bluuebunny/crossref_metadata_2025_split huggingface dataset:
RHOJ controls EMT-associated resistance to chemotherapy
Authors: Debaugnies Maud , Rodríguez-Acebes Sara , Blondeau Jeremy , Parent Marie-Astrid , Zocco Manuel , Song Yura , de Maertelaer Viviane , Moers Virginie , Latil Mathilde , Dubois Christine , Coulonval Katia , Impens Francis , Van Haver Delphi , Dufour Sara , Uemura Akiyoshi , Sotiropoulou Panagiota A. , Méndez Juan , Blanpain Cédric 
Published: March 2023

AbstractThe resistance of cancer cells to therapy is responsible for the death of most patients with cancer1. Epithelial-to-mesenchymal transition (EMT) has been associated with resistance to therapy in different cancer cells2,3. However, the mechanisms by which EMT mediates resistance to therapy remain poorly understood. Here, using a mouse model of skin squamous cell carcinoma undergoing spontaneous EMT during tumorigenesis, we found that EMT tumour cells are highly resistant to a wide range of anti-cancer therapies both in vivo and in vitro. Using gain and loss of function studies in vitro and in vivo, we found that RHOJ—a small GTPase that is preferentially expressed in EMT cancer cells—controls resistance to therapy. Using genome-wide transcriptomic and proteomic profiling, we found that RHOJ regulates EMT-associated resistance to chemotherapy by enhancing the response to replicative stress and activating the DNA-damage response, enabling tumour cells to rapidly repair DNA lesions induced by chemotherapy. RHOJ interacts with proteins that regulate nuclear actin, and inhibition of actin polymerization sensitizes EMT tumour cells to chemotherapy-induced cell death in a RHOJ-dependent manner. Together, our study uncovers the role and the mechanisms through which RHOJ acts as a key regulator of EMT-associated resistance to chemotherapy.
Ultrafast structural changes direct the first molecular events of vision
Authors: Gruhl Thomas , Weinert Tobias , Rodrigues Matthew J. , Milne Christopher J. , Ortolani Giorgia , Nass Karol , Nango Eriko , Sen Saumik , Johnson Philip J. M. , Cirelli Claudio , Furrer Antonia , Mous Sandra , Skopintsev Petr , James Daniel , Dworkowski Florian , Båth Petra , Kekilli Demet , Ozerov Dmitry , Tanaka Rie , Glover Hannah , Bacellar Camila , Brünle Steffen , Casadei Cecilia M. , Diethelm Azeglio D. , Gashi Dardan , Gotthard Guillaume , Guixà-González Ramon , Joti Yasumasa , Kabanova Victoria , Knopp Gregor , Lesca Elena , Ma Pikyee , Martiel Isabelle , Mühle Jonas , Owada Shigeki , Pamula Filip , Sarabi Daniel , Tejero Oliver , Tsai Ching-Ju , Varma Niranjan , Wach Anna , Boutet Sébastien , Tono Kensuke , Nogly Przemyslaw , Deupi Xavier , Iwata So , Neutze Richard , Standfuss Jörg , Schertler Gebhard , Panneels Valerie 
Published: March 2023

AbstractVision is initiated by the rhodopsin family of light-sensitive G protein-coupled receptors (GPCRs)1. A photon is absorbed by the 11-cis retinal chromophore of rhodopsin, which isomerizes within 200 femtoseconds to the all-trans conformation2, thereby initiating the cellular signal transduction processes that ultimately lead to vision. However, the intramolecular mechanism by which the photoactivated retinal induces the activation events inside rhodopsin remains experimentally unclear. Here we use ultrafast time-resolved crystallography at room temperature3 to determine how an isomerized twisted all-trans retinal stores the photon energy that is required to initiate the protein conformational changes associated with the formation of the G protein-binding signalling state. The distorted retinal at a 1-ps time delay after photoactivation has pulled away from half of its numerous interactions with its binding pocket, and the excess of the photon energy is released through an anisotropic protein breathing motion in the direction of the extracellular space. Notably, the very early structural motions in the protein side chains of rhodopsin appear in regions that are involved in later stages of the conserved class A GPCR activation mechanism. Our study sheds light on the earliest stages of vision in vertebrates and points to fundamental aspects of the molecular mechanisms of agonist-mediated GPCR activation.
Influence of Allee effect on the spatiotemporal behavior of a diffusive predator–prey model with Crowley–Martin type response function
Authors: Guin Lakshmi Narayan , Pal Pallav Jyoti , Alzahrani Jawaher , Ali Nijamuddin , Sarkar Krishnendu , Djilali Salih , Zeb Anwar , Khan Ilyas , Eldin Sayed M 
Published: March 2023

AbstractThe present paper is dealt with a predator–prey model in which the growth of the prey population is influenced by the Allee effect while the predator species are contended with the prey population following the Crowley–Martin type response function. The proposed model is comprehensively analyzed in terms of stability and manifestation of bifurcation of the system. The system unveils the bi-stability together with the existence of a separatrix. In view of the eminence of spatial ecology, the dynamical complexity emanating from the induction of the Allee effect in prey species of a Crowley–Martin reaction–diffusion predator–prey model is also investigated profoundly. The results of numerical simulations reveal that the present system dynamics is motivated by both the Allee effect and diffusion-controlled pattern formation growth to hot spots, stripe-hot spot mixtures, stripes, labyrinthine, stripe-cold spot mixtures, and cold spots replication. The theoretical consequences of the spatiotemporal model under study are validated through numerical simulations.
Bioinformatics-based investigation on the genetic influence between SARS-CoV-2 infections and idiopathic pulmonary fibrosis (IPF) diseases, and drug repurposing
Authors: Islam Md. Ariful , Kibria Md. Kaderi , Hossen Md. Bayazid , Reza Md. Selim , Tasmia Samme Amena , Tuly Khanis Farhana , Mosharof Md. Parvez , Kabir Syed Rashel , Kabir Md. Hadiul , Mollah Md. Nurul Haque 
Published: March 2023

AbstractSome recent studies showed that severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections and idiopathic pulmonary fibrosis (IPF) disease might stimulate each other through the shared genes. Therefore, in this study, an attempt was made to explore common genomic biomarkers for SARS-CoV-2 infections and IPF disease highlighting their functions, pathways, regulators and associated drug molecules. At first, we identified 32 statistically significant common differentially expressed genes (cDEGs) between disease (SARS-CoV-2 and IPF) and control samples of RNA-Seq profiles by using a statistical r-package (edgeR). Then we detected 10 cDEGs (CXCR4, TNFAIP3, VCAM1, NLRP3, TNFAIP6, SELE, MX2, IRF4, UBD and CH25H) out of 32 as the common hub genes (cHubGs) by the protein–protein interaction (PPI) network analysis. The cHubGs regulatory network analysis detected few key TFs-proteins and miRNAs as the transcriptional and post-transcriptional regulators of cHubGs. The cDEGs-set enrichment analysis identified some crucial SARS-CoV-2 and IPF causing common molecular mechanisms including biological processes, molecular functions, cellular components and signaling pathways. Then, we suggested the cHubGs-guided top-ranked 10 candidate drug molecules (Tegobuvir, Nilotinib, Digoxin, Proscillaridin, Simeprevir, Sorafenib, Torin 2, Rapamycin, Vancomycin and Hesperidin) for the treatment against SARS-CoV-2 infections with IFP diseases as comorbidity. Finally, we investigated the resistance performance of our proposed drug molecules compare to the already published molecules, against the state-of-the-art alternatives publicly available top-ranked independent receptors by molecular docking analysis. Molecular docking results suggested that our proposed drug molecules would be more effective compare to the already published drug molecules. Thus, the findings of this study might be played a vital role for diagnosis and therapies of SARS-CoV-2 infections with IPF disease as comorbidity risk.
An experimental study of animating-based facial image manipulation in online class environments
Authors: Park Jeong-Ha , Lim Chae-Yun , Kwon Hyuk-Yoon 
Published: March 2023

AbstractRecent advances in artificial intelligence technology have significantly improved facial image manipulation, which is known as Deepfake. Facial image manipulation synthesizes or replaces a region of the face in an image with that of another face. The techniques for facial image manipulation are classified into four categories: (1) entire face synthesis, (2) identity swap, (3) attribute manipulation, and (4) expression swap. Out of them, we focus on expression swap because it effectively manipulates only the expression of the face in the images or videos without creating or replacing the entire face, having advantages for the real-time application. In this study, we propose an evaluation framework of the expression swap models targeting the real-time online class environments. For this, we define three kinds of scenarios according to the portion of the face in the entire image considering actual online class situations: (1) attendance check (Scenario 1), (2) presentation (Scenario 2), and (3) examination (Scenario 3). Considering the manipulation on the online class environments, the framework receives a single source image and a target video and generates the video that manipulates a face of the target video to that in the source image. To this end, we select two models that satisfy the conditions required by the framework: (1) first order model and (2) GANimation. We implement these models in the framework and evaluate their performance for the defined scenarios. Through the quantitative and qualitative evaluation, we observe distinguishing properties of the used two models. Specifically, both models show acceptable results in Scenario 1, where the face occupies a large portion of the image. However, their performances are significantly degraded in Scenarios 2 and 3, where the face occupies less portion of the image; the first order model causes relatively less loss of image quality than GANimation in the result of the quantitative evaluation. In contrast, GANimation has the advantages of representing facial expression changes compared to the first order model. Finally, we devise an architecture for applying the expression swap model to the online video conferencing application in real-time. In particular, by applying the expression swap model to widely used online meeting platforms such as Zoom, Google Meet, and Microsoft Teams, we demonstrate its feasibility for real-time online classes.
Carbon nanotubes as a nitric oxide nano-reservoir improved the controlled release profile in 3D printed biodegradable vascular grafts
Authors: Kabirian Fatemeh , Baatsen Pieter , Smet Mario , Shavandi Amin , Mela Petra , Heying Ruth 
Published: March 2023

AbstractSmall diameter vascular grafts (SDVGs) are associated with a high failure rate due to poor endothelialization. The incorporation of a nitric oxide (NO) releasing system improves biocompatibility by using the NO effect to promote endothelial cell (EC) migration and proliferation while preventing bacterial infection. To circumvent the instability of NO donors and to prolong NO releasing, S-nitroso-N-acetyl-d-penicillamine (SNAP) as a NO donor was loaded in multi-walled carbon nanotubes (MWCNTs). Successful loading was confirmed with a maximum SNAP amount of ~ 5% (w/w) by TEM, CHNS analysis and FTIR spectra. SDVGs were 3D printed from polycaprolactone (PCL) and coated with a 1:1 ratio of polyethylene glycol and PCL dopped with different concentrations of SNAP-loaded matrix and combinations of MWCNTs-OH. Coating with 10% (w/w) SNAP-matrix-10% (w/w) SNAP-MWCNT-OH showed a diminished burst release and 18 days of NO release in the range of 0.5–4 × 10–10 mol cm−2 min−1 similar to the NO release from healthy endothelium. NO-releasing SDVGs were cytocompatible, significantly enhanced EC proliferation and migration and diminished bacterial viability. The newly developed SNAP-loaded MWCNT-OH has a great potential to develop NO releasing biomaterials with a prolonged, controlled NO release promoting in-situ endothelialization and tissue integration in vivo, even as an approach towards personalized medicine.
Speech therapy to overcome dyslexia in primary schoolers
Authors: Nurseitova Zhanar , Shayakhmetova Aisulu 
Published: March 2023

AbstractThis research was aimed to investigate changes in the reading technique and in terms of its semantic charge in primary schoolers diagnosed with dyslexia, which occur as a result of the integrated use of speech therapy techniques. The study was performed between 2016 and 2019 in 6 schools of Moscow and Almaty. It enrolled 194 and 200 children, respectively, who were examined with form I to III inclusive. The study revealed that 13% of children had reading speed disorders; they were constituted group 1. Another 11% had reading comprehension disorders; they constituted group 2. In group 1, by form III, the number of reading repetitions increased twofold. In group 2, the number of children, who read in words and phrases, increased by half; in group 1, it doubled. This research showed clear progress in children with technical dyslexia vs. those with semantic dyslexia. Based on the results, it is possible to develop a methodology for speech therapy techniques that can be suitable not only for speech therapists, but also for primary school teachers, as well as for parents of dyslectic children.
Light scattering in stacked mesophyll cells results in similarity characteristic of solar spectral reflectance and transmittance of natural leaves
Authors: Xu Kai , Ye Hong 
Published: March 2023

AbstractSolar spectral reflectance and transmittance of natural leaves exhibit dramatic similarity. To elucidate the formation mechanism and physiological significance, a radiative transfer model was constructed, and the effects of stacked mesophyll cells, chlorophyll content and leaf thickness on the visible light absorptance of the natural leaves were analyzed. Results indicated that light scattering caused by the stacked mesophyll cells is responsible for the similarity. The optical path of visible light in the natural leaves is increased with the scattering process, resulting in that the visible light transmittance is significantly reduced meanwhile the visible light reflectance is at a low level, thus the visible light absorptance tends to a maximum and the absorption of photosynthetically active radiation (PAR) by the natural leaves is significantly enhanced. Interestingly, as two key leaf functional traits affecting the absorption process of PAR, chlorophyll content and leaf thickness of the natural leaves in a certain environment show a convergent behavior, resulting in the high visible light absorptance of the natural leaves, which demonstrates the PAR utilizing strategies of the natural leaves. This work provides a new perspective for revealing the evolutionary processes and ecological strategies of natural leaves, and can be adopted to guide the improvement directions of crop photosynthesis.
Reduced bimolecular charge recombination in efficient organic solar cells comprising non-fullerene acceptors
Authors: Wu Yue , Li Yungui , van der Zee Bas , Liu Wenlan , Markina Anastasia , Fan Hongyu , Yang Hang , Cui Chaohua , Li Yongfang , Blom Paul W. M. , Andrienko Denis , Wetzelaer Gert-Jan A. H. 
Published: March 2023

AbstractBimolecular charge recombination is one of the most important loss processes in organic solar cells. However, the bimolecular recombination rate in solar cells based on novel non-fullerene acceptors is mostly unclear. Moreover, the origin of the reduced-Langevin recombination rate in bulk heterojunction solar cells in general is still poorly understood. Here, we investigate the bimolecular recombination rate and charge transport in a series of high-performance organic solar cells based on non-fullerene acceptors. From steady-state dark injection measurements and drift–diffusion simulations of the current–voltage characteristics under illumination, Langevin reduction factors of up to over two orders of magnitude are observed. The reduced recombination is essential for the high fill factors of these solar cells. The Langevin reduction factors are observed to correlate with the quadrupole moment of the acceptors, which is responsible for band bending at the donor–acceptor interface, forming a barrier for charge recombination. Overall these results therefore show that suppressed bimolecular recombination is essential for the performance of organic solar cells and provide design rules for novel materials.
Learning to predict RNA sequence expressions from whole slide images with applications for search and classification
Authors: Alsaafin Areej , Safarpoor Amir , Sikaroudi Milad , Hipp Jason D. , Tizhoosh H. R. 
Published: March 2023

AbstractDeep learning methods are widely applied in digital pathology to address clinical challenges such as prognosis and diagnosis. As one of the most recent applications, deep models have also been used to extract molecular features from whole slide images. Although molecular tests carry rich information, they are often expensive, time-consuming, and require additional tissue to sample. In this paper, we propose tRNAsformer, an attention-based topology that can learn both to predict the bulk RNA-seq from an image and represent the whole slide image of a glass slide simultaneously. The tRNAsformer uses multiple instance learning to solve a weakly supervised problem while the pixel-level annotation is not available for an image. We conducted several experiments and achieved better performance and faster convergence in comparison to the state-of-the-art algorithms. The proposed tRNAsformer can assist as a computational pathology tool to facilitate a new generation of search and classification methods by combining the tissue morphology and the molecular fingerprint of the biopsy samples.
Synthesis vs. salvage of ester- and ether-linked phosphatidylethanolamine in the intracellular protozoan pathogen Toxoplasma gondii
Authors: Ren Bingjian , Liang Xiaohan , Brouwers Jos F. , Miron Rosalba Cruz , Shen Bang , Gupta Nishith 
Published: March 2023

AbstractToxoplasma gondii is a prevalent zoonotic pathogen infecting livestock as well as humans. The exceptional ability of this parasite to reproduce in several types of nucleated host cells necessitates a coordinated usage of endogenous and host-derived nutritional resources for membrane biogenesis. Phosphatidylethanolamine is the second most common glycerophospholipid in T. gondii, but how its requirement in the acutely-infectious fast-dividing tachyzoite stage is satisfied remains enigmatic. This work reveals that the parasite deploys de novo synthesis and salvage pathways to meet its demand for ester- and ether-linked PtdEtn. Auxin-mediated depletion of the phosphoethanolamine cytidylyltransferase (ECT) caused a lethal phenotype in tachyzoites due to impaired invasion and cell division, disclosing a vital role of the CDP-ethanolamine pathway during the lytic cycle. In accord, the inner membrane complex appeared disrupted concurrent with a decline in its length, parasite width and major phospholipids. Integrated lipidomics and isotope analyses of the TgECT mutant unveiled the endogenous synthesis of ester-PtdEtn, and salvage of ether-linked lipids from host cells. In brief, this study demonstrates how T. gondii operates various means to produce distinct forms of PtdEtn while featuring the therapeutic relevance of its de novo synthesis.
International corporations trading Brazilian soy are keystone actors for water stewardship
Authors: De Petrillo Elena , Tuninetti Marta , Ridolfi Luca , Laio Francesco 
Published: March 2023

AbstractTransnational corporations play a major, but poorly constrained, role in reallocating global water resources. Here, we couple high-resolution, company-specific trade data with hydrological and crop models to estimate the virtual water trade of the top 9 transnational corporations that trade Brazilian soy. We identify 4429 virtual water flows connecting 1620 Brazilian municipalities with the top-10 soy importing countries and find that the total virtual water flow increased from 43 billion m3 to 100 billion m3 between 2004 and 2018. We find that the largest soy traders displace on average twice as much virtual water as top-importing countries, excluding China. For example, in 2018 one transnational corporation exported 15 Gm3, almost tripling the Netherlands’s virtual water import (the second largest importer at about 5 Gm3). Our findings highlight the importance of transnational corporations for achieving water stewardship and sustainable supply chains to support water resource security at municipal and international scales.
Diversity and function of methyl-coenzyme M reductase-encoding archaea in Yellowstone hot springs revealed by metagenomics and mesocosm experiments
Authors: Lynes Mackenzie M , Krukenberg Viola , Jay Zackary J , Kohtz Anthony J , Gobrogge Christine A , Spietz Rachel L , Hatzenpichler Roland 
Published: March 2023

Abstract
Metagenomic studies on geothermal environments have been central in recent discoveries on the diversity of archaeal methane and alkane metabolism. Here, we investigated methanogenic populations inhabiting terrestrial geothermal features in Yellowstone National Park (YNP) by combining amplicon sequencing with metagenomics and mesocosm experiments. Detection of methyl-coenzyme M reductase subunit A (mcrA) gene amplicons demonstrated a wide diversity of Mcr-encoding archaea inhabit geothermal features with differing physicochemical regimes across YNP. From three selected hot springs we recovered twelve Mcr-encoding metagenome assembled genomes (MAGs) affiliated with lineages of cultured methanogens as well as Candidatus (Ca.) Methanomethylicia, Ca. Hadesarchaeia, and Archaeoglobi. These MAGs encoded the potential for hydrogenotrophic, aceticlastic, hydrogen-dependent methylotrophic methanogenesis, or anaerobic short-chain alkane oxidation. While Mcr-encoding archaea represent minor fractions of the microbial community of hot springs, mesocosm experiments with methanogenic precursors resulted in the stimulation of methanogenic activity and the enrichment of lineages affiliated with Methanosaeta and Methanothermobacter as well as with uncultured Mcr-encoding archaea including Ca. Korarchaeia, Ca. Nezhaarchaeia, and Archaeoglobi. We revealed that diverse Mcr-encoding archaea with the metabolic potential to produce methane from different precursors persist in the geothermal environments of YNP and can be enriched under methanogenic conditions. This study highlights the importance of combining environmental metagenomics with laboratory-based experiments to expand our understanding of uncultured Mcr-encoding archaea and their potential impact on microbial carbon transformations in geothermal environments and beyond.