bluuebunny/crossref_metadata_2025_split huggingface dataset:
Functional genomics uncovers the transcription factor BNC2 as required for myofibroblastic activation in fibrosis
Authors: Bobowski-Gerard Marie , Boulet Clémence , Zummo Francesco P. , Dubois-Chevalier Julie , Gheeraert Céline , Bou Saleh Mohamed , Strub Jean-Marc , Farce Amaury , Ploton Maheul , Guille Loïc , Vandel Jimmy , Bongiovanni Antonino , Very Ninon , Woitrain Eloïse , Deprince Audrey , Lalloyer Fanny , Bauge Eric , Ferri Lise , Ntandja-Wandji Line-Carolle , Cotte Alexia K. , Grangette Corinne , Vallez Emmanuelle , Cianférani Sarah , Raverdy Violeta , Caiazzo Robert , Gnemmi Viviane , Leteurtre Emmanuelle , Pourcet Benoit , Paumelle Réjane , Ravnskjaer Kim , Lassailly Guillaume , Haas Joel T. , Mathurin Philippe , Pattou François , Dubuquoy Laurent , Staels Bart , Lefebvre Philippe , Eeckhoute Jérôme 
Published: September 2022

AbstractTissue injury triggers activation of mesenchymal lineage cells into wound-repairing myofibroblasts, whose unrestrained activity leads to fibrosis. Although this process is largely controlled at the transcriptional level, whether the main transcription factors involved have all been identified has remained elusive. Here, we report multi-omics analyses unraveling Basonuclin 2 (BNC2) as a myofibroblast identity transcription factor. Using liver fibrosis as a model for in-depth investigations, we first show that BNC2 expression is induced in both mouse and human fibrotic livers from different etiologies and decreases upon human liver fibrosis regression. Importantly, we found that BNC2 transcriptional induction is a specific feature of myofibroblastic activation in fibrotic tissues. Mechanistically, BNC2 expression and activities allow to integrate pro-fibrotic stimuli, including TGFβ and Hippo/YAP1 signaling, towards induction of matrisome genes such as those encoding type I collagen. As a consequence, Bnc2 deficiency blunts collagen deposition in livers of mice fed a fibrogenic diet. Additionally, our work establishes BNC2 as potentially druggable since we identified the thalidomide derivative CC-885 as a BNC2 inhibitor. Altogether, we propose that BNC2 is a transcription factor involved in canonical pathways driving myofibroblastic activation in fibrosis.
A multi-state dynamic process confers mechano-adaptation to a biological nanomachine
Authors: Wadhwa Navish , Sassi Alberto , Berg Howard C. , Tu Yuhai 
Published: September 2022

AbstractAdaptation is a defining feature of living systems. The bacterial flagellar motor adapts to changes in the external mechanical load by adding or removing torque-generating (stator) units. But the molecular mechanism behind this mechano-adaptation remains unclear. Here, we combine single motor eletrorotation experiments and theoretical modeling to show that mechano-adaptation of the flagellar motor is enabled by multiple mechanosensitive internal states. Dwell time statistics from experiments suggest the existence of at least two bound states with a high and a low unbinding rate, respectively. A first-passage-time analysis of a four-state model quantitatively explains the experimental data and determines the transition rates among all four states. The torque generated by bound stator units controls their effective unbinding rate by modulating the transition between the bound states, possibly via a catch bond mechanism. Similar force-mediated feedback enabled by multiple internal states may apply to adaptation in other macromolecular complexes.
Genome-scale RNA interference profiling of Trypanosoma brucei cell cycle progression defects
Authors: Marques Catarina A. , Ridgway Melanie , Tinti Michele , Cassidy Andrew , Horn David 
Published: September 2022

AbstractTrypanosomatids, which include major pathogens of humans and livestock, are flagellated protozoa for which cell cycle controls and the underlying mechanisms are not completely understood. Here, we describe a genome-wide RNA-interference library screen for cell cycle defects inTrypanosoma brucei. We induced massive parallel knockdown, sorted the perturbed population using high-throughput flow cytometry, deep-sequenced RNAi-targets from each stage and digitally reconstructed cell cycle profiles at a genomic scale; also enabling data visualisation using an online tool (https://tryp-cycle.pages.dev/). Analysis of several hundred genes that impact cell cycle progression reveals >100 flagellar component knockdowns linked to genome endoreduplication, evidence for metabolic control of the G1-S transition, surface antigen regulatory mRNA-binding protein knockdowns linked to G2M accumulation, and a putative nucleoredoxin required for both mitochondrial genome segregation and for mitosis. The outputs provide comprehensive functional genomic evidence for the known and novel machineries, pathways and regulators that coordinate trypanosome cell cycle progression.
Self-supervised image quality assessment for X-ray tomographic images of Li-ion battery
Authors: Zhang Kai , Nguyen Tuan-Tu , Su Zeliang , Demortière Arnaud 
Published: September 2022

AbstractImage perception plays a fundamental role in the tomography-based approaches for microstructure characterization and has a deep impact on all subsequent stages of image processing, such as segmentation and 3D analysis. The enhancement of image perception, however, frequently involves observer-dependence, which reflects user-to-user dispersion and uncertainties in the calculated parameters. This work presents an objective quantitative method, which uses convolutional neural networks (CNN) for the quality assessment of the X-ray tomographic images. With only dozens of annotations, our method allows to evaluate directly and precisely the quality of tomographic images. Different metrics were employed to evaluate the correlation between our predicted scores and subjective human annotations. The evaluation results demonstrate that our method can be a direct tool to guide the enhancement process in order to produce reliable segmentation results. The processing of the tomographic image can thus evolve into a robust observer-independent procedure and advance towards the development of an efficient self-supervised approach.
Evolution of electronic and magnetic properties of Sr2IrO4 under strain
Authors: Pärschke Ekaterina M. , Chen Wei-Chih , Ray Rajyavardhan , Chen Cheng-Chien 
Published: September 2022

AbstractMotivated by properties-controlling potential of the strain, we investigate strain dependence of structure, electronic, and magnetic properties of Sr2IrO4 using complementary theoretical tools: ab-initio calculations, analytical approaches (rigid octahedra picture, Slater-Koster integrals), and extended $$t-{{{\mathcal{J}}}}$$

t
−
J

model. We find that strain affects both Ir-Ir distance and Ir-O-Ir angle, and the rigid octahedra picture is not relevant. Second, we find fundamentally different behavior for compressive and tensile strain. One remarkable feature is the formation of two subsets of bond- and orbital-dependent carriers, a compass-like model, under compression. This originates from the strain-induced renormalization of the Ir-O-Ir superexchange and O on-site energy. We also show that under compressive (tensile) strain, Fermi surface becomes highly dispersive (relatively flat). Already at a tensile strain of 1.5%, we observe spectral weight redistribution, with the low-energy band acquiring almost purely singlet character. These results can be directly compared with future experiments.
Terahertz lattice and charge dynamics in ferroelectric semiconductor SnxPb1−xTe
Authors: Okamura Y. , Handa H. , Yoshimi R. , Tsukazaki A. , Takahashi K. S. , Kawasaki M. , Tokura Y. , Takahashi Y. 
Published: September 2022

AbstractThe symmetry breaking induced by the ferroelectric transition often triggers the emergence of topological electronic states such as Weyl fermions in polar metals/semimetals. Such strong coupling between the lattice deformation and electronic states is therefore essentially important for the control of versatile topological phases. Here, we study the terahertz lattice and charge dynamics in ferroelectric semiconductor SnxPb1-xTe thin films hosting versatile topological phases by means of the terahertz time-domain spectroscopy. With lowering the temperature, the resonant frequency of transverse optical (TO) phonon shows the significant softening and upturn. This temperature anomaly of lattice dynamics directly indicates the displacive-type ferroelectric transition. The resulting phase diagram suggests the enhancement of ferroelectricity in the films possibly due to compressive strain compared with the bulk crystals. The low-energy TO phonon induces the large DC and terahertz dielectric constant even in metallic state. Furthermore, we find that the Born effective charge of phonon mode is enhanced at around the compositions showing the band gap closing associated with the topological transition.
Sharkipedia: a curated open access database of shark and ray life history traits and abundance time-series
Authors: Mull Christopher G. , Pacoureau Nathan , Pardo Sebastián A. , Ruiz Luz Saldaña , García-Rodríguez Emiliano , Finucci Brittany , Haack Max , Harry Alastair , Judah Aaron B. , VanderWright Wade , Yin Jamie S. , Kindsvater Holly K. , Dulvy Nicholas K. 
Published: September 2022

AbstractA curated database of shark and ray biological data is increasingly necessary both to support fisheries management and conservation efforts, and to test the generality of hypotheses of vertebrate macroecology and macroevolution. Sharks and rays are one of the most charismatic, evolutionary distinct, and threatened lineages of vertebrates, comprising around 1,250 species. To accelerate shark and ray conservation and science, we developed Sharkipedia as a curated open-source database and research initiative to make all published biological traits and population trends accessible to everyone. Sharkipedia hosts information on 58 life history traits from 274 sources, for 170 species, from 39 families, and 12 orders related to length (n = 9 traits), age (8), growth (12), reproduction (19), demography (5), and allometric relationships (5), as well as 871 population time-series from 202 species. Sharkipedia relies on the backbone taxonomy of the IUCN Red List and the bibliography of Shark-References. Sharkipedia has profound potential to support the rapidly growing data demands of fisheries management, international trade regulation as well as anchoring vertebrate macroecology and macroevolution.
A global dataset of microbial community in ticks from metagenome study
Authors: Liu Mei-Chen , Zhang Jing-Tao , Chen Jin-Jin , Zhu Ying , Fu Bo-Kang , Hu Zhen-Yu , Fang Li-Qun , Zhang Xiao-Ai , Liu Wei 
Published: September 2022

AbstractTicks are important vectors of various zoonotic pathogens that can infect animals and humans, and most documented tick-borne pathogens have a strong bias towards microorganisms with strong disease phenotypes. The recent development of next-generation sequencing (NGS) has enabled the study of microbial communities, referred to as microbiome. Herein, we undertake a systematic review of published literature to build a comprehensive global dataset of microbiome determined by NGS in field-collected ticks. The dataset comprised 4418 records from 76 literature involving geo-referenced occurrences for 46 species of ticks and 219 microorganism families, revealing a total of 83 emerging viruses identified from 24 tick species belonging to 6 tick genera since 1980. The viral, bacterial and eukaryotic composition was compared regarding the tick species, their live stage and types of the specimens, or the geographic location. The data can assist the further investigation of ecological, biogeographical and epidemiological features of the tick-borne disease.
Limit cycles and chaos in the hybrid atom-optomechanics system
Authors: Xu Xingran , Krisnanda Tanjung , Liew Timothy C. H. 
Published: September 2022

AbstractWe consider atoms in two different periodic potentials induced by different lasers, one of which is coupled to a mechanical membrane via radiation pressure force. The atoms are intrinsically two-level systems that can absorb or emit photons, but the dynamics of their position and momentum are treated classically. On the other hand, the membrane, the cavity field, and the intrinsic two-level atoms are treated quantum mechanically. We show that the mean excitation of the three systems can be stable, periodically oscillating, or in a chaotic state depending on the strength of the coupling between them. We define regular, limit cycle, and chaotic phases, and present a phase diagram where the three phases can be achieved by manipulating the field-membrane and field-atom coupling strengths. We also computed other observable quantities that can reflect the system’s phase such as position, momentum, and correlation functions. Our proposal offers a new way to generate and tune the limit cycle and chaotic phases in a well-established atom-optomechanics system.
Vascular refilling coefficient is not a good marker of whole-body capillary hydraulic conductivity in hemodialysis patients: insights from a simulation study
Authors: Pstras Leszek , Waniewski Jacek , Lindholm Bengt 
Published: September 2022

AbstractRefilling of the vascular space through absorption of interstitial fluid by micro vessels is a crucial mechanism for maintaining hemodynamic stability during hemodialysis (HD) and allowing excess fluid to be removed from body tissues. The rate of vascular refilling depends on the imbalance between the Starling forces acting across the capillary walls as well as on their hydraulic conductivity and total surface area. Various approaches have been proposed to assess the vascular refilling process during HD, including the so-called refilling coefficient (Kr) that describes the rate of vascular refilling per changes in plasma oncotic pressure, assuming that other Starling forces and the flow of lymph remain constant during HD. Several studies have shown that Kr decreases exponentially during HD, which was attributed to a dialysis-induced decrease in the whole-body capillary hydraulic conductivity (LpS). Here, we employ a lumped-parameter mathematical model of the cardiovascular system and water and solute transport between the main body fluid compartments to assess the impact of all Starling forces and the flow of lymph on vascular refilling during HD in order to explain the reasons behind the observed intradialytic decrease in Kr. We simulated several HD sessions in a virtual patient with different blood priming procedures, ultrafiltration rates, session durations, and constant or variable levels of LpS. We show that the intradialytic decrease in Kr is not associated with a possible reduction of LpS but results from the inherent assumption that plasma oncotic pressure is the only variable Starling force during HD, whereas in fact other Starling forces, in particular the oncotic pressure of the interstitial fluid, have an important impact on the transcapillary fluid exchange during HD. We conclude that Kr is not a good marker of LpS and should not be used to guide fluid removal during HD or to assess the fluid status of dialysis patients.
Simulation of optical radiation force distribution in interference patterns and necessary conditions for chiral structure formation on dielectrics
Authors: Nakata Yoshiki , Tsubakimoto Koji , Shiraga Hiroyuki , Miyanaga Noriaki , Kosaka Yuki , Yoshida Masataka 
Published: September 2022

AbstractA chiral structure is formed by the optical radiation force induced by a circularly polarized light that has spin angular momentum; chiral structures are expected to be used for light control devices and molecular chirality discrimination devices. In this paper, we clarify the relationship between the differences in the distributions of the optical radiation force and the possibility of formation of chiral structures. We first simulate the optical radiation force distribution in the case of a Gaussian beam that successfully forms a chiral structure. Given a vector $${\varvec{r}}$$

r

with a centre of the light spot $$\mathrm{O}$$
O
and polar coordinates $$R(\left|{\varvec{r}}\right|, \theta )$$

R
(

r

,
θ
)

, and an optical radiation force vector $${\varvec{F}}$$

F

at $$R$$
R
, the angle $${\theta }^{\mathrm{^{\prime}}}=\mathrm{\angle }({\varvec{r}}, {\varvec{F}})$$

θ

′

=
∠

(

r

,

F

)

and $$\left|{\varvec{F}}\right|$$

F

must be constant with respect to the declination angle $$\theta$$
θ
for a chiral structure to form. These conditions are fulfilled in the case of a 6-beam interference pattern, but not in the case of a 4-beam interference pattern, which is consistent with the result that no chiral structure is formed in the latter case. The equations derived for simulation of optical radiation force distribution can be used for any optical intensity distribution, and will be of great help in the research of any dielectrics deformation.
Investigating the nature of mass distribution surrounding the Galactic supermassive black hole
Authors: Chan Man Ho , Lee Chak Man , Yu Chi Wai 
Published: September 2022

AbstractIn the past three decades, many stars orbiting about the supermassive black hole (SMBH) at the Galactic Centre (Sgr A*) were identified. Their orbital nature can give stringent constraints for the mass of the SMBH. In particular, the star S2 has completed at least one period since our first detection of its position, which can provide rich information to examine the properties of the SMBH, and the astrophysical environment surrounding the SMBH. Here, we report an interesting phenomenon that if a significant amount of dark matter or stellar mass is distributed around the SMBH, the precession speed of the S2 stellar orbit could be ‘slow down’ by at most 27% compared with that without dark matter surrounding the SMBH, assuming the optimal dark matter scenario. We anticipate that future high quality observational data of the S2 stellar orbit or other stellar orbits can help reveal the actual mass distribution near the SMBH and the nature of dark matter.
Aqueous column changes in the episcleral veins after the instillation of ripasudil versus latanoprost: a randomized, double-blind, crossover clinical trial
Authors: Suzuki Marie , Suzuki Yohei , Komori Ryohei , Orii Yusuke , Arimura Shogo , Iwasaki Kentaro , Takamura Yoshihiro , Inatani Masaru 
Published: September 2022

AbstractTo investigate whether the topical administration of ripasudil ophthalmic solution enhances aqueous outflow in the episcleral vein of the human eye. Two-sequence, prospective, randomized, double-blind, crossover trial. Sixteen eyes of 16 healthy participants were recruited in this study. Participants were randomized into one of the two crossover sequences to the instillation of ripasudil or the control drug, latanoprost, followed by a washout period of more than 2 days, and crossed over to the alternative instillation. The aqueous columns in the episcleral veins were recorded using a video capture system connected to a slit-light microscope (hemoglobin video imaging) before and 2 and 8 h after the instillation. Comparisons between ripasudil and latanoprost for the changes of the aqueous column width after the instillation. Two hours after the instillation, the ripasudil group had significantly greater dilation of the aqueous column width than the latanoprost group. Eight hours after the instillation, the ripasudil group had significantly greater dilation of the aqueous column width than the latanoprost group. Hemoglobin video imaging revealed that the topical administration of ripasudil ophthalmic solution enhanced aqueous outflow in the episcleral vein of the human eye.
Single cell RNA sequencing confirms retinal microglia activation associated with early onset retinal degeneration
Authors: Kumari Asha , Ayala-Ramirez Raul , Zenteno Juan Carlos , Huffman Kristyn , Sasik Roman , Ayyagari Radha , Borooah Shyamanga 
Published: September 2022

AbstractMutations in the Membrane-type frizzled related protein (Mfrp) gene results in an early-onset retinal degeneration associated with retinitis pigmentosa, microphthalmia, optic disc drusen and foveal schisis. In the current study, a previously characterized mouse model of human retinal degeneration carrying homozygous c.498_499insC mutations in Mfrp (MfrpKI/KI) was used. Patients carrying this mutation have retinal degeneration at an early age. The model demonstrates subretinal deposits and develops early-onset photoreceptor degeneration. We observed large subretinal deposits in MfrpKI/KI mice which were strongly CD68 positive and co-localized with autofluorescent spots. Single cell RNA sequencing of MfrpKI/KI mice retinal microglia showed a significantly higher number of pan-macrophage marker Iba-1 and F4/80 positive cells with increased expression of activation marker (CD68) and lowered microglial homeostatic markers (TMEM119, P2ry13, P2ry13, Siglech) compared with wild type mice confirming microglial activation as observed in retinal immunostaining showing microglia activation in subretinal region. Trajectory analysis identified a small cluster of microglial cells with activation transcriptomic signatures that could represent a subretinal microglia population in MfrpKI/KI mice expressing higher levels of APOE. We validated these findings using immunofluorescence staining of retinal cryosections and found a significantly higher number of subretinal Iba-1/ApoE positive microglia in MfrpKI/KI mice with some subretinal microglia also expressing lowered levels of microglial homeostatic marker TMEM119, confirming microglial origin. In summary, we confirm that MfrpKI/KI mice carrying the c.498_499insC mutation had a significantly higher population of activated microglia in their retina with distinct subsets of subretinal microglia. Further, studies are required to confirm whether the association of increased subretinal microglia in MfrpKI/KI mice are causal in degeneration.
CBCT artefact-burden of zirconia-based as compared to titanium implants for different beam energies: an analytical approach
Authors: Schulze Ralf 
Published: September 2022

AbstractBeam hardening artefacts induced by highly-dense material (e.g. metal) is a common quality issue in maxillofacial Cone Beam Computed Tomography (CBCT-) images. This experimental and analytical study investigated attenuation patterns of two typical dental implant materials: zirconia-ceramic and pure titanium. By application of different x-ray beam energies (60, 70, 80, 90 [kVp]) energy-dependent attenuation of these materials is assessed and the resulting artefact induction in the resulting CBCT-images evaluated. A zirconia (Y-TZP-) implant ($$\varnothing$$
∅
: 4.1 mm) and a pure titanium rod ($$\varnothing$$
∅
: 4.0 mm) were exposed in a commercial CBCT (3D Accuitomo 170). The raw two-dimensional (2D) projection radiographs the CBCT utilizes for three-dimensional reconstruction applied for acquisition of attenuation profiles through the circular central slice of the implant-phantom images. Distances the x-rays traverse through the implant-phantoms at this location were computed. Using this information and the linear attenuation coefficient, transmission and attenuation was computed for each material and beam energy. These data were related to beam hardening artefacts that were assessed in the axial reconstructions of the implants’ CBCT images. Transmission of titanium for all peak kilovoltages (kVp) was higher and approximately 200% that of Y-TZP at 60 kVp versus 530% at 90 kVp. At 4 mm diameter transmission for Y-TZP was only approximately 5 % for all four beam-energies. In agreement with this finding, beam hardening artefacts for Y-TZP could not be reduced using higher energies, whereas for titanium they decreased with increasing energy. For the energy spectrum used in this study (60–90 kVp), beam hardening caused by titanium can be reduced using higher energies while this is not the case for zirconia-ceramic (Y-TZP).