bluuebunny/crossref_metadata_2025 huggingface dataset:
Chaparral wildfire shifts the functional potential for soil pyrogenic organic matter and nitrogen cycling
Authors: Pulido-Chavez M. Fabiola , Nelson Amelia R , Wilkins Michael R , Glassman Sydney I
Published: August 2024

Wildfires alter soil chemistry and microbial communities, opening niche space for pyrophilous or "fire-loving" microbes to initiate secondary succession. However, wildfires also increase soil nitrogen (N) and transform woody vegetation into difficult-to-degrade pyrogenic organic matter (PyOM), a potential carbon (C) source for pyrophilous microbes. Whether pyrophilous microbes can degrade these post-fire resources has significant implications for global C and N cycling, including C sequestration and greenhouse gas emissions. To determine temporal patterns in the functional potential for PyOM degradation and N cycling, we performed shotgun metagenomics on 30 burned and unburned soils collected at 17, 25, 34, 131, and 376 days after a high-severity wildfire in a Southern California fire-adapted chaparral shrubland. Not only did overall profiles of C and N cycling genes differ between burned and unburned plots, but burned plots showed dramatic increases from 17 to 376 days in genes responsible for degrading PyOM (167%) and cycling N (117%). In contrast, gene abundances for PyOM degradation and N cycling remained stable over time in unburned plots. Genes encoding the degradation pathways for two PyOM degradation intermediate pathways, catechol and protocatechuate, revealed that the easier-to-degrade ortho-cleavage pathways dominated all time points in the burned plots. Genes encoding N retention pathways (assimilatory and dissimilatory nitrate reduction) dominated N cycling pathways in burned plots for the entire year. Finally, dominant pyrophilous bacterial taxa in the genera Massilia and Noviherbaspirillium encoded different PyOM and N processing pathways, suggesting that traits enabling adaptation to wildfires, like post-fire resource acquisition, drive microbial secondary succession.
Modeling vascular dynamics at the initial stage of endochondral ossification on a microfluidic chip using a human embryonic-stem-cell-derived organoid
Authors: Kesharwani Abhiraj , Tani Shoichiro , Nishikawa Masaki , Sakai Yasuyuki , Okada Hiroyuki , Ohba Shinsuke , Chung Ung-il , Hojo Hironori
Published: August 2024

Vascular interactions play a crucial role in embryogenesis, including skeletal development. During endochondral ossification, vascular networks are formed as mesenchymal cells condense and later invade skeletal elements to form the bone marrow. We and other groups developed a model of endochondral ossification by implanting human embryonic stem cell (hESC)–derived sclerotome into immunodeficient mice. However,in vitromodels of endochondral ossification, particularly vascular interaction with mesenchymal cells at its initial stage, are yet to be established. Therefore, we developed a method to model the initial stage of endochondral ossification using a microfluidic chip-based platform, with a particular focus on the vascular interaction. On the chip, we found that the fibrin gel helped align mCherry-expressing human umbilical vein endothelial cells (HUVECs) better than the collagen-I gel, suggesting that the fibrin gel is more suitable for the formation of a vascular-like network. The perfusability of the vascular-like networks was partially confirmed using fluorescein isothiocyanate (FITC)-dextran and fluorescent microbeads. We then mixed hESC-derived sclerotome with enhanced green fluorescent protein (EGFP)-expressing HUVECs and applied this mixture on the chip. We named this mixture of cells SH organoids. The SH organoids showed superior abilities to maintain the vascular-like network, which was formed by the mCherry-expressing HUVECs, compared with the sclerotome spheroids on the chip. The EGFP-expressing HUVECs migrated from the SH organoid, formed a vascular-like networks, and partially interacted with the mCherry-expressing vascular-like networks on the chip. Histological analysis showed that SRY-box transcription factor 9 (SOX9) and type I collagen were expressed mutually exclusively in the condensed mesenchymal cells and perichondrial-like cells, respectively. This study demonstrates that our SH organoid-on-a-chip method reproduces vascular networks that are formed at the initial stage of endochondral ossification. This model may provide insights into human endochondral ossification and has potential applications in bone disease modeling and drug screening.
Benchmarking macaque brain gene expression for horizontal and vertical translation
Authors: Luppi Andrea I , Liu Zhen-Qi I , Hansen Justine Y , Cofre Rodrigo , Kuzmin Elena , Froudist-Walsh Seán , Palomero-Gallagher Nicola , Misic Bratislav
Published: August 2024

The spatial patterning of gene expression shapes cortical organization and emergent function. Advances in spatial transcriptomics make it possible to comprehensively map cortical gene expression in both humans and model organisms. The macaque is a particularly valuable model organism, due to its evolutionary similarity with the human. The translational potential of macaque gene expression rests on the assumption that it is a good proxy for spatial patterns of corresponding proteins (vertical translation) and for spatial patterns of ortholog human genes (horizontal translation). Here we systematically benchmark the spatial distribution of gene expression in the macaque cortex against (a) cortical receptor density in the macaque and (b) cortical gene expression in the human. We find that there is moderate cortex-wide correspondence between gene expression and protein density in the macaque, which is improved by considering layer specific gene expression. We find greater correspondence between orthologous gene expression in the macaque and human. Inter-species correspondence of gene expression exhibits systematic regional heterogeneity, with greater correspondence in unimodal than transmodal cortex, mapping onto patterns of evolutionary cortical expansion. We extend these results to additional micro-architectural features using macaque immunohistochemistry and T1w:T2w ratio, and replicate them using macaque RNA-seq and human RNA-seq gene expression. Collectively, the present results showcase both the potential and limitations of macaque spatial transcriptomics as an engine of translational discovery within and across species.
Genome-resolved diversity and biosynthetic potential of the coral reef microbiome
Authors: Paoli Lucas , Wiederkehr Fabienne , Ruscheweyh Hans-Joachim , Miravet-Verde Samuel , Bistolas Kalia S.I. , Sawyer Teresa , Labadie Karine , Mayer Kim-Isabelle , Perdereau Aude , Reddy Maggie M. , Moulin Clémentine , Boissin Emilie , Bourdin Guillaume , Cailliau Juliette , Iwankow Guillaume , Poulain Julie , Romac Sarah ,   Tara Pacific Consortium Coordinators, Planes Serge , Allemand Denis , Agostini Sylvain , Bowler Chris , Douville Eric , Forcioli Didier , Galand Pierre E. , Lombard Fabien , Oliveira Pedro H. , Piel Jörn , Thomas Olivier , Thurber Rebecca Vega , Troublé Romain , Voolstra Christian R. , Wincker Patrick , Ziegler Maren , Sunagawa Shinichi
Published: August 2024

Coral reefs are marine biodiversity hotspots that provide a wide range of ecosystem services. They are also reservoirs of bioactive compounds, many of which are produced by microbial symbionts associated with reef invertebrate hosts. However, for the keystone species of coral reefs, the reef-building corals themselves, we still lack a systematic assessment of their microbially encoded biosynthetic potential, and thus the molecular resources that may be at stake due to the alarming decline in reef biodiversity and cover. Here, we analysed microbial genomes reconstructed from 820 reef-building coral samples of three representative coral genera collected at 99 reefs across 32 islands during a two-year expedition throughout the Pacific Ocean (Tara Pacific). By contextualising our analyses with the microbiomes of other reef species, we found that genomic information was previously available for only 10% of the 4,224 microbial species overall and for less than 1% of the 645 species exclusively identified in Tara Pacific samples. We found reef-building coral microbiomes to be host-specific and their biosynthetic potential to rival or even surpass that found in traditional targets for natural product discovery, such as sponges and soft corals. Fire corals were not only particularly diverse in microbially encoded biosynthetic gene clusters (BGCs), but also in BGC-rich bacteria, including Acidobacteriota spp., which have been recently highlighted for their promising natural product repertoire. Together, this study unveils new candidate sources for bioactive compound discovery, prioritises targets for microbial isolation, and underscores the importance of conservation efforts by linking macro-organismal biodiversity loss to host-specific microbiomes and their biotechnological potential.
BMP signalling attenuates intercellular adhesion to drive mesenchyme migration during fin fold morphogenesis
Authors: Saha Bitan , Mahabaleshwar Harsha , Ho Min Charmaine , Leong Leslie Boon Haw , Chua Levene Wenqian , Kwok Samuel , Carney Tom J
Published: August 2024

The development of the vertebrate limb bud is a multifactorial process involving the coordinated activity of diverse signalling pathways and cell types. BMP signalling has been consistently shown to play an integral role during the patterning of mouse and chick limbs. However, the molecular mechanisms and cellular processes underlying its contribution to limb development are poorly understood. Using zebrafish embryos, we demonstrate a novel role of BMPs in driving median fin fold morphogenesis, an evolutionary related structure. Our findings indicated that a graded BMP signal is established in the emerging fin fold along the proximo-distal axis, with the fin mesenchymal cells being identified as the primary target of the signalling cue. Pharmacological and genetic ablation of BMP signalling in the fin fold inhibited the normal migration of the mesenchymal cells into the fin fold. The observed inhibition of migration was accompanied by the elongation in mesenchymal cell shape, which hinted at the possibility of altered physical forces acting on the cell population. We observed that loss of BMP signalling led to the cellular re-distribution and altered membrane dynamics of N-cadherin in the fin mesenchymal cells, which manifested as an increase in homotypic cell adhesion. This change in cell-adhesion serves as the mechanistic basis for the observed defect in migration. Furthermore, inability to detach due to loss of BMP signalling occurs independently of sphingosine-1-phosphate signalling that generates a gradient of mesenchyme adhesion to the underlying matrix. Overall, this study highlights the cellular and molecular mechanism underlying the role of BMPs in coordinating early fin bud morphogenesis.
High-Resolution Spatial Mapping of Electrocorticographic Activities with a 4096-Channel, Multiplexed Thin-Film Transistor Array
Authors: Sheng Xing
Published: August 2024

Advanced brain-machine interfaces (BMIs) demand implantable devices that offer flexibility, high-density and high-throughput capabilities. Conventional neural electrodes are constrained by the wiring strategy. Here we present a flexible and implantable electrocorticography (ECoG) device array (NeuroCam) based on metal-oxide semiconductor thin-film transistors (TFTs), to record brain activities at a large scale. Employing a multiplexing technique, the system is capable to record ECoG signals with up to 4096 channels and a density of 44 sites/mm2, while compressing the fan-in/fan-out leads to around a hundred. In a rabbit model with epilepsy, the NeuroCam array maps abnormal spike-wave discharges with an exceptional spatial resolution (150 um) across extensive brain areas. The device strategy provides a promising route towards high-throughput BMIs with potential applications in fundamental neuroscience studies and practical biomedicine.
Differential cytoophidium assembly betweenSaccharomyces cerevisiae andSchizosaccharomyces pombe
Authors: Deng Ruolan , Li Yi-Lan , Liu Ji-Long
Published: August 2024

The de novo synthesis of cytidine 5’-triphosphate (CTP) is catalyzed by the enzyme CTP synthase (CTPS), which is known to form cytoophidia across all three domains of life. In this study, we use the budding yeastSaccharomyces cerevisiaeand the fission yeastSchizosaccharomyces pombeas model organisms to compare cytoophidium assembly under external environmental and intracellular CTPS alterations. We observe that under low and high temperature conditions, cytoophidia in fission yeast gradually disassembled, while cytoophidia in budding yeast remain unaffected. The effect of pH changes on cytoophidia maintenance in the two yeast species is different. When cultured in the yeast saturated cultured medium, cytoophidia in fission yeast disassemble, while cytoophidia in budding yeast gradually form. Overexpression of CTPS leads to the presence and maintenance of cytoophidia in both yeast species from the log phase to the stationary phase. In summary, our results demostrate differential cytoophidium assembly betweenSaccharomyces cerevisiaeandSchizosaccharomyces pombe, the two most studied yeast species.
Cell type and locus-specific epigenetic editing of memory expression
Authors: Coda Davide Martino , WATT LISA , glauser liliane , Batiuk Mykhailo , Burns Allison , Stahl Cora , Graeff Johannes
Published: August 2024

Epigenetic modifications parallel multiple memory processes, but evidence that the epigenetic makeup of a single site can guide learnt behaviors has so far been lacking. Here, we developed CRISPR-based epigenetic editing tools to address this question in a cell type-specific, locus-restricted and temporally controllable manner in the adult mouse brain. Focusing on learning-induced neuronal populations, we provide a proof-of-principle that site-specific epigenetic dynamics are causally implicated in memory expression.
Novel Mouse Model of Alternating Hemiplegia of Childhood Exhibits Prominent Motor and Seizure Phenotypes
Authors: Hawkins Nicole , DeKeyser Jean-Marc , Kearney Jennifer A , George Alfred L
Published: August 2024

Pathogenic variants in ATP1A3 encoding the neuronal Na/K-ATPase cause a spectrum of neurodevelopmental disorders including alternating hemiplegia of childhood (AHC). Three recurrent ATP1A3 variants are associated with approximately half of known AHC cases and mouse models of two of these variants (p.D801N, p.E815K) replicated key features of the human disorder, which include paroxysmal hemiplegia, dystonia and seizures. Epilepsy occurs in 40-50% of individuals affected with AHC, but detailed investigations of seizure phenotypes were limited in the previously reported mouse models. Using gene editing, we generated a novel AHC mouse expressing the third most recurrent ATP1A3 variant (p.G947R) to model neurological phenotypes of the disorder. Heterozygous Atp1a3-G947R mice on a pure C57BL/6J background were born at a significantly lower frequency than wildtype (WT) littermates, but in vitro fertilization or outcrossing to a different strain (C3HeB/FeJ) generated offspring at near-Mendelian genotype ratios, suggesting a defect in reproductive fitness rather than embryonic lethality. Heterozygous mutant mice were noticeably smaller and exhibited premature lethality, hyperactivity, anxiety-like behaviors, severe motor dysfunction including low grip strength, impaired coordination with abnormal gait and balance, and cooling-induced hemiplegia and dystonia. We also observed a prominent seizure phenotype with lower thresholds to chemically (flurothyl, kainic acid) and electrically induced seizures, post-handling seizures, sudden death following seizures, and abnormal EEG activity. Together, our findings support face validity of a novel AHC mouse model with quantifiable traits including co-morbid epilepsy that will be useful as an in vivo platform for investigating pathophysiology and testing new therapeutic strategies for this rare neurodevelopmental disorder.
Platelet-derived LPA16:0 inhibits adult neurogenesis and stress resilience in anxiety disorder
Authors: Larrieu Thomas , Carron Charline , Grieco Fabio , Weber Crystal , Ginggen Kyllian , Delacrétaz Aurélie , Gallart-Ayala Hector , Tsuda Mumeko , Cameron Heather A. , Eap Chin B. , Ivanisevic Julijana , Magistretti Pierre , Telley Ludovic , Dayer Alexandre , Piguet Camille , Toni Nicolas
Published: August 2024

Anxiety disorders are accompanied by changes in brain plasticity, stress vulnerability and heightened risk of depression. Here, we found that serum LPA16:0 abundance increased with trait anxiety in both human and mice and was sufficient to reduce the proliferation of adult hippocampal neural stem/progenitor cells. In humans, the main LPA receptor, LPA1, bears single nucleotide polymorphism variants associated with anxiety. In mice, LPA16:0 decreased hippocampal neurogenesis and stress resilience, whereas LPA1antagonism or the reduction of platelets, the main source of circulating LPA16:0, increased adult neurogenesis and resilience to acute stress. Finally, the inhibition of adult neurogenesis abolished the beneficial effect of LPA1antagonism on resilience against both acute and chronic stress.

Together, these findings identify LPA16:0-LPA1signaling as a regulation mechanism of adult neurogenesis and a potential therapeutic target for mood disorders.
Experimental and Computational Insights into the Structural Dynamics of the Fc Fragment of IgG1 Subtype from Biosimilar VEGF-Trap
Authors: Destan Ebru , Turkut Engin , Aldeniz Alper , Kang Jungmin , Tosha Takehiko , Yabashi Makina , Yilmaz Baris , Timucin Ahmet Can , Matsuura Hiroaki , Kawano Yoshiaki , Cinkaya Irfan , DeMirci Hasan
Published: August 2024

The constant fragment (Fc) of the Immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half-life. A prime example is VEGF-Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)-1 and VEGFR-2. The Fc region's role in N-glycosylation is particularly important, as it significantly influences protein stability. In this study, we present the first near-physiological temperature structures of the N-glycan-bound Fc fragment of IgG1 subtype from a biosimilar VEGF-Trap, determined using the SPring-8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including our own data, reveals alternate conformations within the glycan-binding pocket. Furthermore, molecular dynamics (MD) simulations highlight an unexpected degree of structural plasticity. These findings offer new insights into the molecular basis of Fc-mediated functions and provide valuable information for the design of next-generation therapeutics.
Ligand-Mediated Endocytosis Is Regulated in A Sexually Dimorphic Way in Osteocytesin vivo
Authors: Matthews Melia , Saffari Alexander , Mukul Nuzhat , Hai Lanlan , Naguib Nada , Wiesner Ulirich B. , Lewis Karl J.
Published: August 2024

Endocytosis is a critical cellular process involved in many physiological functions. Most research on endocytosis has been performedin vitro, however, understanding this processin vivois necessary in tissues like bone that have a unique 3D extra-cellular matrix. Here, we present a live-cell study of endocytosis in osteocytes, mechanosensory cells embedded in mouse bone. We visualized real-time fluorescent nanoparticle uptake and trafficking in osteocytes by using intravital imaging combined with multiphoton microscopy within living animals. We applied pharmacologic inhibitors to distinguish between general and receptor-specific endocytosis pathwaysin vivo. Our findings reveal rapid nanoparticle uptake in osteocytes, with marked differences in the timescale and pattern of uptake depending on nanoparticle surface functionality. We also discovered differences in dynamin-dependent endocytosis in osteocytes between male and female animals. These results offer the firstin vivoderived insights into how osteocytes take up materials and provide new evidence for chemically altering receptor-mediated endocytosis in live bone tissue.
Improving the value utilization of tuna peptide powder for the cosmetics field through ozone oxidation
Authors: Zheng Haolong , Gu Shiyang , Huang Shiqi , Zhang Yan , Xu Feng , Lv Daofei , Yuan Wenbing , Zhu Kongyu , Chen Xin
Published: August 2024

To improve the utilization efficiency of small molecule peptides in marine proteins and promote their application in cosmetics, this study adopts ozone oxidation to conduct deodorization research on tuna small molecule peptides. To devise a method for the ozone oxidation and deodorization of tuna peptide powder suitable for the cosmetics field, orthogonal tests were carried out. The time, ozone concentration, and temperature were adjusted to determine the optimal conditions for ozonation and deodorization of tuna peptide powder. The results showed that at 50°C and an ozone concentration of 99.10 × 103 mg/m3, wet ozone oxidation for 40 min can also significantly reduce the fishy smell. Under these conditions, the color of tuna peptide powder treated with wet ozone was lighter. In addition, the main volatile compounds were detected by gas chromatography–mass spectrometry (GC-MS). The content of the main fishy volatile substance, hexanal, decreased by 66.4%, and two octyl aldehydes were observed. The results also showed that the protein activity of tuna peptide powder after ozonation remained unchanged. Thus, this study presents an approach to the ozone oxidation of tuna peptide powder that is suitable for cosmetics.
Dimerization GAS2 mediates microtubule and F-actin crosslinking
Authors: An Jiancheng , Imasaki Tsuyoshi , Narita Akihiro , Niwa Shinsuke , Sasaki Ryohei , Makino Tsukasa , Nitta Ryo , Kikkawa Masahide
Published: August 2024

GAS2 was originally identified as a growth arrest-specific protein, and recent studies have revealed its involvement in multiple cellular processes. Its dual interaction with actin filaments and microtubules highlights its essential role in cytoskeletal organization, such as cell division, apoptosis, and possibly tumorigenesis. However, the structural bases by which GAS2 regulates cytoskeletal dynamics remain unclear. In this study, we present cryo-EM structures of the GAS2- CH3 domain in complex with F-actin at 2.8 Å resolution, representing the first type 3 CH domain structure bound to F-actin, confirming its actin-binding activity. We also provide the first near- atomic resolution cryo-EM structure of the GAS2-GAR domain bound to microtubules and identified conserved microtubule-binding residues. Our biochemical experiments show that GAS2 promotes microtubule nucleation and polymerization and its C-terminal region is essential for dimerization, bundling of both F-actin and microtubules, and microtubule nucleation. Based on these results, we propose how GAS2 controls cytoskeletal organization.
Haploid Asexual Blastocyst Fitness Varies Across Mouse Strains Related to Efficiency of Exit From Totipotency
Authors: Crasta Daphne Norma , Lee Si Won , Fredrickson Jolene , Thejo Theodore , Adiga Satish K. , Zhao Yulian , Kalthur Guruprasad , Kannan Nagarajan
Published: August 2024

In vitroactivation, both sexually and asexually, facilitates assessing the reproductive mode and fitness of mammalian oocytes. Herein, we present evidence of the enhancement of asexual haploid blastocyst fitness in one selectively-inbredMus musculuspopulation. We tracked sexually and asexually activated-oocytes as they exited totipotency and self-organized into blastocyst-stage embryos. We examined haploid and diploid parthenogenetic potential of activated-oocytes. Unexpectedly, ∼90% of selectively-inbred mouse oocytes that were asexually activated successfully generated haploid blastocysts, contrasting with ∼90% failure in randomly-outbred mice. Furthermore, by closely tracking the timeline of exit from totipotency, we propose a novel ‘self-correcting’ ‘totipotency clock’, crucial for timely exit from totipotency and successful embryogenesis across mammals. Insufficiency in this ‘self-correcting’ prerequisite, will alter the fitness landscape in different reproductive modes. Collectively, this work provides a quantitative framework to investigate the unknown disruptive evolutionary trajectories of reproductive modes and fitness of females in anisogamous species.

Highlights

Serendipitious discovery of disruptive evolution of haploid asexual reproductive mode and preimplantation embryogenetic fitness in FVB strain of mice.

Novel self-correcting totipotency clock regulates blastulation potential in mammals including humans and limits haploid asexual embryogenesis

Evolution of haploid asexual reproductive mode and preimplantation embryogenetic fitness in FVB mouse is linked to a superior self-correcting totipotency clock lacking in other animals.

Graphical Summary
Metabolization of microbial postbiotic pentanoate drives anti-cancer CAR T cells
Authors: Staudt Sarah , Nikolka Fabian , Perl Markus , Franz Julia , Leblay Noemie , Yuan Xiaoli-Kat , Larrayoz Marta , Lozano Teresa , Warmuth Linda , Fante Matthias A , Skorpskaite Aiste , Fei Teng , Bromberg Maria , San Martin-Uriz Patxi , Rodriguez-Madoz Juan Roberto , Ziegler-Martin Kai , Adil-Gholam Nazdar , Benz Pascal , Tran Huu Phuc , Stein-Thoeringer Christoph , Schmitt Michael , Kleigrewe Karin , Freitag Fabian , Riester Zeno , Weber Justus , Mangold Kira , Ho Patrick , Einsele Hermann , Prosper Felipe , Ellmeier Wilfried , Busch Dirk , Visekruna Alexander , Slingerland John , Shouval Roni , Hiller Karsten , Lasarte Juan Jose , Martinez-Climent Jose Angel , Pausch Patrick , Neri Paola , van den Brink Marcel , Poeck Hendrik , Hudecek Michael , Luu Maik
Published: August 2024

The microbiome is a complex host factor and key determinant of the outcome of antibody-based and cellular immunotherapy. Its postbiotics are a blend of soluble commensal byproducts that are released into the host environment and have been associated with the regulation of immune homeostasis, particularly through impacts on epigenetics and cell signaling. In this study, we show that the postbiotic pentanoate is metabolized to citrate within the TCA cycle via both the acetyl- and succinyl-CoA entry points, a feature uniquely enabled by the chemical structure of the C5 aliphatic chain. We identified ATP-citrate lyase as the crucial factor that redirects pentanoate-derived citrate from the succinyl-CoA route to the nucleus, thereby linking metabolic output and histone acetylation. This epigenetic-metabolic crosstalk mitigated T cell exhaustion and promoted naive-like differentiation in pentanoate-programmed chimeric antigen receptor (CAR) T cells. The predictive and therapeutic potential of pentanoate was corroborated in two independent patient cohorts and three syngeneic models of CAR T adoptive therapy. Our data demonstrate that postbiotics are integrated into mitochondrial metabolism and subsequently incorporated as epigenetic imprints. This bridge between microbial and mammalian interspecies communication can ultimately impact T cell differentiation and efficacy.
The stretch-shortening cycle effect is not associated with cortical or spinal excitability modulations
Authors: Rissmann Lea-Fedia , Raiteri Brent James , Seiberl Wolfgang , Siebert Tobias , Hahn Daniel
Published: August 2024

It is unclear whether cortical and spinal excitability modulations contribute to enhanced SSC performance. Therefore, this study investigated cortical and spinal excitability modulations during and following shortening of stretch-shortening cycle (SSC) contractions compared with pure shortening (SHO) contractions. Participants (N = 18) performed submaximal voluntary plantar flexion contractions while prone on the dynamometer bench. The right foot was strapped onto the dynamometer’s footplate attachment and the resultant ankle joint torque and crank arm angle were recorded. Cortical and spinal excitability modulations of the soleus muscle were analyzed by eliciting compound muscle actional potentials via electrical nerve stimulation, cervicomedullary motor-evoked potentials (CMEPs) via electrical stimulation of the spinal cord, and motor-evoked potentials (MEPs) via magnetic stimulation of the motor cortex. Mean torque following stretch was significantly increased by 7±3% (p=0.029) compared with the fixed-end reference (REF) contraction and mean torque during shortening of SSC compared with SHO was significantly increased by 12±24% (p=0.046). Mean steady-state torque was significantly lower by 13±3% (p=0.006) and 9±12% (p=0.011) following SSC compared with REF and SHO, respectively. Mean steady-state torque was not significantly lower following SHO compared with REF (7±8%, p=0.456). CMEPs and MEPs were also not significantly different during shortening of SSC compared with SHO (p≥0.885) or during the steady state of SSC, SHO, and REF (p≥0.727). Therefore, our results indicate that SSC performance was not associated with cortical or spinal excitability modulations during or after shortening, but rather driven by mechanical mechanisms triggered during active stretch.

Key points

A stretch-shortening cycle (SSC) effect of 12% was observed during EMG-matched submaximal voluntary contractions of the human plantar flexors

The SSC effect was neither associated with cortical or spinal excitability modulations nor with stretch-reflex activity

The SSC effect was likely driven by mechanical mechanisms related to active muscle stretch, which have long-lasting effects during shortening

Residual force depression following SSC was not attenuated by the long-lasting mechanical mechanisms triggered during active muscle stretch

Steady-state torques were lower following shortening of SSCs versus pure shortening and fixed-end contractions at the same final ankle joint angle, but the torque differences were not correlated with cortical or spinal excitability modulations
Neural Mechanisms of Feedback Processing and Regulation Recalibration during Neurofeedback Training
Authors: Pamplona Gustavo S. P. , Zweerings Jana , Lor Cindy S. , deErney Lindsay , Roecher Erik , Taebi Arezoo , Hellrung Lydia , Amano Kaoru , Scheinost Dustin , Krause Florian , Rosenberg Monica D. , Ionta Silvio , Brem Silvia , Hermans Erno J. , Mathiak Klaus , Scharnowski Frank
Published: August 2024

The acquisition of new skills is facilitated by providing individuals with feedback that reflects their performance. This process creates a closed loop that involves feedback processing and regulation recalibration to promote effective training. Functional magnetic resonance imaging (fMRI)-based neurofeedback is unique in applying this principle by delivering direct feedback on the self-regulation of brain activity. Understanding how feedback-driven learning occurs requires examining how feedback is evaluated and how regulation adjusts in response to feedback signals. In this pre-registered mega-analysis, we re-analyzed data from eight intermittent fMRI neurofeedback studies (N = 153 individuals) to investigate brain regions where activity and connectivity are linked to feedback processing and regulation recalibration (i.e., regulation after feedback) during training. We harmonized feedback scores presented during training in these studies and computed their linear associations with brain activity and connectivity using parametric general linear model analyses. We observed that, during feedback processing, feedback scores were positively associated with (1) activity in the reward system, dorsal attention network, default mode network, and cerebellum; and with (2) reward system-related connectivity within the salience network. During regulation recalibration, no significant associations were observed between feedback scores and either activity or associative learning-related connectivity. Our results suggest that neurofeedback is processed in the reward system, supporting the theory that reinforcement learning shapes this form of brain training. In addition, the involvement of large-scale networks in feedback processing, continuously transitioning between evaluating external feedback and internally assessing the adopted cognitive state, suggests that higher-level processing is integral to this type of learning. Our findings highlight the pivotal role of performance-related feedback as a driving force in learning, potentially extending beyond neurofeedback training to other feedback-based processes.

Key Points

We conducted a pre-registered mega-analysis integrating data from eight fMRI neurofeedback studies to examine feedback processing and regulation recalibration during neurofeedback training.

During feedback processing, feedback was associated with activity in the reward system, dorsal attention network, default mode network, and cerebellum; as well as with reward system-related connectivity within the salience network.

We found no positive results during regulation blocks; however, additional analyses suggest that recalibration may have already occurred during feedback presentation.
One-Pot Dual Protein Labelling for Simultaneous Mechanical and Fluorescent Readouts in Optical Tweezers
Authors: Silbermann Laura-Marie , Fottner Maximilian , Migdad Nora , Lang Kathrin , Tych Katarzyna (Kasia)
Published: August 2024

Optical tweezers are widely used in the study of biological macromolecules but are limited by their one-directional probing capability, potentially missing critical conformational changes. Combining fluorescence microscopy with optical tweezers, employing Förster resonance energy transfer (FRET) pairs, addresses this issue. Moreover, attaching one FRET probe to a tethered protein and the other to a protein in solution allows precise localisation of interaction sites, while probing mechanical properties. When integrating fluorescence microscopy with optical tweezers, orthogonal protein conjugation methods are needed to enable simultaneous, site-specific attachment of fluorophores and DNA handles, commonly used to apply force to molecules of interest. In this study, we utilized commercially available reagents for dual site-specific labelling of the homodimeric heat shock protein 90 (Hsp90) using thiol-maleimide and inverse electron demand Diels–Alder cycloaddition (IEDDAC) bioorthogonal reactions. In a one-pot approach, Hsp90 modified with a cysteine mutation and the non-canonical amino acid cyclopropene-L-lysine (CpK) was labelled with the FRET pair maleimide-Atto550 and maleimide-Atto647N, alongside single- stranded methyltetrazine-modified DNA oligonucleotide. Optical tweezers experiments with this labelled Hsp90 construct revealed structural transitions consistent with previous studies, validating the approach. Fluorescence measurements confirmed the proximity of FRET pairs in the N-terminally closed state of Hsp90 in this experimental setup. This integrative method provides a powerful tool for probing protein conformational dynamics and protein interactions beyond the limitations of traditional optical tweezers.

Statement

The developed method combines fluorescence microscopy with optical tweezers, enhancing single-molecule protein studies by overcoming the limitations of one- directional mechanical probing. Utilizing two orthogonal protein conjugation methods for one-pot dual labelling, the heat shock protein 90 was labelled with a FRET pair and single-stranded DNA oligonucleotides. Validated by comparison with published conformational changes, mechanical unfolding signatures, and FRET pair distances, this approach provides a powerful tool to explore single-molecule conformational dynamics and protein interactions.
Demonstration of a tunable interface between Rydberg atoms and superconducting microwave circuits with differential polarizability nulling
Authors: Brown L. L. , Grondin J. A. L. , Hogan S. D.
Published: August 2024

Microwave-dressed Rydberg atoms in pairs of states that are optically accessible and engineered so that the frequency of the transition between them is tunable while exhibiting a low sensitivity to stray electric fields have been interfaced with a superconducting coplanar waveguide (CPW) microwave resonator. This was achieved with helium atoms in triplet Rydberg states with principal quantum numbers n=55 and 56. The atoms were dressed with two strong microwave fields—a control field and a differential polarizability nulling field. The control field allowed the atoms to be coupled to the resonator using the two-color two-photon transition between the equal parity 1s55sS13≡|55s〉 and 1s56sS13≡|56s〉 Rydberg states, with one photon supplied by it and the other provided by the resonator. The nulling field was detuned from the field-free 1s55sS13→1s55pPJ3≡|55p〉 transition to admix |55p〉 character into the |55s〉 state and eliminate the differential static electric dipole polarizability of the |55s〉 and |56s〉 states. The experiments were performed with atoms located ∼300µm above a

λ

/

4

niobium nitride superconducting CPW resonator operated at temperatures between 3.59 and 3.73K. The measured ac and dc Stark shifts of the Rydberg states at this atom-circuit interface in the presence of the dressing fields are in good quantitative agreement with the results of Floquet calculations. The differential polarizability nulling fields used in the experiments allowed the difference in the Stark shifts of the |55s〉 and |56s〉 states over the range of dc fields offset from the residual stray field by ±65 mV/cm to be reduced from 2π×2.1 MHz to 2π×125 kHz.

Published by the American Physical Society
2024
Heavy-flavor hadron production in relativistic heavy ion collisions at energies available at BNL RHIC and at the CERN LHC in the EPOS4HQ framework
Authors: Zhao Jiaxing , Aichelin Joerg , Gossiaux Pol Bernard , Ozvenchuk Vitalii , Werner Klaus
Published: August 2024

Employing the recently developed EPOS4HQ event generator, we study the production of different heavy-flavor mesons in relativistic heavy-ion collisions at BNL Relativistic Heavy Ion Collider and CERN Large Hadron Collider energies. The transverse momentum spectra, yield ratio, nuclear modification factor, and elliptic flow can be well described in the EPOS4HQ framework. We furthermore analyze the processes which modify these observables as compared to pp collisions and are at the origin of the experimentally determined nuclear modification factor RAA.

Published by the American Physical Society
2024
Doubly-charged
Tcc++
states in the dynamical diquark model
Authors: Mutuk Halil
Published: August 2024

One of the celebrated tools in explaining the hydrogen atom is Born-Oppenheimer approximation. The resemblance of QQq¯q¯ tetraquarks to hydrogen atom within quantum chromodynamics implies usage of Born-Oppenheimer approximation for these multiquark states. In this work, we use dynamical diquark model to calculate mass spectra and sizes of doubly charmed and charged tetraquark states denoted as Tcc++. Our results for mass spectra indicate some bound-state candidates with respect to corresponding two-meson thresholds. Calculation of expectation values of ⟨r2⟩ reflects that doubly charmed and charged tetraquark states are compact.

Published by the American Physical Society
2024
Cosmological dynamics of string theory axion strings
Authors: Benabou Joshua N. , Bonnefoy Quentin , Buschmann Malte , Kumar Soubhik , Safdi Benjamin R.
Published: August 2024

The quantum chromodynamics (QCD) axion may solve the strong CP problem and explain the dark matter (DM) abundance of our Universe. The axion was originally proposed to arise as the pseudo-Nambu-Goldstone boson of global U(1)PQ Peccei-Quinn (PQ) symmetry breaking, but axions also arise generically in string theory as zero modes of higher-dimensional gauge fields. In this work we show that string theory axions behave fundamentally differently from field theory axions in the early Universe. Field theory axions may form axion strings if the PQ phase transition takes place after inflation. In contrast, we show that string theory axions do not generically form axion strings. In special inflationary paradigms, such as D-brane inflation, string theory axion strings may form; however, their tension is parametrically larger than that of field theory axion strings. We then show that such QCD axion strings overproduce the DM abundance for all allowed QCD axion masses and are thus ruled out, except in scenarios with large warping. A loop-hole to this conclusion arises in the axiverse, where an axion string could be composed of multiple different axion mass eigenstates; a heavier eigenstate could collapse the network earlier, allowing for the QCD axion to produce the correct DM abundance and also generating observable gravitational wave signals.

Published by the American Physical Society
2024
Cascade
Ξ0
baryon spectroscopy in the relativistic framework of an independent quark model
Authors: Patel Rameshri V. , Shah Manan N.
Published: August 2024

The spectroscopy of Ξ0 is performed within the relativistic framework of independent quark model. The equal mixture of scalar and vector components in the potential having Martin-like form is considered for the confinement. With the suitable potential parameters for Ξ0, mass spectra for high radial and orbital excitation is calculated. The experimentally observed values of the ground-state magnetic moment, branching ratios, and asymmetry parameters for radiative weak decays, Ξ0→Λ0+γ0 and Ξ0→Σ0+γ0 are obtained to validate the model. The spin parity of experimentally known resonances like Ξ(1530), Ξ(1820), and Ξ(2030) are confirmed through the Regge trajectories in (J,M2) plane. The spin parity of Ξ(1950), Ξ(2130), and Ξ(2250) are predicted using those Regge trajectories. The radiative decay width and magnetic moment of first resonance is also predicted.

Published by the American Physical Society
2024
Post-conflict marketing: the role of former conflict stakeholder on post-conflict product/service valuation across countries
Authors: Rodriguez Brayan , Reinoso-Carvalho Felipe , Motoki Kosuke , Velasco Carlos
Published: August 2024

Purpose

This research examined the role of post-conflict marketing in supporting businesses within conflict-affected regions, aligning with the objectives of UN Sustainable Development Goal 16 to foster peaceful societies amid increasing global conflicts.

Design/methodology/approach

Drawing from the theories of social egalitarianism and consumer discrimination, the study explored the moderating influence of conflict stakeholder on consumer willingness to pay (WTP). Understanding such stakeholder roles underscores post-conflict marketing's potential for economic growth and stability. Two experiments assessed the WTP, WTP a premium price and expected attractiveness of strategic products and services developed by key stakeholders (ex-guerrilla, ex-paramilitaries, ex-militaries, victims and other citizens) in the Colombian post-conflict context among both local (Colombian) and foreign (Japanese) consumers.

Findings

Results revealed that products associated with victims consistently received higher ratings. A notable contrast emerged as Japanese consumers favoured products of victims over those of regular citizens while rating offerings from ex-paramilitary and retired military stakeholders similarly, unlike their Colombian counterparts.

Research limitations/implications

The study acknowledges limitations regarding participants' geographic location and experimental design, providing insights for future research and potential refinements.

Practical implications

The findings offer insights into the impact of consumer attitudes on post-conflict stakeholder entrepreneurship in foreign and local markets, thus contributing relevant knowledge to support market success.

Originality/value

This is the first study assessing the role of various post-conflict stakeholders in influencing consumer evaluations of products and services. Consequently, these findings contribute to the foundational understanding of post-conflict marketing and offer a benchmark for business development in conflict-affected areas.
Research on the correlation between the degree of digitization of manufacturing process links and economic benefits
Authors: Wang Heyong , Gu Long , Hong Ming
Published: August 2024

Purpose

This paper aims to provide a reference for the development of digital transformation from the perspective of manufacturing process links.

Design/methodology/approach

This paper applies canonical correlation analysis based on digital technology patents in the key links of manufacturing industries (product design, procurement, product manufacturing, warehousing and transportation, and wholesale and retail) and the related indicators of economic benefits of regions in China.

Findings

(1) The degree of digitalization of manufacturing process links is significantly correlated with economic benefits. (2) The improvement of the degree of digitalization in the “product design” link, the “warehousing and transportation” link, the “product manufacturing” link and the “wholesale and retail” link has significant impacts on the economic benefits of manufacturing industry. (3) The digital degree of the “procurement” link has no obvious influence on the economic benefits of manufacturing industry.

Practical implications

The research results can provide reference for the formulation and implementation of micro policies. The strategy of improving the level of digital transformation of key links of manufacturing industry is put forward to better promote both the digital transformation of manufacturing industry and economic development.

Originality/value

This paper innovatively studies the relationship between digitalization of manufacturing process links and economic benefits. The findings can provide theoretical and empirical support for the digital transformation of China's manufacturing industry and high-quality development of economy.
The roles of entrepreneurial orientation and government support in the open innovation of manufacturing firms: empirical evidence from South Korea
Authors: Yoon Jungwon , Oh Soo Jung
Published: August 2024

Purpose

This study investigates the effect of entrepreneurial orientation and government support on the innovation openness of South Korean manufacturing firms. By compartmentalizing entrepreneurial orientation and government support, this study seeks to elucidate their effects on the breadth and depth of firms' knowledge searches.

Design/methodology/approach

The study utilizes Poisson regression analysis with empirical data from 2,353 South Korean manufacturing firms collected from Korean Innovation Survey data.

Findings

Analysis reveals nuanced influences of various factors on firms' open innovation activities. Innovativeness positively affects knowledge search breadth and depth, highlighting the role of innovation-oriented processes, while competitive aggressiveness influences depth, thereby underscoring the pursuit of specialized knowledge acquisition. Proactiveness positively affects breadth but negatively affects depth, suggesting the importance of maintaining broad perspectives. Government support scope positively affects both breadth and depth, reflecting the significance of external support in encouraging inclusive knowledge exploration. The importance of government support positively influences depth, emphasizing its vital role in establishing collaborative relationships to enhance in-depth knowledge acquisition.

Originality/value

This study provides novel insights by exploring the nuanced implementation of open innovation in latecomer economies, especially South Korea, which experienced rapid economic development by leveraging innovation. The identification of specific factors influencing knowledge search breadth and depth contributes to the literature on open innovation by providing strategic guidelines for firms and policymakers. This practical implications of this study suggest that firms should align their strategies with entrepreneurial orientation while leveraging pertinent government support.