bluuebunny/crossref_metadata_2025_split huggingface dataset:
Light-sheet photonic force optical coherence elastography for high-throughput quantitative 3D micromechanical imaging
Authors: Lin Yuechuan , Leartprapun Nichaluk , Luo Justin C. , Adie Steven G. 
Published: August 2021

AbstractMicroscale mechanical properties of the extracellular matrix (ECM) and dynamic cell-ECM interactions play an important role in physiological processes and disease. However, it remains a challenge for current mechanical characterization methods to combine quantitative 3D imaging of ECM mechanics with cellular-scale resolution and dynamic monitoring of cell-mediated changes to pericellular viscoelasticity. Here, we present light-sheet photonic force optical coherence elastography (LS-pfOCE) to address these challenges by leveraging a light-sheet for parallelized, non-invasive, and localized mechanical loading. We demonstrate the capabilities of LS-pfOCE by imaging the micromechanical heterogeneity of fibrous 3D collagen matrices and perform a live-cell study to image micromechanical heterogeneity induced by NIH-3T3 cells seeded in 3D fibrin constructs. We also show that LS-pfOCE is able to quantify temporal variations in pericellular viscoelasticity in response to altered cellular activity. By providing access to the spatiotemporal variations in the micromechanical properties of 3D complex biopolymer constructs and engineered cellular systems, LS-pfOCE has the potential to drive new discoveries in the rapidly growing field of mechanobiology.
LRcell: detecting the source of differential expression at the sub-cell type level from bulk RNA-seq data
Authors: Ma Wenjing , Sharma Sumeet , Jin Peng , Gourley Shannon L. , Qin Zhaohui 
Published: August 2021

AbstractGiven most tissues are consist of abundant and diverse sub cell-types, an important yet unaddressed problem in bulk RNA-seq analysis is to identify at which sub cell-type(s) the differential expression occur. Single-cell RNA-sequencing (scRNA-seq) technologies can answer the question, but they are often labor-intensive and cost-prohibitive. Here, we present LRcell, a computational method aiming to identify specific sub-cell type(s) that drives the changes observed in a bulk RNA-seq experiment. In addition, LRcell provides pre-embedded marker genes computed from putative single-cell RNA-seq experiments as options to execute the analyses. Using three different real datasets, we show that LRcell successfully identifies known cell types involved in psychiatric disorders and LRcell is more sensitive than even the leading deconvolution methods.
Neural network-based predictions of antimicrobial resistance inSalmonellaspp. using k-mers counting from whole-genome sequences
Authors: Barros Cristian C. 
Published: August 2021

AbstractArtificial intelligence-based predictions have emerged as a friendly and reliable tool for the surveillance of the antimicrobial resistance (AMR) worldwide. In this regard, genome databases typically include whole-genome sequencing (WGS) data containing AMR meta-data that can be used to train machine learning (ML) models, in order to predict phenotype features from genome samples. In this study, using a Neural Network (NN) architecture and the SGD-ADAM algorithm, we build ML antibiotic resistance models that can predict Minimum Inhibitory Concentrations (MICs) and antimicrobial susceptibility profiles ofSalmonellaspp. Data analysis was based on 7,268 genomes publicly available in PATRIC database, containing about 75,000 AMR annotations. ML models were built using reference-freek-mer analysis of whole-genome sequences, MIC measurements and susceptibility categories, obtaining robust and accurate results for 9 antibiotics belonging to beta-lactam, fluoroquinolone, phenicol, aminoglycoside, tetracycline and sulphonamide classes. Al-though the accuracy of predicting the actual MIC reaches modest levels, the within ± 1 2-fold dilution accuracy per antibiotic reaches significant levels with values that varies from 85% to 95%, with narrow 95% CIs of about 5% and individual accuracies per MIC ≳ 80%. For differentiation between “susceptible” and “resistant” values, by measuring the accuracy and error of model’s susceptibility predictions to different antibiotics, the accuracy is the same as before and ranges from 85% to 95%, with 95% CIs of about 5%, the recall extends from 75% to 85%, the precision from 60% to 90%, whereas the very major error is ≲ 20%. In summary, these results show that NN-based models are able to learn and predict the AMR phenotype from bacterial genomes based on a gene-freek-mer analysis.
Cryo-EM structure of disease-related prion fibrils provides insights into seeding barriers
Authors: Li Qiuye , Jaroniec Christopher P. , Surewicz Witold K. 
Published: August 2021

ABSTRACTOne of the least understood aspects of prion diseases is the structure of infectious prion protein aggregates. Here we report a high-resolution cryo-EM structure of amyloid fibrils formed by human prion protein with Y145Stop mutation that is associated with a familial prion disease. This structural insight allows us not only to explain previous biochemical findings, but also provides direct support for the conformational adaptability model of prion transmissibility barriers.
Incompatibility of DFHBI based fluorescent RNA aptamers with particular commercial cell-free expression systems
Authors: Speakman Alexander J. , Dunn Katherine E. 
Published: August 2021

ABSTRACTFluorescent RNA aptamers are an increasingly used tool for quantifying transcription and for visualising RNA interactions, bothin vitroandin vivo. However when tested in the commercially available,E. coliextract based Expressway™ cell-free expression system, no fluorescence is detected. The same experimental setup is shown to successfully produce fluorescent RNA aptamers when tested in another buffer designed forin vitrotranscription, and RNA purification of the Expressway™ reaction products show that transcription does occur, but does not result in a fluorescent product. In this paper we demonstrate the incompatibility of a narrow selection of RNA aptamers in one particular cell-free expression system, and consider that similar issues may arise with other cell-free expression systems, RNA aptamers, and their corresponding fluorophores.
Typhoid toxin sorting and exocytic transport fromSalmonellaTyphi infected cells
Authors: Chang Shu-Jung , Lin Yen-Yi , Lara-Tejero Maria , Galán Jorge E. 
Published: August 2021

SUMMARYTyphoid toxin is an essential virulence factor forSalmonellaTyphi, the cause of typhoid fever in humans. This toxin has an unusual biology in that it is produced bySalmonellaTyphi only when located within host cells. Once synthesized, the toxin is secreted to the lumen of theSalmonella-containing vacuole from where it is transported to the extracellular space by vesicle carrier intermediates. Here we report the identification of the typhoid toxin sorting receptor and the cellular machinery that packages the toxin into vesicle carriers, and exports it to the extracellular space. We found that the cation- independent mannose-6-phosphate receptor serves as typhoid toxin sorting receptor and that the coat protein COPII and the GTPase Sar1 mediate its packaging into vesicle carriers. Formation of the typhoid toxin carriers requires the specific environment of theSalmonellaTyphi-containing vacuole, which is determined by the activities of specific effectors of its type III protein secretion systems. We also found that Rab11B and its interacting protein Rip11 control the intracellular transport of the typhoid toxin carriers, and the SNARE proteins VAMP7, SNAP23, and Syntaxin 4 their fusion to the plasma membrane. Typhoid toxin’s cooption of specific cellular machinery for its transport to the extracellular space illustrates the remarkable adaptation of an exotoxin to exert its function in the context of an intracellular pathogen.
Caveats and nuances of model-based and model-free representational connectivity analysis
Authors: Karimi-Rouzbahani Hamid , Woolgar Alexandra , Henson Richard , Nili Hamed 
Published: August 2021

AbstractBrain connectivity analyses have conventionally relied on statistical relationship between one-dimensional summaries of activation in different brain areas. However, summarising activation patterns within each area to a single dimension ignores the potential statistical dependencies between their multi-dimensional activity patterns. Representational Connectivity Analyses (RCA) is a method that quantifies the relationship between multi-dimensional patterns of activity without reducing the dimensionality of the data. We consider two variants of RCA. In model-free RCA, the goal is to quantify the shared information for two brain regions. In model-based RCA, one tests whether two regions have shared information about a specific aspect of the stimuli/task, as defined by a model. However, this is a new approach and the potential caveats of model-free and model-based RCA are still understudied. We first explain how model-based RCA detects connectivity through the lens of models, and then present three scenarios where model-based and model-free RCA give discrepant results. These conflicting results complicate the interpretation of functional connectivity. We highlight the challenges in three scenarios: complex intermediate models, common patterns across regions and transformation of representational structure across brain regions. The paper is accompanied by scripts that reproduce the results. In each case, we suggest potential ways to mitigate the difficulties caused by inconsistent results. The results of this study shed light on some understudied aspects of RCA, and allow researchers to use the method more effectively.
Modeling myosin Va liposome transport through actin filament networks reveals a percolation threshold that modulates transport properties
Authors: Walcott S. , Warshaw D. M. 
Published: August 2021

AbstractMyosin Va (myoVa) motors transport membrane-bound cargo through three-dimensional, intracellular actin filament networks. We developed a coarse-grained, in silico model to predict how actin filament density (3-800 filaments) within a randomly oriented actin network affects fluid-like liposome (350nm vs. 1,750nm) transport by myoVa motors. 5,000 simulated liposomes transported within each network adopted one of three states: transport, tug of war, or diffusion. Diffusion due to liposome detachment from actin rarely occurred given at least 10 motors on the liposome surface. However, with increased actin density, liposomes transitioned from primarily directed transport on single actin filaments to an apparent random walk, resulting from a mixture of transport and tug of wars as the probability of encountering additional actin filaments increased. This phase transition arises from a percolation phase transition at a critical number of accessible actin filaments, Nc. Nc, is a geometric property of the actin network that depends only on the position and polarity of the actin filaments and the liposome diameter, as evidenced by a five-fold increase in liposome diameter resulting in a five-fold decrease in Nc. Thus, in cells, actin network density and cargo size may be regulated to match cargo delivery to the cell’s physiological demands.
Artemisinin-independent inhibitory activity ofArtemisiasp. infusions against differentPlasmodiumstages including relapse-causing hypnozoites
Authors: Ashraf Kutub , Tajeri Shahin , Arnold Christophe-Sébastien , Amanzougaghene Nadia , Franetich Jean-François , Vantaux Amélie , Soulard Valérie , Bordessoulles Mallaury , Cazals Guillaume , Bousema Teun , van Gemert Geert-Jan , Grand Roger Le , Dereuddre-Bosquet Nathalie , Barale Jean-Christophe , Witkowski Benoit , Snounou Georges , Duval Romain , Botté Cyrille Y. , Mazier Dominique 
Published: August 2021

AbstractArtemisinin-based combination therapies (ACT) are the frontline treatments against malaria worldwide. Recently the use of traditional infusions fromArtemisia annua(from which artemisinin is obtained) orA. afra(lacking artemisinin) has been controversially advocated. Such unregulated plant-based remedies are strongly discouraged as they might constitute sub-optimal therapies and promote drug resistance. Here, we conducted the first comparative study of the anti-malarial effects of both plant infusionsin vitroagainst the asexual erythrocytic stages ofP. falciparumand the pre-erythrocytic (i. e., liver) stages of variousPlasmodiumspecies. Low concentrations of either infusion accounted for significant inhibitory activities across every parasite species and stage studied. We show that these antiplasmodial effects were essentially artemisinin-independent and were additionally monitored by observations of the parasite apicoplast and mitochondrion. In particular, the infusions significantly incapacitated sporozoites, and forP. vivaxandP. cynomolgi,disrupted the hypnozoites. This provides the first indication that compounds other than 8-aminoquinolines could be effective antimalarials against relapsing parasites. These observations advocate for further screening to uncover urgently needed novel antimalarial lead compounds.
No need to choose: independent regulation of cognitive stability and flexibility challenges the stability-flexibility tradeoff
Authors: Geddert Raphael , Egner Tobias 
Published: August 2021

AbstractAdaptive behavior requires the ability to focus on a current task and protect it from distraction (cognitive stability) as well as the ability to rapidly switch to another task in light of changing circumstances (cognitive flexibility). Cognitive stability and flexibility have been conceptualized as opposite endpoints on astability-flexibility tradeoffcontinuum, implying an obligatory reciprocity between the two: greater flexibility necessitates less stability, and vice versa. Surprisingly, rigorous empirical tests of this critical assumption are lacking. Here, we acquired simultaneous measurements of cognitive stability (congruency effects) and flexibility (switch costs) on the same stimuli within the same task, while independently varying contextual demands on these functions with block-wise manipulations of the proportion of incongruent trials and task switches, respectively. If cognitive stability and flexibility are reciprocal, increases in flexibility in response to higher switch rates should lead to commensurate decreases in stability, and increases in stability in response to more frequent incongruent trials should result in decreased flexibility. Across three experiments, using classic cued task switching (Experiments 1 and 3) and attentional set shifting (Experiment 2) protocols, we found robust evidence against an obligatory stability-flexibility tradeoff. Although we observed the expected contextual adaptation of stability and flexibility to changing demands, strategic adjustments in stability had little influence on flexibility, and vice versa. These results refute the long-held assumption of a stability-flexibility tradeoff, documenting instead that the cognitive processes mediating these functions can be regulated independently – it is possible to be both stable and flexible at the same time.
Polysorbate 80 Controls Morphology, Structure and Stability of Human Insulin Amyloid-Like Spherulites
Authors: Zhou Xin , Galparsoro Dirk Fennema , Madsen Anders Østergaard , Vetri Valeria , van de Weert Marco , Nielsen Hanne Mørck , Foderà Vito 
Published: August 2021

AbstractAmyloid protein aggregates are not only associated with neurodegenerative diseases and may also occur as unwanted by-products in protein-based therapeutics. Surfactants are often employed to stabilize protein formulations and reduce the risk of aggregation. However, surfactants alter protein-protein interactions and may thus modulate the physicochemical characteristics of any aggregates formed. Human insulin aggregation was induced at low pH in the presence of varying concentrations of the surfactant polysorbate 80. Various spectroscopic and imaging methods were used to study the aggregation kinetics, as well as structure and morphology of the formed aggregates. Molecular dynamics simulations were employed to investigate the initial interaction between the surfactant and insulin. Addition of polysorbate 80 slowed down, but did not prevent, aggregation of insulin. Amyloid spherulites formed under all conditions, with a higher content of intermolecular beta-sheets in the presence of the surfactant above its critical micelle concentration. In addition, a denser packing was observed, leading to a more stable aggregate. Molecular dynamics simulations suggested a tendency for insulin to form dimers in the presence of the surfactant, indicating a change in protein-protein interactions. It is thus shown that surfactants not only alter aggregation kinetics, but also affect physicochemical properties of any aggregates formed.
Stable Flow-induced Expression of KLK10 Inhibits Endothelial Inflammation and Atherosclerosis
Authors: Williams Darian , Mahmoud Marwa , Liu Renfa , Andueza Aitor , Kumar Sandeep , Kang Dong-Won , Zhang Jiahui , Tamargo Ian , Villa-Roel Nicolas , Baek Kyung-In , Lee Hwakyoung , An Yongjin , Zhang Leran , Tate Edward W. , Bagchi Pritha , Pohl Jan , Mosnier Laurent O. , Diamandis Eleftherios P. , Mihara Koichiro , Hollenberg Morley D. , Dai Zhifei , Jo Hanjoong 
Published: August 2021

AbstractIntroductionAtherosclerosis preferentially occurs in arterial regions exposed to disturbed blood flow (d-flow), while regions exposed to stable flow (s-flow) are protected. The proatherogenic and atheroprotective effects ofd-flowands-floware mediated in part by the global changes in endothelial cell gene expression, which regulates endothelial dysfunction, inflammation, and atherosclerosis. Previously, we identified Kallikrein-Related Peptidase 10 (KLK10, a secreted serine protease) as a flow-sensitive gene in arterial endothelial cells, but its role in endothelial biology and atherosclerosis was unknown.Methods and ResultsHere, we show that KLK10 is upregulated unders-flowconditions and downregulated underd-flowconditions usingin vivomouse models andin vitrostudies with cultured endothelial cells (ECs). Single-cell RNA sequencing (scRNAseq) and scATAC sequencing (scATACseq) study using the partial carotid ligation mouse model showed flow-regulated KLK10 expression at the epigenomic and transcription levels. Functionally, KLK10 protected againstd-flow-induced inflammation and permeability dysfunction in human artery ECs (HAECs). Further, treatment of micein vivowith rKLK10 decreased arterial endothelial inflammation ind-flowregions. Additionally, rKLK10 injection or ultrasound-mediated transfection of KLK10-expressing plasmids inhibited atherosclerosis inApoE-/-mice. Studies using pharmacological inhibitors and siRNAs revealed that the anti-inflammatory effects of KLK10 were mediated by a Protease Activated Receptors (PAR1/2)-dependent manner. However, unexpectedly, KLK10 did not cleave the PARs. Through a proteomics study, we identified HTRA1 (High-temperature requirement A serine peptidase 1), which bound and cleaved KLK10. Further, siRNA knockdown of HTRA1 prevented KLK10’s anti-inflammatory and barrier protective function in HAECs, suggesting that HTRA1 regulates KLK10 function. Moreover, KLK10 expression was significantly reduced in human coronary arteries with advanced atherosclerotic plaques compared to those with less severe plaques.ConclusionKLK10 is a flow-sensitive endothelial protein and, in collaboration with HTRA1, serves as an anti-inflammatory, barrier-protective, and anti-atherogenic factor.
Localized hypermutation drives the evolution of unstable colistin resistance inPseudomonas aeruginosa
Authors: Kapel Natalia , Caballero Julio Diaz , MacLean R. Craig 
Published: August 2021

AbstractColistin has emerged as an important last line of defence for the treatment of infections caused by antibiotic resistant Gram-negative pathogens. Here we investigate the responses of ≈1,000 populations of an MDR strain ofP. aeruginosato a high dose of colistin. Colistin exposure resulted in rapid cell death, but a sub-set of populations eventually recovered due to the outgrowth of heteroresistant cells. Genome sequencing revealed that heteroresistance was primarily driven by mutations in the PmrAB two-component system that occurred at a rate (≈2×10-5per cell division) that was 103-104fold higher than typical resistance mutation rates. Crucially, this elevated mutation rate was only found inpmrB, demonstrating that hypermutability is localized to this gene. PmrAB provides resistance to antimicrobial peptides that are involved in host immunity, suggesting that this pathogen may have evolved a high mutation rate as an adaption to generate mutants that are resistant to host antimicrobial peptides that are secreted during infection. Interestingly, we found no mutations in 1/3 of populations that recovered from colistin treatment, suggesting that phenotypic plasticity and/or persister cells contribute to the ability ofPseudomonasto adapt to colistin.
Crosstalk between Ethylene and ABA during changes in soil water content reveals a role of ACC in coffee anthesis regulation
Authors: López Marlon Enrique , Santos Iasminy Silva , Gutiérrez Robert Márquez , Mesa Andrea Jaramillo , Cardon Carlos Henrique , Espindola Lima Juliana Maria , Lima André Almeida , Chalfun-Junior Antonio 
Published: August 2021

SummaryCoffee (Coffea arabicaL.) presents an asynchronous flowering regulated by endogenous and environmental stimulus, and anthesis occurs once plants are rehydrated after a period of water deficit.We evaluated the evolution of Abscisic Acid (ABA), ethylene, 1-aminocyclopropane-1-carboxylate (ACC) content, ACC oxidase (ACO) activity, and expression analysis of theLysine Histidine Transporter1 (LHT1)transporter, in roots, leaves and, flower buds from three coffee genotypes (Coffea arabicaL. cv Oeiras, Acauã, andSemperflorens) cultivated under field conditions with two experiments. In a third field experiment, the effect of exogenous supply of ACC in coffee anthesis was evaluated.We found an increased ACC level in all tissues from the three coffee genotypes in the re-watering period just before anthesis for all tissues and high expression of theLHT1gene in flower buds and leaves. Ethylene content and ACO activity decreased from rainy to dry period whereas ABA content increased. Higher number of opened and G6 stage flower buds were observed in the treatment with exogenous ACC.The results showed that the interaction of ABA-ACO-ethylene and intercellular ACC transport among leaves, buds, and roots in coffee favors an increased level of ACC that is most likely, involved as a modulator in coffee anthesis.
Improved blind demixing methods for recovering dense neuronal morphology from barcode imaging data
Authors: Chen Shuonan , Loper Jackson , Zhou Pengcheng , Paninski Liam 
Published: August 2021

AbstractCellular barcoding methods offer the exciting possibility of ‘infinite-pseudocolor’ anatomical reconstruction — i.e., assigning each neuron its own random unique barcoded ‘pseudocolor,’ and then using these pseudocolors to trace the microanatomy of each neuron. Here we use simulations, based on densely-reconstructed electron microscopy microanatomy, with signal structure matched to real barcoding data, to quantify the feasibility of this procedure. We develop a new blind demixing approach to recover the barcodes that label each neuron. We also develop a neural network which uses these barcodes to reconstruct the neuronal morphology from the observed fluorescence imaging data, ‘connecting the dots’ between discontiguous amplicon signals. We find that accurate recovery should be feasible, provided that the barcode signal density is sufficiently high. This study suggests the possibility of mapping the morphology and projection pattern of many individual neurons simultaneously, at high resolution and at large scale, via conventional light microscopy.