensitivity and selectivity in the biological H2S concentration range. The three-channel platform was also feasible for identifying the difference in the plasma H2S concentrations of AP and normal mice. More importantly, the precision of AP serodiagnosis was significantly improved (>99.0%) using the three-signal method based on the three-channel platform and an optimized threshold, which was clearly higher than that of the single- or two-signal methods (79.5%–94.1%). Our study highlights the importance of constructing a multichannel platform for the simultaneous multi-signal quantification of bio-indicators, and provides rigorous ways to improve the precision of medical serodiagnosis.
Styrene maleic acid recovers proteins from mammalian cells and tissues while avoiding significant cell death
Authors: Smith Andrew J. , Wright Kathleen E. , Muench Stephen P. , Schumann Sophie , Whitehouse Adrian , Porter Karen E. , Colyer John 
Published: November 2019

AbstractDetection of protein biomarkers is an important tool for medical diagnostics, typically exploiting concentration of particular biomarkers or biomarker release from tissues. We sought to establish whether proteins not normally released by living cells can be extracted without harming cells, with a view to extending this into biomarker harvest for medical diagnosis and other applications. Styrene maleic acid (SMA) is a polymer that extracts nanodiscs of biological membranes (containing membrane proteins) from cells. Hitherto it has been used to harvest SMA-lipid-membrane protein particles (SMALP) for biochemical study, by destroying the living cellular specimen. In this study, we applied SMA at low concentration to human primary cardiovascular cells and rat vascular tissue, to ‘biopsy’ cell proteins while avoiding significant reductions in cell viability. SMA at 6.25 parts per million harvested proteins from cells and tissues without causing significant release of cytosolic dye (calcein) or reduction in cell viability at 24 and 72 hours post-SMA (MTT assay). A wide range of proteins were recovered (20–200 kDa) and a number identified by mass spectrometry: this confirmed protein recovery from plasma membrane, intracellular membranes and cell cytosol without associated cell death. These data demonstrate the feasibility of non-lethally sampling proteins from cells, greatly extending our sampling capability, which could yield new physiological and/or pathological biomarkers.
Stability of cellulase in ionic liquids: correlations between enzyme activity and COSMO-RS descriptors
Authors: Pedersen Jacob Nedergaard , Pérez Bianca , Guo Zheng 
Published: November 2019

AbstractIonic liquids (ILs) are effective in pretreating cellulose for enhanced enzymatic saccharification, however ILs can inactivate cellulases. To guide the selection of ILs, the activity of cellulase was correlated with COSMO-RS calculations and descriptors of ILs including hydrogen bond (H-bond) basicity/acidity, polarity and ion size. Trends were deduced using an anion-series and a cation-series of ionic liquids in aqueous solutions. The activity in the cation-series was best correlated with the size of varied cations, whereas the activity in the anion-series showed a pronounced correlation to H-bond basicity and polarity of different anions. COSMO-RS was further used to predict the solubility of cellulose in ILs, which was correlated with cellulase activity on IL-pretreated cellulose. The best correlations were found between the enzyme activity in the anion-series ILs and the logarithmic activity coefficients, the H-bond energy, H-bond basicity and polarizability, underlining that the anion plays a crucial role in cellulose dissolution.
Gastric acid inhibitor aggravates indomethacin-induced small intestinal injury via reducing Lactobacillus johnsonii
Authors: Nadatani Yuji , Watanabe Toshio , Suda Wataru , Nakata Akinobu , Matsumoto Yuji , Kosaka Satoshi , Higashimori Akira , Otani Koji , Hosomi Shuhei , Tanaka Fumio , Nagami Yasuaki , Kamata Noriko , Taira Koichi , Yamagami Hirokazu , Tanigawa Tetsuya , Hattori Masahira , Fujiwara Yasuhiro 
Published: November 2019

AbstractProton pump inhibitors (PPIs) alter the composition of the intestinal microbiome, exacerbating indomethacin (IND)-induced small intestinal damage. Vonoprazan fumarate inhibits gastric acid secretion using a different mechanism from PPIs. We investigated the effects of both drugs on the intestinal microbiome and IND-induced small intestinal damage. We sought to clarify whether PPI-induced dysbiosis and worsening of the damage were due to a specific drug class effect of PPIs. Rabeprazole administration increased operational taxonomic unit numbers in the small intestines of C57BL/6 J mice, whereas the difference was not significant in the vonoprazan-treated group but exhibited a trend. Permutational multivariate analysis of variance of the unweighted UniFrac distances showed significant differences between vehicle- and vonoprazan- or rabeprazole-treated groups. L. johnsonii was the predominant microbial species, and the population ratio decreased after vonoprazan and rabeprazole administration. The vonoprazan- and rabeprazole-treated groups showed increased IND-induced damage. This high sensitivity to IND-induced damage was evaluated by transplantation with contents from the small intestine of mice treated with either vonoprazan or rabeprazole. Supplementation of L. johnsonii orally in mice treated with rabeprazole and vonoprazan prevented the increase in IND-induced small intestinal damage. In conclusion, both rabeprazole and vonoprazan aggravated NSAID-induced small intestinal injury by reducing the population of L. johnsonii in the small intestine via suppressing gastric acid secretion.
Phenomenological models of NaV1.5. A side by side, procedural, hands-on comparison between Hodgkin-Huxley and kinetic formalisms
Authors: Andreozzi Emilio , Carannante Ilaria , D’Addio Giovanni , Cesarelli Mario , Balbi Pietro 
Published: November 2019

AbstractComputational models of ion channels represent the building blocks of conductance-based, biologically inspired models of neurons and neural networks. Ion channels are still widely modelled by means of the formalism developed by the seminal work of Hodgkin and Huxley (HH), although the electrophysiological features of the channels are currently known to be better fitted by means of kinetic Markov-type models. The present study is aimed at showing why simplified Markov-type kinetic models are more suitable for ion channels modelling as compared to HH ones, and how a manual optimization process can be rationally carried out for both. Previously published experimental data of an illustrative ion channel (NaV1.5) are exploited to develop a step by step optimization of the two models in close comparison. A conflicting practical limitation is recognized for the HH model, which only supplies one parameter to model two distinct electrophysiological behaviours. In addition, a step by step procedure is provided to correctly optimize the kinetic Markov-type model. Simplified Markov-type kinetic models are currently the best option to closely approximate the known complexity of the macroscopic currents of ion channels. Their optimization can be achieved through a rationally guided procedure, and allows to obtain models with a computational burden that is comparable with HH models one.
ctDNA detected by ddPCR reveals changes in tumour load in metastatic malignant melanoma treated with bevacizumab
Authors: Forthun Rakel Brendsdal , Hovland Randi , Schuster Cornelia , Puntervoll Hanne , Brodal Hans Petter , Namløs Heidi Maria , Aasheim Lars Birger , Meza-Zepeda Leonardo A. , Gjertsen Bjørn Tore , Knappskog Stian , Straume Oddbjørn 
Published: November 2019

AbstractBevacizumab is included in an increasing number of clinical trials. To find biomarkers to predict and monitor treatment response, cancer and angiogenesis relevant mutations in tumour and circulating tumour DNA (ctDNA) were investigated in 26 metastatic melanoma patients treated with bevacizumab. Patients with >1% BRAF/NRAS ctDNA at treatment start had significantly decreased progression free survival (PFS) and overall survival (OS) (PFS: p = 0.019, median 54 vs 774 days, OS: p = 0.026, median 209 vs 1064 days). Patients with >1% BRAF/NRAS ctDNA during treatment showed similar results (PFS: p = 0.002, OS: p = 0.003). ≤1% BRAF/NRAS ctDNA and normal lactate dehydrogenase (LDH) levels both significantly predicted increased response to treatment, but BRAF/NRAS ctDNA was better at predicting response compared to LDH at treatment start (OR 16.94, p = 0.032 vs OR 4.57, p = 0.190), and at predicting PFS (HR 6.76, p = 0.002) and OS (HR 6.78, p = 0.002) during therapy. ctDNA BRAF p.V600D/E/K and NRAS p.G12V/p.Q61K/L/R were better biomarkers for response prediction than TERT promoter mutations (OR 1.50, p = 0.657). Next generation sequencing showed that all patients with ≥2 mutations in angiogenesis-relevant genes had progressive disease, but did not reveal other biomarkers identifying responders. To conclude, ctDNA and LDH are useful biomarkers for both monitoring and predicting response to bevacizumab.
Evidence for confounding eye movements under attempted fixation and active viewing in cognitive neuroscience
Authors: Thielen Jordy , Bosch Sander E. , van Leeuwen Tessa M. , van Gerven Marcel A. J. , van Lier Rob 
Published: November 2019

AbstractEye movements can have serious confounding effects in cognitive neuroscience experiments. Therefore, participants are commonly asked to fixate. Regardless, participants will make so-called fixational eye movements under attempted fixation, which are thought to be necessary to prevent perceptual fading. Neural changes related to these eye movements could potentially explain previously reported neural decoding and neuroimaging results under attempted fixation. In previous work, under attempted fixation and passive viewing, we found no evidence for systematic eye movements. Here, however, we show that participants’ eye movements are systematic under attempted fixation when active viewing is demanded by the task. Since eye movements directly affect early visual cortex activity, commonly used for neural decoding, our findings imply alternative explanations for previously reported results in neural decoding.
Couleurs et émaux. Des décors de la Manufacture de Sèvres à la réactivité des pigments
Authors: Verger Louisiane , Dargaud Olivier , Cormier Laurent 
Published: November 2019

Un décor de porcelaine est obtenu à l’aide de mélanges de pigments et de composants incolores qui, en se vitrifiant, fixent l’émail à la surface de l’objet et révèlent ainsi la couleu.
Cet article s’intéresse à la stabilité d’un pigment de type spinelle au cours de la cuisson du décor. La caractérisation d’un grain de ce pigment par microscopie électronique, spectroscopie optique et absorption des rayons X, a permis de montrer que le changement de couleur parfois observé après cuisson résulte d’un enrichissement en chrome de la périphérie des grains de spinelle.
Physique de l’archéomagnétisme pour la datation de bâtiments du haut Moyen Âge
Authors: Lanos Philippe 
Published: November 2019

La physique de l’archéomagnétisme, basée sur la mesure des aimantations thermorémanentes et sur l’étude du champ magnétique terrestre dans le passé, permet de dater les terres cuites archéologiques restées en place depuis leur dernière cuisson, mais aussi celles qui ont été déplacées depuis leur lieu de fabrication jusqu’au lieu de la construction.
La datation de monuments du haut Moyen Âge a permis de nouvelles interprétations des mesures d’aimantation effectuées sur les briques mises en œuvre dans les maçonneries. Ces avancées récentes sont illustrées ici dans le cas de la tour-clocher de la collégiale Saint‑Martin à Angers.
Social and Economic Factors of Sports Activity in Russian Regions
Authors: Kramin T.V. , Miftahov M.R. , Andreff W. , Eroshkina S.B. 
Published: November 2019

In this study, the key factors of sports activity in the Russian regions were identified and substantiated. The regional panel data for the period 2007–2017 was used as data for the study. It is shown that traditional material factors are highly significant in models for assessing the level of sports activity in the Russian regions. These include, in particular, the following indicators: the one-time carrying capacity of sports facilities, the per capita expenditures for physical culture and sports development, the number of sports facilities per 100 thousand people, the number of full-time physical culture and sports personnel per capita. Consequently, forecasting based on them will give a stable and reliable result.
Along with the evidence of the significance of the material factors of sports activity, a justification of the influence of a number of intangible, institutional factors is given. Such factors include the awareness about the benefits of systematic physical education and sports, institutions of public encouragement and support for those involved in sports and physical culture, etc.