bluuebunny/crossref_metadata_2025_split huggingface dataset:
Near-perfect precise on-target editing of human hematopoietic stem and progenitor cells
Authors: Cloarec-Ung Fanny-Meï , Beaulieu Jamie , Suthananthan Arunan , Lehnertz Bernhard , Sauvageau Guy , Sheppard Hilary M , Knapp David JHF 
Published: May 2023

AbstractPrecision gene editing in primary hematopoietic stem and progenitor cells (HSPCs) would facilitate both curative treatments for monogenic disorders as well as disease modelling. Precise efficiencies even with the CRISPR/Cas system, however, remain limited. Through an optimization of guide RNA delivery, donor design, and additives, we have now obtained mean precise editing efficiencies >90% on primary cord blood HSCPs with minimal toxicity and without observed off-target editing. The main protocol modifications needed to achieve such high efficiencies were the addition of the DNA-PK inhibitor AZD7648, and the inclusion of spacer-breaking silent mutations in the donor in addition to mutations disrupting the PAM sequence. Critically, editing was even across the progenitor hierarchy, did not substantially distort the hierarchy or affect lineage outputs in colony-forming cell assays or the frequency of high self-renewal potential long-term culture initiating cells. As modelling of many diseases requires heterozygosity, we also demonstrated that the overall editing and zygosity can be tuned by adding in defined mixtures of mutant and wild-type donor. With these optimizations, editing at near-perfect efficiency can now be accomplished directly in human HSPCs. This will open new avenues in both therapeutic strategies and disease modelling.
The reaction-diffusion basis of animated patterns in eukaryotic flagella
Authors: Cass James , Bloomfield-Gadêlha Hermes 
Published: May 2023

AbstractWe show that the flagellar beat of bull spermatozoa andChlamydomonas Reinhardtiican be modelled by a minimal, geometrically nonlinear, sliding-controlled, reaction-diffusion system. Model solutions are spatio-temporallyanimated patternsdescribing flagellar bending waves, further connecting beating patterns of cilia and flagella with, seemly unrelated, chemical patterns from classical reaction-diffusion systems. Instead of chemical species freely reacting and diffusing in space, our system describes the tug-of-war reaction-kinetics of molecular motors that are anchored in the flagellar structure, but the shear deformation that they generate candiffuseaway via the bending elasticity of the flagellum. Synchronization of the reaction-kinetics in neighbouring elements occurs via asliding-controlmechanism. We derive from first principles the reaction-diffusion basis of animated patterns, and show that this is a direct consequence of the highinternalenergy dissipation by the flagellum relative to theexternaldissipation by the fluid environment. By fitting, for the first time, nonlinear, large-amplitude solutions of a specific motor cross-bridge reaction-kinetics, we show that reaction-diffusion successfully accounts for beating patterns of bothbull spermandChlamydomonas(wild-type and mbo2-mutant), unifying these distant eukaryotic species under the same minimal model. Our results suggest that the flagellar beat occurs far from equilibrium, in the strongly nonlinear regime, and that in contrary to the conclusions of small amplitude studies, a unified mechanism may exist for dynein molecular motor control that is regulated by axonemal sliding, without requiring curvature-sensing or the fine-tuning of basal compliance, and only weakly influenced by hydrodynamic dissipation and the cell body boundary condition. High internal dissipation allows the emergence of base-to-tip autonomous travelling waves, independently of, and without relying on, the external fluid viscosity, when small. This enables progressive swimming, otherwise not possible, in low viscosity environments, and may be critical for external fertilizers and aquatic microorganisms. The reaction-diffusion model may prove a powerful tool for studying the pattern formation of movement in flagella, cilia, and more generally, oscillations of animated filament-bundles at the microscale.
Motor cortex latent dynamics encode spatial and temporal arm movement parameters independently
Authors: Colins Rodriguez Andrea , Perich Matthew G. , Miller Lee , Humphries Mark D. 
Published: May 2023

AbstractThe fluid movement of an arm requires multiple spatiotemporal parameters to be set independently. Recent studies have argued that arm movements are generated by the collective dynamics of neurons in motor cortex. An untested prediction of this hypothesis is that independent parameters of movement must map to independent components of the neural dynamics. Using a task where monkeys made a sequence of reaching movements to randomly placed targets, we show that the spatial and temporal parameters of arm movements are independently encoded in the low-dimensional trajectories of population activity in motor cortex: Each movement’s direction corre-sponds to a fixed neural trajectory through neural state space and its speed to how quickly that trajectory is traversed. Recurrent neural network models show this coding allows independent control over the spatial and temporal parameters of movement by separate network parameters. Our results support a key prediction of the dynamical systems view of motor cortex, but also argue that not all parameters of movement are defined by different trajectories of population activity.Significance StatementFrom delicate strokes while drawing to ballistic swings while playing tennis, a skilled arm movement requires precise control of both its direction and speed. Motor cortex is thought to play a key role in controlling both, but it is unclear how they are jointly controlled. We show here that the population activity in motor cortex represents both the spatial and temporal properties of arm movements in the same low-dimensional signal. This representation was remarkably simple: the movement’s direction is represented by the trajectory that signal takes; the movement’s speed by how quickly the signal moves along its trajectory. Our network modelling shows this encoding allows an arm movement’s direction and speed to be simultaneously and independently controlled.
Transcriptomic landscape of posterior regeneration in the annelidPlatynereis dumerilii
Authors: Paré Louis , Bideau Loïc , Baduel Loeiza , Dalle Caroline , Benchouaia Médine , Schneider Stephan Q. , Laplane Lucie , Clément Yves , Vervoort Michel , Gazave Eve 
Published: May 2023

AbstractBackground:Restorative regeneration, the capacity to reform a lost body part following amputation or injury, is an important and still poorly understood process in animals. Annelids, or segmented worms, show amazing regenerative capabilities, and as such are a crucial group to investigate. Elucidating the molecular mechanisms that underpin regeneration in this major group remains a key goal. Among annelids, the nereididaePlatynereis dumerilii(re)emerged recently as a front-line regeneration model. Following amputation of its posterior part,Platynereisworms can regenerate both differentiated tissues of their terminal part as well as a growth zone that contains putative stem cells. While this regeneration process follows specific and reproducible stages that have been well characterized, the transcriptomic landscape of these stages remains to be uncovered.Results:We generated a high qualityde novoReference transcriptome for the annelidPlatynereis dumerilii. To do so, we produced and analyzed three RNA-sequencing datasets, encompassing five stages of posterior regeneration, along with blastema stages and non-amputated tissues as controls. We included these regeneration RNA-seq datasets, as well as embryonic and tissue-specific datasets from the literature to produce a Reference transcriptome. We used this Reference transcriptome to perform in depth analyzes of RNA-seq data during the course of regeneration to reveal the important dynamics of the gene expression, process with thousands of genes differentially expressed between stages, as well as unique and specific genes expression at each regeneration stage. The study of these genes highlighted the importance of the nervous system at both early and late stages of regeneration, as well as the enrichment of RNA-binding proteins (RBPs) during almost the entire regeneration process.Conclusions:In this study, we provided a high-qualityde novoReference transcriptome for the annelidPlatynereisthat is useful for investigating various developmental processes, including regeneration. Our extensive stage-specific transcriptional analysis during the course of posterior regeneration shed light upon major molecular mechanisms and pathways, and will foster many specific studies in the future.
Dilated cardiomyopathy variant R14del increases phospholamban pentamer stability, blunting dynamic regulation of cardiac calcium handling
Authors: Cleary Sean R. , Teng Allen C. T. , Kongmeneck Audrey Deyawe , Fang Xuan , Phillips Taylor A. , Cho Ellen E. , Kekenes-Huskey Peter , Gramolini Anthony O. , Robia Seth L. 
Published: May 2023

ABSTRACTThe sarco(endo)plasmic reticulum Ca2+ATPase (SERCA) is a membrane transporter that creates and maintains intracellular Ca2+stores. In the heart, SERCA is regulated by an inhibitory interaction with the monomeric form of the transmembrane micropeptide phospholamban (PLB). PLB also forms avid homo-pentamers, and dynamic exchange of PLB between pentamers and the regulatory complex with SERCA is an important determinant of cardiac responsiveness to exercise. Here, we investigated two naturally occurring pathogenic mutations of PLB, a cysteine substitution of arginine 9 (R9C) and an in-frame deletion of arginine 14 (R14del). Both mutations are associated with dilated cardiomyopathy. We previously showed that the R9C mutation causes disulfide crosslinking and hyperstabilization of pentamers. While the pathogenic mechanism of R14del is unclear, we hypothesized that this mutation may also alter PLB homo-oligomerization and disrupt the PLB-SERCA regulatory interaction. SDS-PAGE revealed a significantly increased pentamer:monomer ratio for R14del-PLB when compared to WT-PLB. In addition, we quantified homo-oligomerization and SERCA-binding in live cells using fluorescence resonance energy transfer (FRET) microscopy. R14del-PLB showed an increased affinity for homo-oligomerization and decreased binding affinity for SERCA compared to WT, suggesting that, like R9C, the R14del mutation stabilizes PLB in its pentameric form, decreasing its ability to regulate SERCA. Moreover, the R14del mutation reduces the rate of PLB unbinding from the pentamer after a transient Ca2+elevation, limiting the rate of re-binding to SERCA. A computational model predicted that hyperstabilization of PLB pentamers by R14del impairs the ability of cardiac Ca2+handling to respond to changing heart rates between rest and exercise. We postulate that impaired responsiveness to physiological stress contributes to arrhythmogenesis in human carriers of the R14del mutation.
Polarized Mechanosensitive Signaling Domains Protect Arterial Endothelial Cells Against Inflammation
Authors: Hong Soon-Gook , Ashby Julianne W. , Kennelly John P. , Wu Meigan , Chattopadhyay Eesha , Foreman Rob , Tontonoz Peter , Turowski Patric , Gallagher-Jones Marcus , Mack Julia J. 
Published: May 2023

AbstractEndothelial cells (ECs) in the descending aorta are exposed to high laminar shear stress, which supports an anti-inflammatory phenotype that protects them from atherosclerosis. High laminar shear stress also supports flow-aligned cell elongation and front-rear polarity, but whether this is required for athero-protective signaling is unclear. Here, we show that Caveolin-1-rich microdomains become polarized at the downstream end of ECs exposed to continuous high laminar flow. These microdomains are characterized by higher membrane rigidity, filamentous actin (F-actin) and lipid accumulation. Transient receptor potential vanilloid-type 4 (Trpv4) ion channels, while ubiquitously expressed, mediate localized Ca2+entry at these microdomains where they physically interact with clustered Caveolin-1. The resultant focal bursts in Ca2+activate the anti-inflammatory factor endothelial nitric oxide synthase (eNOS) within the confines of these domains. Importantly, we find that signaling at these domains requires both cell body elongation and sustained flow. Finally, Trpv4 signaling at these domains is necessary and sufficient to suppress inflammatory gene expression. Our work reveals a novel polarized mechanosensitive signaling hub that induces an anti-inflammatory response in arterial ECs exposed to high laminar shear stress.
Metabolic disruption impacts tick fitness and microbial relationships
Authors: Samaddar Sourabh , O’Neal Anya J. , Marnin Liron , Rolandelli Agustin , Singh Nisha , Wang Xiaowei , Butler L. Rainer , Rangghran Parisa , Laukaitis Hanna J. , Cabrera Paz Francy E. , Fiskum Gary M. , Polster Brian M. , Pedra Joao H. F. 
Published: May 2023

AbstractArthropod-borne microbes rely on the metabolic state of a host to cycle between evolutionarily distant species. For instance, arthropod tolerance to infection may be due to redistribution of metabolic resources, often leading to microbial transmission to mammals. Conversely, metabolic alterations aids in pathogen elimination in humans, who do not ordinarily harbor arthropod-borne microbes. To ascertain the effect of metabolism on interspecies relationships, we engineered a system to evaluate glycolysis and oxidative phosphorylation in the tickIxodes scapularis. Using a metabolic flux assay, we determined that the rickettsial bacteriumAnaplasma phagocytophilumand the Lyme disease spirocheteBorrelia burgdorferi, which are transstadially transmitted in nature, induced glycolysis in ticks. On the other hand, the endosymbiontRickettsia buchneri,which is transovarially maintained, had a minimal effect onI. scapularisbioenergetics. Importantly, the metabolite β-aminoisobutyric acid (BAIBA) was elevated duringA. phagocytophiluminfection of tick cells following an unbiased metabolomics approach. Thus, we manipulated the expression of genes associated with the catabolism and anabolism of BAIBA inI. scapularisand detected impaired feeding on mammals, reduced bacterial acquisition, and decreased tick survival. Collectively, we reveal the importance of metabolism for tick-microbe relationships and unveil a valuable metabolite forI. scapularisfitness.
Cortical microtubules oppose actomyosin-driven membrane ingression duringC. elegansmeiosis I polar body extrusion
Authors: Quiogue Alyssa R. , Sumiyoshi Eisuke , Fries Adam , Chuang Chien-Hui , Bowerman Bruce 
Published: May 2023

AbstractDuringC. elegansoocyte meiosis I, cortical actomyosin is locally remodeled to assemble a contractile ring near the spindle. In contrast to mitosis, when most cortical actomyosin converges into a contractile ring, the small oocyte ring forms within and remains part of a much larger and actively contractile cortical actomyosin network. This network both mediates contractile ring dynamics and generates shallow ingressions throughout the oocyte cortex during polar body extrusion. Based on our analysis of requirements for CLS-2, a member of the CLASP family of proteins that stabilize microtubules, we recently proposed that a balance of actomyosin-mediated tension and microtubule-mediated stiffness are required for contractile ring assembly within the oocyte cortical actomyosin network. Here, using live cell imaging and fluorescent protein fusions, we show that CLS-2 is part of a complex of kinetochore proteins, including the scaffold KNL-1 and the kinase BUB-1, that also co-localize to patches distributed throughout the oocyte cortex during meiosis I. By reducing their function, we further show that KNL-1 and BUB-1, like CLS-2, are required for cortical microtubule stability, to limit membrane ingression throughout the oocyte, and for meiotic contractile ring assembly and polar body extrusion. Moreover, nocodazole or taxol treatment to destabilize or stabilize oocyte microtubules, respectively, leads to excess or decreased membrane ingression throughout the oocyte and defective polar body extrusion. Finally, genetic backgrounds that elevate cortical microtubule levels suppress the excess membrane ingression incls-2mutant oocytes. These results support our hypothesis that CLS-2, as part of a sub-complex of kinetochore proteins that also co-localize to patches throughout the oocyte cortex, stabilizes microtubules to stiffen the oocyte cortex and limit membrane ingression throughout the oocyte, thereby facilitating contractile ring dynamics and the successful completion of polar body extrusion during meiosis I.
Comprehensive screening of a light-inducible split Cre recombinase with domain insertion profiling
Authors: Tague Nathan , Andreani Virgile , Fan Yunfan , Timp Winston , Dunlop Mary J. 
Published: May 2023

AbstractSplitting proteins with light- or chemically-inducible dimers provides a mechanism for post-translational control of protein function. However, current methods for engineering stimulus-responsive split proteins often require significant protein engineering expertise and laborious screening of individual constructs. To address this challenge, we use a pooled library approach that enables rapid generation and screening of nearly all possible split protein constructs in parallel, where results can be read out using sequencing. We perform our method on Cre recombinase with optogenetic dimers as a proof of concept, resulting in comprehensive data on split sites throughout the protein. To improve accuracy in predicting split protein behavior, we develop a Bayesian computational approach to contextualize errors inherent to experimental procedures. Overall, our method provides a streamlined approach for achieving inducible post-translational control of a protein of interest.
Complex films formed on Al alloy surface via vapor phase assembly of benzotriazole and dodecyltrimethoxysilane
Authors: Wang Qiang , Zhang Hongliang , Zhang Da Quan , Zheng Hongai , Gao Lixin 
Published: May 2023

Purpose
The purpose of this paper is to study the effect of vapor assembly sequence and assembly temperature on the corrosion protection of the complex silane films Al alloy. The performance and application range of silane films are enhanced.

Design/methodology/approach
The complex silane films were successfully prepared on the surface of aluminum alloy using via vapor phase assembly of 1,2,3-benzotriazole (BTA) and dodecyltrimethoxysilanes (DTMS). The protection of the assembly films against corrosion of Al alloy is investigated by the electrochemical measurements and the alkaline solution accelerated corrosion test. Thickness and hydrophobicity of the complex films are studied using ellipsometric spectroscopy and contact angle tests.

Findings
It shows that the anti-corrosion ability of the complex films is overall superior to that of the single-component assembled films. DTMS-BTA films have larger thickness and best anti-corrosion ability. The alkyl chains in DTMS have better compatibility with BTA molecules. The rigid BTA molecule can permeate into the long alkyl chain of DTMS as fillers and improve the barrier properties of the complex films.

Originality/value
In this paper, a green and efficient method of vapor phase assembly is proposed to rust prevention during manufacture of Al alloy workpiece.
Higher education by fields and foreign direct investments: insights from OECD countries
Authors: Şeri̇foğlu Müzeyyen Merve , Öge Güney Pelin 
Published: May 2023

PurposeThis paper investigates the two-way relationship between foreign direct investment (FDI) inflows and higher education across 36 Organisation for Economic Co-operation and Development (OECD) countries for 1998–2019 periods. To demonstrate this relationship, the authors take into account the total number of graduates as well as the number of graduates from different fields. Accordingly, the authors gathered graduates in four groups which are education, social sciences, technical sciences (tech) and health. In addition to investigating two-way relationship between FDI and graduates, the authors also examined the contribution of primary and secondary level education to FDI.Design/methodology/approachThe authors use two models to investigate the bidirectional relationship between FDI inflows and graduates from four fields. In the first model, the dependent variable is FDI inflows, and in the second model, graduates from each field are the dependent variable. To investigate the dual relationship, the authors employ ordinary least squares (OLS) and two-step system generalized method of moments (GMM) developed by Arellano Bover (1995) and Blundell Bond (1998).FindingsFor the first model, the results show that secondary level and higher education have a positive impact on FDI. In terms of graduates by fields, it is seen that education and health graduates contributed the most to FDI. For the second model in which the authors analysed the effect of FDI on total graduates and graduates from different fields, the authors find that FDI positively affects the number of graduates from all fields, and the strongest effect is on graduates from the social science field.Practical implicationsBased on the results, the authors can say that well-educated people promote FDI inflows to OECD countries, and FDI is also a driving force in raising highly educated people. So, the authors think that the results will help design higher education policies in accordance with FDI and higher education connection.Originality/valueTo the best of the authors’ knowledge, this paper is the first to examine the impact of FDI inflows on graduates by fields and also to investigate the impact of graduates by fields on FDI.
One-to-one LEGO® SERIOUS PLAY® positive psychology coaching for emerging adults: a single-participant case study
Authors: Moore Maurissa , O'Sullivan David 
Published: May 2023

PurposeThis study explores one-to-one LEGO® Serious Play® in positive psychology coaching (1-1 LSP in PPC) as an intervention to help emerging adults (EAs) in higher education develop a growth mindset.Design/methodology/approachThis is a qualitative single-participant case study of an EA undergraduate student's experience with 1-1 LSP in PPC to help him navigate uncertainty about making a decision that he felt would influence his future career.Findings1-1 LSP in PPC enabled the participant to create a metaphoric representation of how a growth mindset operated for him, promoting self-awareness and reflectivity. The LEGO® model that the participant built during his final session acted as a reminder of the resources and processes he developed during coaching, which helped him navigate future challenges.Research limitations/implicationsThis study contributes to the emerging literature on the impact of using LSP as a tool in one-to-one coaching in higher education. The participant's experience demonstrates that 1-1 LSP in PPC may be an effective way to support positive EA development. More research is needed to explore its potential.Practical implicationsThis study provides a possible roadmap to incorporate 1-1 LSP in PPC into coaching in higher education as a reflective tool to build a growth mindset in EA students.Originality/valueBecause most undergraduates are EAs navigating the transition from adolescence into adulthood, universities would benefit from adopting developmentally informed coaching practices. 1-1 LSP in PPC may be an effective intervention that provides the structured and psychologically safe environment EAs need to develop lasting personal resources.