bluuebunny/crossref_metadata_2025_split huggingface dataset:
The force loading rate drives cell mechanosensing through both reinforcement and cytoskeletal softening
Authors: Andreu Ion , Falcones Bryan , Hurst Sebastian , Chahare Nimesh , Quiroga Xarxa , Le Roux Anabel-Lise , Kechagia Zanetta , Beedle Amy E. M. , Elosegui-Artola Alberto , Trepat Xavier , Farré Ramon , Betz Timo , Almendros Isaac , Roca-Cusachs Pere 
Published: July 2021

AbstractCell response to force regulates essential processes in health and disease. However, the fundamental mechanical variables that cells sense and respond to remain unclear. Here we show that the rate of force application (loading rate) drives mechanosensing, as predicted by a molecular clutch model. By applying dynamic force regimes to cells through substrate stretching, optical tweezers, and atomic force microscopy, we find that increasing loading rates trigger talin-dependent mechanosensing, leading to adhesion growth and reinforcement, and YAP nuclear localization. However, above a given threshold the actin cytoskeleton softens, decreasing loading rates and preventing reinforcement. By stretching rat lungs in vivo, we show that a similar phenomenon may occur. Our results show that cell sensing of external forces and of passive mechanical parameters (like tissue stiffness) can be understood through the same mechanisms, driven by the properties under force of the mechanosensing molecules involved.
Transcription coordinates histone amounts and genome content
Authors: Claude Kora-Lee , Bureik Daniela , Chatzitheodoridou Dimitra , Adarska Petia , Singh Abhyudai , Schmoller Kurt M. 
Published: July 2021

AbstractBiochemical reactions typically depend on the concentrations of the molecules involved, and cell survival therefore critically depends on the concentration of proteins. To maintain constant protein concentrations during cell growth, global mRNA and protein synthesis rates are tightly linked to cell volume. While such regulation is appropriate for most proteins, certain cellular structures do not scale with cell volume. The most striking example of this is the genomic DNA, which doubles during the cell cycle and increases with ploidy, but is independent of cell volume. Here, we show that the amount of histone proteins is coupled to the DNA content, even though mRNA and protein synthesis globally increase with cell volume. As a consequence, and in contrast to the global trend, histone concentrations decrease with cell volume but increase with ploidy. We find that this distinct coordination of histone homeostasis and genome content is already achieved at the transcript level, and is an intrinsic property of histone promoters that does not require direct feedback mechanisms. Mathematical modeling and histone promoter truncations reveal a simple and generalizable mechanism to control the cell volume- and ploidy-dependence of a given gene through the balance of the initiation and elongation rates.
Observation of laser-assisted electron scattering in superfluid helium
Authors: Treiber Leonhard , Thaler Bernhard , Heim Pascal , Stadlhofer Michael , Kanya Reika , Kitzler-Zeiler Markus , Koch Markus 
Published: July 2021

AbstractLaser-assisted electron scattering (LAES), a light–matter interaction process that facilitates energy transfer between strong light fields and free electrons, has so far been observed only in gas phase. Here we report on the observation of LAES at condensed phase particle densities, for which we create nano-structured systems consisting of a single atom or molecule surrounded by a superfluid He shell of variable thickness (32–340 Å). We observe that free electrons, generated by femtosecond strong-field ionization of the core particle, can gain several tens of photon energies due to multiple LAES processes within the liquid He shell. Supported by Monte Carlo 3D LAES and elastic scattering simulations, these results provide the first insight into the interplay of LAES energy gain/loss and dissipative electron movement in a liquid. Condensed-phase LAES creates new possibilities for space-time studies of solids and for real-time tracing of free electrons in liquids.
A mechanochromic donor-acceptor torsional spring
Authors: Raisch Maximilian , Maftuhin Wafa , Walter Michael , Sommer Michael 
Published: July 2021

AbstractMechanochromic polymers are intriguing materials that allow to sense force of specimens under load. Most mechanochromic systems rely on covalent bond scission and hence are two-state systems with optically distinct “on” and “off” states where correlating force with wavelength is usually not possible. Translating force of different magnitude with gradually different wavelength of absorption or emission would open up new possibilities to map and understand force distributions in polymeric materials. Here, we present a mechanochromic donor-acceptor (DA) torsional spring that undergoes force-induced planarization during uniaxial elongation leading to red-shifted absorption and emission spectra. The DA spring is based on ortho-substituted diketopyrrolopyrrole (o-DPP). Covalent incorporation of o-DPP into a rigid yet ductile polyphenylene matrix allows to transduce sufficiently large stress to the DA spring. The mechanically induced deflection from equilibrium geometry of the DA spring is theoretically predicted, in agreement with experiments, and is fully reversible upon stress release.
The evolution of convex trade-offs enables the transition towards multicellularity
Authors: Bernardes Joana P. , John Uwe , Woltermann Noemi , Valiadi Martha , Hermann Ruben J. , Becks Lutz 
Published: July 2021

AbstractThe evolutionary transition towards multicellular life often involves growth in groups of undifferentiated cells followed by differentiation into soma and germ-like cells. Theory predicts that germ soma differentiation is facilitated by a convex trade-off between survival and reproduction. However, this has never been tested and these transitions remain poorly understood at the ecological and genetic level. Here, we study the evolution of cell groups in ten isogenic lines of the unicellular green algaeChlamydomonas reinhardtiiwith prolonged exposure to a rotifer predator. We confirm that growth in cell groups is heritable and characterized by a convex trade-off curve between reproduction and survival. Identical mutations evolve in all cell group isolates; these are linked to survival and reducing associated cell costs. Overall, we show that just 500 generations of predator selection were sufficient to lead to a convex trade-off and incorporate evolved changes into the prey genome.
Native flagellar MS ring is formed by 34 subunits with 23-fold and 11-fold subsymmetries
Authors: Kawamoto Akihiro , Miyata Tomoko , Makino Fumiaki , Kinoshita Miki , Minamino Tohru , Imada Katsumi , Kato Takayuki , Namba Keiichi 
Published: July 2021

AbstractThe bacterial flagellar MS ring is a transmembrane complex acting as the core of the flagellar motor and template for flagellar assembly. The C ring attached to the MS ring is involved in torque generation and rotation switch, and a large symmetry mismatch between these two rings has been a long puzzle, especially with respect to their role in motor function. Here, using cryoEM structural analysis of the flagellar basal body and the MS ring formed by full-length FliF from Salmonella enterica, we show that the native MS ring is formed by 34 FliF subunits with no symmetry variation. Symmetry analysis of the C ring shows a variation with a peak at 34-fold, suggesting flexibility in C ring assembly. Finally, our data also indicate that FliF subunits assume two different conformations, contributing differentially to the inner and middle parts of the M ring and thus resulting in 23- and 11-fold subsymmetries in the inner and middle M ring, respectively. The internal core of the M ring, formed by 23 subunits, forms a hole of the right size to accommodate the protein export gate.
Integration of photocatalytic and dark-operating catalytic biomimetic transformations through DNA-based constitutional dynamic networks
Authors: Wang Chen , O’Hagan Michael P. , Neumann Ehud , Nechushtai Rachel , Willner Itamar 
Published: July 2021

AbstractNucleic acid-based constitutional dynamic networks (CDNs) have recently emerged as versatile tools to control a variety of catalytic processes. A key challenge in the application of these systems is achieving intercommunication between different CDNs to mimic the complex interlinked networks found in cellular biology. In particular, the possibility to interface photochemical ‘energy-harvesting’ processes with dark-operating ‘metabolic’ processes, in a similar way to plants, represents an up to now unexplored yet enticing research direction. The present study introduces two CDNs that allow the intercommunication of photocatalytic and dark-operating catalytic functions mediated by environmental components that facilitate the dynamic coupling of the networks. The dynamic feedback-driven intercommunication of the networks is accomplished via information transfer between the two CDNs effected by hairpin fuel strands in the environment of the system, leading to the coupling of the photochemical and dark-operating modules.
Identification of small molecules that interfere with c-di-GMP signaling and induce dispersal of Pseudomonas aeruginosa biofilms
Authors: Andersen Jens Bo , Hultqvist Louise Dahl , Jansen Charlotte Uldahl , Jakobsen Tim Holm , Nilsson Martin , Rybtke Morten , Uhd Jesper , Fritz Blaine Gabriel , Seifert Roland , Berthelsen Jens , Nielsen Thomas Eiland , Qvortrup Katrine , Givskov Michael , Tolker-Nielsen Tim 
Published: July 2021

AbstractMicrobial biofilms are involved in a number of infections that cannot be cured, as microbes in biofilms resist host immune defenses and antibiotic therapies. With no strict biofilm-antibiotic in the current pipelines, there is an unmet need for drug candidates that enable the current antibiotics to eradicate bacteria in biofilms. We used high-throughput screening to identify chemical compounds that reduce the intracellular c-di-GMP content in Pseudomonas aeruginosa. This led to the identification of a small molecule that efficiently depletes P. aeruginosa for c-di-GMP, inhibits biofilm formation, and disperses established biofilm. A combination of our lead compound with standard of care antibiotics showed improved eradication of an implant-associated infection established in mice. Genetic analyses provided evidence that the anti-biofilm compound stimulates the activity of the c-di-GMP phosphodiesterase BifA in P. aeruginosa. Our work constitutes a proof of concept for c-di-GMP phosphodiesterase-activating drugs administered in combination with antibiotics as a viable treatment strategy for otherwise recalcitrant infections.
Deep learning for visualization and novelty detection in large X-ray diffraction datasets
Authors: Banko Lars , Maffettone Phillip M. , Naujoks Dennis , Olds Daniel , Ludwig Alfred 
Published: July 2021

AbstractWe apply variational autoencoders (VAE) to X-ray diffraction (XRD) data analysis on both simulated and experimental thin-film data. We show that crystal structure representations learned by a VAE reveal latent information, such as the structural similarity of textured diffraction patterns. While other artificial intelligence (AI) agents are effective at classifying XRD data into known phases, a similarly conditioned VAE is uniquely effective at knowing what it doesn’t know: it can rapidly identify data outside the distribution it was trained on, such as novel phases and mixtures. These capabilities demonstrate that a VAE is a valuable AI agent for aiding materials discovery and understanding XRD measurements both ‘on-the-fly’ and during post hoc analysis.
Towards an odour-baited trap to control Musca sorbens, the putative vector of trachoma
Authors: Robinson Ailie , Bickford-Smith Jack , Abdurahman Shafi Oumer , Abraham Aga Muluadam , Shuka Gemeda , Debela Dereje , Hordofa Gebreyes , Alemayehu Wondu , Sarah Virginia , Last Anna , MacLeod David , Burton Matthew J. , Logan James G. 
Published: July 2021

AbstractMusca sorbens is a synanthropic filth fly that aggressively attacks people to feed from mucous membranes of the eyes, nose or mouth, from open sores, or from sweat. It has long been suspected that this fly contributes to the transmission of eye infections, particularly trachoma, and recent work has added to the evidence base that M. sorbens is a trachoma vector in Ethiopia. There are few options to control M. sorbens, largely due to a lack of evidence. Space spraying with insecticides is effective, but an environmentally sound and long-term sustainable solution would be better, for example, mass trapping. We tested commercially available and homemade trap types in a pilot (laboratory) study and three field studies. A homemade design, built from a bucket and two empty water bottles, baited with a commercially available lure, The Buzz, was found to be most effective. This trap caught 3848 M. sorbens over 26 trap ‘events’ (3- or 4-day periods); mean/median per 24 h 43.6 (standard deviation 137.10)/2.25 (IQR 0.25–12.67). The Buzz lure is cheap and effective for 4 weeks, and trap components cheap and locally available. Further studies are needed to understand the impact of this trap on local fly populations and the local transmission of trachoma.
Parametric excitation and mode control using an Oersted field in a NiFe nanowire
Authors: Hwang S. , Yoon Seungha , Seo Dongpyo , Han S. H. , Cho B. K. 
Published: July 2021

AbstractParametric pumping is a nonlinear wave phenomenon and a promising technique for electronic devices based on spin waves, so-called “magnonics”. For parametric excitation, a magnetic nanowire system that has a built-in dc current line to produce an Oersted field is designed, and for spin wave detection, a micro-Brillouin light scattering (μ-BLS) system is used. A spin wave with a frequency of fsw = 5.6 GHz is observed when a pumping microwave with a frequency of fmw = 11.2 GHz is applied. The wave is found to be of the n = 1 width mode (n is the antinode number), and its mode changes to an edge-localized (or possibly n > 1) mode when the Oersted field (or current) varies. Joule heating effects are not observed in the pumping process. Thus, spin wave mode control by the built-in current would be a convenient and useful method to enhance the efficiency and compatibility in applications of spin-based electronics.
Low-temperature and atmospheric pressure plasma for palm biodiesel hydrogenation
Authors: Kongprawes Grittima , Wongsawaeng Doonyapong , Ngaosuwan Kanokwan , Kiatkittipong Worapon , Assabumrungrat Suttichai 
Published: July 2021

AbstractPartially hydrogenated fatty acid methyl ester (H-FAME) is conventionally produced through partial hydrogenation under high pressure and elevated temperature in the presence of a catalyst. Herein, a novel green, catalyst-free, non-thermal and atmospheric pressure dielectric barrier discharge (DBD) plasma was employed instead of a conventional method to hydrogenate palm FAME. H-FAME became more saturated with the conversion of C18:2 and C18:3 of 47.4 and 100%, respectively, at 100 W input power, 1 mm gas-filled gap size and 80% H2 in the mixed gas at room temperature for 5 h, causing a reduction of the iodine value from 50.2 to 43.5. Oxidation stability increased from 12.8 to 20 h while a cloud point changed from 13.5 to 16 °C. Interestingly, DBD plasma hydrogenation resulted in no trans-fatty acid formation which provided a positive effect on the cloud point. This green DBD plasma system showed a superior performance to a conventional catalytic reaction. It is an alternative method that is safe from explosion due to the mild operating condition, as well as being highly environmentally friendly by reducing waste and energy utilization from the regeneration process required for a catalytic process. This novel green plasma hydrogenation technique could also be applied to other liquid-based processes.
The benefit of the diffusion kurtosis imaging in presurgical evaluation in patients with focal MR-negative epilepsy
Authors: Bartoňová Michaela , Bartoň Marek , Říha Pavel , Vojtíšek Lubomír , Brázdil Milan , Rektor Ivan 
Published: July 2021

AbstractThe effectivity of diffusion-weighted MRI methods in detecting the epileptogenic zone (EZ) was tested. Patients with refractory epilepsy (N=25) who subsequently underwent resective surgery were recruited. First, the extent of white matter (WM) asymmetry from mean kurtosis (MK) was calculated in order to detect the lobe with the strongest impairment. Second, a newly developed metric was used, reflecting a selection of brain areas with concurrently increased mean Diffusivity, reduced fractional Anisotropy, and reduced mean Kurtosis (iDrArK). A two-step EZ detection was performed as (1) lobe-specific detection, (2) iDrArK voxel-wise detection (with a possible lobe-specific restriction if the result of the first step was significant in a given subject). The method results were compared with the surgery resection zones. From the whole cohort (N=25), the numbers of patients with significant results were: 10 patients in lobe detection and 9 patients in EZ detection. From these subsets of patients with significant results, the impaired lobe was successfully detected with 100% accuracy; the EZ was successfully detected with 89% accuracy. The detection of the EZ using iDrArK was substantially more successful when compared with solo diffusional parameters (or their pairwise combinations). For a subgroup with significant results from step one (N=10), iDrArK without lobe restriction achieved 37.5% accuracy; lobe-restricted iDrArK achieved 100% accuracy. The study shows the plausibility of MK for detecting widespread WM changes and the benefit of combining different diffusional voxel-wise parameters.
Long range correlations and slow time scales in a boundary driven granular model
Authors: Plati Andrea , Puglisi Andrea 
Published: July 2021

AbstractWe consider a velocity field with linear viscous interactions defined on a one dimensional lattice. Brownian baths with different parameters can be coupled to the boundary sites and to the bulk sites, determining different kinds of non-equilibrium steady states or free-cooling dynamics. Analytical results for spatial and temporal correlations are provided by analytical diagonalisation of the system’s equations in the infinite size limit. We demonstrate that spatial correlations are scale-free and time-scales become exceedingly long when the system is driven only at the boundaries. On the contrary, in the case a bath is coupled to the bulk sites too, an exponential correlation decay is found with a finite characteristic length. This is also true in the free cooling regime, but in this case the correlation length grows diffusively in time. We discuss the crucial role of boundary driving for long-range correlations and slow time-scales, proposing an analogy between this simplified dynamical model and dense vibro-fluidized granular materials. Several generalizations and connections with the statistical physics of active matter are also suggested.
Morphological, molecular characterization, plant pathogenicity and biocontrol of Cladosporium complex groups associated with faba beans
Authors: El-Dawy Eman Gamal Abd Elnaser Mohamed , Gherbawy Youssuf Ahmed , Hussein Mohamed Ahmed 
Published: July 2021

AbstractVicia faba (faba bean) is one of the most significant leguminous crops. The faba bean is specialized by maximum nutritional value, in energy and protein content, which leads it to be suitable for food and feed production. Diseases caused with fungi are amongst the biotic factors responsible for decreasing in faba bean yields. In this work, Cladosporium isolates were recorded in cultivated faba bean leaves and pods collected from markets in Qena, Upper Egypt; morphological features and molecular characterization based on actin gene were performed. The ability of the pathogens to cause disease in faba bean seedlings and the biocontrol method to avoid the pathogenic effect of Cladosporium were determined. Results showed that Cladosporium is the main genera isolated from faba beans, and the morphological criteria showed presence of three species complex groups of Cladosporium (C. cladosporioides, C. herbarum and C. sphaerospermum) and the confirmation with molecular characterization revealed the existence of four species in the three groups. All the 26 tested strains of Cladosporium were able to cause leaf lesions on Vicia faba seedlings with different levels. Chaetomium globosum is a biocontrol agent could inhibit the growth of the majority strains of Cladosporium.
Time course profiling of host cell response to herpesvirus infection using nanopore and synthetic long-read transcriptome sequencing
Authors: Maróti Zoltán , Tombácz Dóra , Moldován Norbert , Torma Gábor , Jefferson Victoria A. , Csabai Zsolt , Gulyás Gábor , Dörmő Ákos , Boldogkői Miklós , Kalmár Tibor , Meyer Florencia , Boldogkői Zsolt 
Published: July 2021

AbstractThird-generation sequencing is able to read full-length transcripts and thus to efficiently identify RNA molecules and transcript isoforms, including transcript length and splice isoforms. In this study, we report the time-course profiling of the effect of bovine alphaherpesvirus type 1 on the gene expression of bovine epithelial cells using direct cDNA sequencing carried out on MinION device of Oxford Nanopore Technologies. These investigations revealed a substantial up- and down-regulatory effect of the virus on several gene networks of the host cells, including those that are associated with antiviral response, as well as with viral transcription and translation. Additionally, we report a large number of novel bovine transcript isoforms identified by nanopore and synthetic long-read sequencing. This study demonstrates that viral infection causes differential expression of host transcript isoforms. We could not detect an increased rate of transcriptional readthroughs as described in another alphaherpesvirus. According to our knowledge, this is the first report on the use of LoopSeq for the analysis of eukaryotic transcriptomes. This is also the first report on the application of nanopore sequencing for the kinetic characterization of cellular transcriptomes. This study also demonstrates the utility of nanopore sequencing for the characterization of dynamic transcriptomes in any organisms.