bluuebunny/crossref_metadata_2025_split huggingface dataset:
ThirdPeak: A flexible tool designed for the robust analysis of two- and three-dimensional (single-molecule) tracking data
Authors: Müller Thomas , Meiser Elisabeth , Engstler Markus 
Published: January 2024

AbstractThirdPeak is an open-source tool tailored for the comprehensive analysis of two– and three-dimensional track data across various scales. Its versatile import options facilitate seamless integration into established workflows, and the user interface allows for swift visualization and analysis of the data. When applied to live-cell diffusion data, this software unveils the advantages of combining both 2D and 3D analysis, providing valuable insights into the understanding of biological processes.
Neurometabolic predictors of mental effort in the frontal cortex
Authors: Barakat Arthur , Clairis Nicolas , Brochard Jules , Pessiglione Mathias , Godin Jean-Philippe , Cuenoud Bernard , Xin Lijing , Sandi Carmen 
Published: January 2024

AbstractMotivation drives individuals to overcome costs to achieve desired outcomes, such as rewards or avoidance of punishment, with significant variability across individuals. The dorsomedial prefrontal cortex/dorsal anterior cingulate cortex (dmPFC/dACC) and anterior insula are key brain regions implicated in effort-based decision-making. Here, we utilized proton magnetic resonance spectroscopy (1H-MRS) at 7 Tesla on 69 healthy participants in these brain regions to uncover the neurometabolic factors that influence these differences. We designed and applied an effort-based decision-making task requiring mental and physical effort to probe motivated behavior, complemented by computational modeling to extract key behavioral parameters. Gradient boosting machine learning was applied to explore the predictive role of specific metabolites in motivated behavior. Our results reveal that a model established on dmPFC/dACC metabolites explains decisions to exert high mental effort and sensitivity to mental effort. In particular, glutamate, aspartate, and lactate in dmPFC/dACC, three metabolites linked through the tricarboxylic acid cycle and glycolysis, were identified as key discriminative metabolites in the dmPFC/dACC, predictive of mental effort choices, underpinning energy supply and cognitive processes. Anterior insula metabolites did not significantly relate to effort-related decisions. Notably, glutamine and lactate levels between the periphery (plasma) and the dmPFC/dACC were correlated, suggesting a metabolic link between peripheral and central biomarkers of effort. Our findings provide novel insights into the neurometabolic underpinnings of motivated behavior and propose novel biomarkers for mental effort-based decision-making. Importantly, our study highlights the relevance of multivariate approaches in elucidating complex cognitive functions.
Single-domain antibodies reveal unique borreliacidal epitopes on the Lyme disease vaccine antigen, Outer surface protein A (OspA)
Authors: Vance David J , Basir Saiful , Piazza Carol Lyn , Willsey Graham , Haque H M Emranul , Tremblay Jacque M , Rudolph Michael J , Muriuki Beatrice , Cavacini Lisa A , Weis David D , Shoemaker Charles B , Mantis Nicholas J 
Published: January 2024

ABSTRACTCamelid-derived, single-domain antibodies (VHHs) have proven to be extremely powerful tools in defining the antigenic landscape of immunologically heterogeneous surface proteins. In this report, we generated a phage-displayed VHH library directed against the candidate Lyme disease vaccine antigen, Outer surface protein A (OspA). Two alpacas were immunized with recombinant OspA serotype 1 (ST1) fromBorrelia burgdorferisensu stricto strain B31, in combination with the canine vaccine RECOMBITEK®Lyme containing lipidated OspA. The phage library was subjected to two rounds of affinity enrichment (“panning”) against recombinant OspA, yielding 21 unique VHHs within two epitope bins, as determined through competition ELISAs with a panel of OspA-specific human monoclonal antibodies. Epitope refinement was conducted by hydrogen exchange-mass spectrometry (HX-MS). Six of the monovalent VHHs were expressed as human IgG1-Fc fusion proteins and shown to have functional properties associated with protective human monoclonal antibodies, includingB. burgdorferiagglutination, outer membrane damage, and complement-dependent borreliacidal activity. The VHHs displayed unique reactivity profiles with the seven OspA serotypes associated withB. burgdorferigenospecies in the United States and Europe consistent with there being conserved epitopes across OspA serotypes that should be considered when designing and evaluating multivalent Lyme disease vaccines.
Dynamic Nature ofStaphylococcus aureusType I Signal Peptidases
Authors: Madsen Jesper J. , Yu Wenqi 
Published: January 2024

SUMMARYMolecular dynamics simulations are used to interrogate the dynamic nature ofStaphylococcus aureusType I signal peptidases, SpsA and SpsB, including the impact of the P29S mutation of SpsB. Fluctuations and plasticity-rigidity characteristics vary among the proteins, particularly in the extracellular domain. Intriguingly, the P29S mutation, which influences susceptibility to arylomycin antibiotics, affect the mechanically coupled motions in SpsB. The integrity of the active site is crucial for catalytic competency, and variations in sampled structural conformations among the proteins are consistent with diverse peptidase capabilities. We also explored the intricate interactions between the proteins and the modelS. aureusmembrane. It was observed that certain membrane-inserted residues in the loop around residue 50 (50s) and C-terminal loops, beyond the transmembrane domain, give rise to direct interactions with lipids in the bilayer membrane. Our findings are discussed in the context of functional knowledge about these signal peptidases, offering additional understanding of dynamic aspects relevant to some cellular processes with potential implications for drug targeting strategies.HighlightsDynamics ofS. aureusSpsA and SpsB (wild-type and P29S) is analyzed.Differences in flexibility and plasticity are relevant for function.P29S mutation decouples mechanical motions in SpsB.Extracellular domain loops insert differently into the membrane in SpsA and SpsB.S. aureusmodel membrane properties are elucidated.
A marine sponge-associated mycobacterium closely related toMycobacterium tuberculosis
Authors: Pidot Sacha J. , Klatt Stephan , Ates Louis S. , Frigui Wafa , Sayes Fadel , Majlessi Laleh , Izumi Hiroshi , Monk Ian R. , Porter Jessica L. , Bennett-Wood Vicki , Seemann Torsten , Otter Ashley , Taiaroa George , Cook Gregory M. , West Nicholas , Tobias Nicholas J. , Fuerst John A. , Stutz Michael D. , Pellegrini Marc , McConville Malcolm , Brosch Roland , Stinear Timothy P. 
Published: January 2024

AbstractReconstructing the evolutionary origins ofMycobacterium tuberculosis, the causative agent of human tuberculosis, has helped identify bacterial factors that have led to the tubercle bacillus becoming such a formidable human pathogen. Here we report the discovery and detailed characterization of an exceedingly slow growing mycobacterium that is closely related toM. tuberculosisfor which we have proposed the species nameMycobacterium spongiaesp. nov., (strain ID: FSD4b-SM). The bacterium was isolated from a marine sponge, taken from the waters of the Great Barrier Reef in Queensland, Australia. Comparative genomics revealed that, after the opportunistic human pathogenMycobacterium decipiens,M. spongiaeis the most closely related species to theM. tuberculosiscomplex reported to date, with 80% shared average nucleotide identity and extensive conservation of keyM. tuberculosisvirulence factors, including intact ESX secretion systems and associated effectors. Proteomic and lipidomic analyses showed that these conserved systems are functional in FSD4b-SM, but that it also produces cell wall lipids not previously reported in mycobacteria. We investigated the virulence potential of FSD4b-SM in mice and found that, while the bacteria persist in lungs for 56 days after intranasal infection, no overt pathology was detected. The similarities withM. tuberculosis, together with its lack of virulence, motivated us to investigate the potential of FSD4b-SM as a vaccine strain and as a genetic donor of the ESX-1 genetic locus to improve BCG immunogenicity. However, neither of these approaches resulted in superior protection againstM. tuberculosischallenge compared to BCG vaccination alone. The discovery ofM. spongiaeadds to our understanding of the emergence of theM. tuberculosiscomplex and it will be another useful resource to refine our understanding of the factors that shaped the evolution and pathogenesis ofM. tuberculosis.
Phylogenomics reveals coincident divergence between giant host sea anemones and the clownfish adaptive radiation
Authors: De Jode Aurelien , Quattrini Andrea M. , Chiodo Tommaso , Daly Marymegan , McFadden Catherine S. , Berumen Michael L. , Meyer Christopher P. , Mills Suzanne , Beldade Ricardo , Bartholomew Aaron , Scott Anna , Reimer James D , Yanagi Kensuke , Fuji Takuma , Rodríguez Estefanía , Titus Benjamin M. 
Published: January 2024

AbstractThe mutualism between clownfishes (or anemonefishes) and their giant host sea anemones are among the most immediately recognizable animal interactions on the planet and have attracted a great deal of popular and scientific attention [1-5]. However, our evolutionary understanding of this iconic symbiosis comes almost entirely from studies on clownfishes— a charismatic group of 28 described species in the genusAmphiprion[2]. Adaptation to venomous sea anemones (Anthozoa: Actiniaria) provided clownfishes with novel habitat space, ultimately triggering the adaptive radiation of the group [2]. Clownfishes diverged from their free-living ancestors 25-30 MYA with their adaptive radiation to sea anemones dating to 13.2 MYA [2, 3]. Far from being mere habitat space, the host sea anemones also receive substantial benefits from hosting clownfishes, making the mutualistic and co-dependent nature of the symbiosis well established [4, 5]. Yet the evolutionary consequences of mutualism with clownfishes have remained a mystery from the host perspective. Here we use bait-capture sequencing to fully resolve the evolutionary relationships among the 10 nominal species of clownfish-hosting sea anemones for the first time (Figure 1). Using time-calibrated divergence dating analyses we calculate divergence times of less than 25 MYA for each host species, with 9 of 10 host species having divergence times within the last 13 MYA (Figure 1). The clownfish-hosting sea anemones thus diversified coincidently with clownfishes, potentially facilitating the clownfish adaptive radiation, and providing the first strong evidence for co-evolutionary patterns in this iconic partnership.
PP2B-dependent cerebellar plasticity sets the amplitude of an innate reflex during juvenile development
Authors: Wu Bin , Post Laura , Lin Zhanmin , Schonewille Martijn 
Published: January 2024

AbstractThroughout life, the cerebellum plays a central role in the coordination and optimization of movements, using cellular plasticity to adapt a range of behaviors. If these plasticity processes establish a fixed setpoint during development, or continuously adjust behaviors throughout life, is currently unclear. Here, by spatiotemporally manipulating the activity of protein phosphatase 2B (PP2B), an enzyme critical for cerebellar plasticity, we examined the consequences of disrupted plasticity on the performance and adaptation of the vestibulo-ocular reflex (VOR). We find that, in contrast to Purkinje cell specific deletion starting early postnatally, acute pharmacological as well as adult-onset genetic deletion of PP2B affects all forms of VOR adaptation, but not the level of VOR itself. Next, we show that Purkinje cell-specific genetic deletion of PP2B in juvenile mice leads to a progressive loss of the protein PP2B and a concurrent change in the VOR, in addition to the loss of adaptive abilities. Finally, re-expressing PP2B in adult mice that lack PP2B expression from early in development, rescues VOR adaptation, but does not affect the performance of the reflex. Together, our results indicate that chronic or acute, genetic or pharmacological block of PP2B disrupts the adaptation of the VOR. In contrast, only the absence of plasticity during cerebellar development affects the setpoint of VOR, an effect that cannot be corrected after maturation of the cerebellum. These findings suggest that cerebellar plasticity influences behavior in two ways, through direct control of behavioral adaptation and via long-term effects initiated in the juvenile period.Significance StatementEarly damage to motor adaptation structures, such as the cerebellum, has been linked to neurodevelopmental disorders persisting into adulthood. Understanding these long-term effects requires disentangling the persistent, long-term effects of disrupted development from the acute, ongoing effects directly caused by the continuous presence of the disruption. Here, we demonstrate that disruptions during early development affect both basal level and adaptation, whereas late, adult-onset disruption of cerebellar plasticity only affects the ability to adapt, not the setpoint of an innate reflex. Our findings that specifically the absence of plasticity during cerebellar development affects the setpoint of VOR, which cannot be corrected by re-instating plasticity after maturation of the cerebellum, supports the concept of a sensitive developmental period for setting innate reflexes.
A potential role of inefficient and non-specific piRNA production from the whole transcriptome
Authors: Shoji Keisuke , Tomari Yukihide 
Published: January 2024

AbstractPIWI-interacting RNAs (piRNAs) are small RNAs that play a critical role in repressing transposons in the germline by guiding PIWI proteins to complementary target sequences. It is well known that the 5’ ends of piRNAs are typically defined through cleavage by PIWI proteins or by the endonuclease Zucchini, and piRNAs are amplified via reciprocal cleavage of sense and antisense transcripts by PIWI proteins. Here, we show that low levels of sense-stranded piRNAs are produced from the whole transcriptome in silkworms, flies, and mice, in a manner independent from the known biogenesis pathways. Notably, this mechanism is utilized in silkworm cultured cells for the production of piRNAs derived from the extremely abundant sub-genomic RNAs ofBombyx morilatent virus, which have been suggested to play a role in suppressing viral replication. We propose that this inefficient and non-specific piRNA-production pathway acts as a primitive sensor for aberrantly abundant transcripts in the germline, potentially seeding piRNA sequence repertoire for more efficient and established biogenesis pathways.
A Deep Learning Pipeline for Mapping in situ Network-level Neurovascular Coupling in Multi-photon Fluorescence Microscopy
Authors: Rozak Matthew , Mester James , Attarpour Ahmadreza , Dorr Adrienne , Patel Shruti , Koletar Margaret , Hill Mary , McLaurin JoAnne , Goubran Maged , Stefanovic Bojana 
Published: January 2024

1AbstractFunctional hyperaemia is a well-established hallmark of healthy brain function, whereby local brain blood flow adjusts in response to a change in the activity of the surrounding neurons. Although functional hyperemia has been extensively studied at the level of both tissue and individual vessels, vascular network-level coordination remains largely unknown. To bridge this gap, we developed a deep learning-based computational pipeline that uses two-photon fluorescence microscopy images of cerebral microcirculation to enable automated reconstruction and quantification of the geometric changes across the microvascular network, comprising hundreds of interconnected blood vessels, pre and post-activation of the neighbouring neurons. The pipeline’s utility was demonstrated in the Thy1-ChR2 optogenetic mouse model, where we observed network-wide vessel radius changes to depend on the photostimulation intensity, with both dilations and constrictions occurring across the cortical depth, at an average of 16.1±14.3 μm (mean±stddev) away from the most proximal neuron for dilations; and at 21.9±14.6 μm away for constrictions. We observed a significant heterogeneity of the vascular radius changes within vessels, with radius adjustment varying by an average of 24 ± 28% of the resting diameter, likely reflecting the heterogeneity of the distribution of contractile cells on the vessel walls. A graph theory-based network analysis revealed that the assortativity of adjacent blood vessel responses rose by 152 ± 65% at 4.3 mW/mm2of blue photostimulationvs. the control, with a 4% median increase in the efficiency of the capillary networks during this level of blue photostimulation in relation to the baseline. Interrogating individual vessels is thus not sufficient to predict how the blood flow is modulated in the network. Our computational pipeline, to be made openly available, enables tracking of the microvascular network geometry over time, relating caliber adjustments to vessel wall-associated cells’ state, and mapping network-level flow distribution impairments in experimental models of disease.
Review on impact, crushing response and applications of re-entrant core sandwich structures
Authors: Al-Khazraji Mustafa S. 
Published: January 2024

Purpose
Auxetic sandwich structures are gaining attention because of the negative Poisson’s ratio effect offered by these structures. Re-entrant core was one configuration of the auxetic structures. There is a growing concern about the design and behavior of re-entrant cores in aerospace, marine and protection applications. Several researchers proposed various designs of re-entrant core sandwiches with various materials. The purpose of this study is to review the most recent advances in re-entrant core sandwich structures. This review serves as a guide for researchers conducting further research in this wide field of study.

Design/methodology/approach
The re-entrant core sandwich structures were reviewed in terms of their design improvements, impact and quasi-static crushing responses. Several design improvements were reviewed including 2D cell, 3D cell, gradient, hierarchical and hybrid configurations. Some common applications of the re-entrant core sandwiches were given at the end of this paper with suggestions for future developments in this field.

Findings
Generally, the re-entrant configuration showed improved energy absorption and impact response among auxetic structures. The main manufacturing method for re-entrant core manufacturing was additive manufacturing. The negative Poisson’s ratio effect of the re-entrant core provided a wide area of research.

Originality/value
Generally, re-entrant cores were mentioned in the review articles as part of other auxetic structures. However, in this review, the focus was solely made on the re-entrant core sandwiches with their mechanics.
Sustainable tourism development activities and planning systems in Vhembe district, Limpopo province, South Africa: A comprehensive eco-touristic and sustainability perspective
Authors: Ramaano Azwindini Isaac 
Published: January 2024

PurposeThis study aims to examine Musina municipality’s tourism development status and plans with existing documents and respondents’ responses on their envisaged implications on tourism development and sustainability initiatives in Vhembe District, Limpopo Province, South Africa.Design/methodology/approachSurveys, interviews and focus group discussions, supplemented by field observation and document reviews, gray literature alongside published literature, were applied. Subsequently, Microsoft Excel and cross-tabulation analysis orchestrated the analysis of the data.FindingsThe policy and strategy aspects contributing to the previous and actual tourism statuses in Musina municipality are defined. The study concludes that Musina Municipality has rich tourism possibilities but lacks a better tourism strategy to empower local communities. Nonetheless, it dwells in the most tourism-based landscape within the Vhembe District of Limpopo.Originality/valueMusina Municipality is one of the driest areas in the north of Limpopo Province in South Africa. It is also marked by impoverished rural communities. Studies on sustainable tourism and development have increased in recent years. However, rare studies specialize in synergies within various forms of tourism. Also, significant resources to advance local communities in rural areas are not sufficiently appreciated.
Effect of nano-AlN, Al2O3 on friction and wear properties of copper-steel clad plate immersed in the lubricants
Authors: Lin Xiaoxuan , Sang Xiong , Zhu Yuyan , Zhang Yichen 
Published: January 2024

Purpose
This paper aims to investigate the preparation of AlN and Al2O3, as well as the effect of nano-AlN and nano-Al2O3, on friction and wear properties of copper-steel clad plate immersed in the lubricants.

Design/methodology/approach
Nano-AlN or nano-Al2O3 (0.1, 0.2, 0.3, 0.4 and 0.5 Wt.%) functional fluids were prepared. Their tribological properties were tested by an MRS-10A four-ball friction tester and a ball-on-plate configuration, and scanning electron microscope observed the worn surface of the plate.

Findings
An increase in nano-AlN and Al2O3 content enhances the extreme pressure and anti-wear performance of the lubricant. The best performance is achieved at 0.5 Wt.% of nano-AlN and 0.3 Wt.% of nano-Al2O3 with PB of 834 N and 883 N, a coefficient of friction (COF) of approximately 0.07 and 0.06, respectively. Furthermore, the inclusion of nano-AlN and nano-Al2O3 particles in the lubricant enhances its extreme pressure performance and reduces wear, leading to decreased wear spot depth. The lubricating effect of the nano-Al2O3 lubricant on the surface of the copper-steel composite plate is slightly superior to that of the nano-AlN lubricant, with a COF reaching 0.07. Both lubricants effectively fill and lubricate the holes on the surface of the copper-steel composite plate.

Originality/value
AlN and Al2O3 as water-based lubricants have excellent lubrication performance and can reduce the COF. It can provide some reference for the practical application of nano-water-based lubricants.

Peer review
The peer review history for this article is available at: https://publons.com/publon/10.1108/ILT-08-2023-0255/