bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deficiency of Orexin Receptor Type 1 in Dopaminergic Neurons Increases Novelty-Induced Locomotion and Exploration
Authors: Xiao Xing , Yeghiazaryan Gagik , Eggersmann Fynn , Cremer Anna L. , Backes Heiko , Kloppenburg Peter , Hausen A. Christine 
Published: August 2023

AbstractOrexin signaling in the ventral tegmental area and substantia nigra promotes locomotion and reward processing, but it is not clear whether dopaminergic neurons directly mediate these effects. We show that dopaminergic neurons in these areas mainly express orexin receptor subtype 1 (Ox1R). In contrast, only a minor population in the medial ventral tegmental area express orexin receptor subtype 2 (Ox2R). To analyze the functional role of Ox1R signaling in dopaminergic neurons, we deleted Ox1R specifically in dopamine transporter-expressing neurons of mice and investigated the functional consequences. Deletion of Ox1R increased locomotor activity and exploration during exposure to novel environments or when intracerebroventricularely injected with orexin A. Spontaneous activity in home cages, anxiety, reward processing, and energy metabolism did not change. Positron emission tomography imaging revealed that Ox1R signaling in dopaminergic neurons affected distinct neural circuits depending on the stimulation mode. In line with an increase of neural activity in the lateral paragigantocellular nucleus (LPGi) of Ox1RΔDATmice, we found that dopaminergic projections innervate the LPGi in regions where the inhibitory dopamine receptor subtype D2 but not the excitatory D1 subtype resides. These data suggest a crucial regulatory role of Ox1R signaling in dopaminergic neurons in novelty-induced locomotion and exploration.
Approximating conformational Boltzmann distributions with AlphaFold2 predictions
Authors: Brown Benjamin P. , Stein Richard A. , Meiler Jens , Mchaourab Hassane 
Published: August 2023

AbstractProtein dynamics are intimately tied to biological function and can enable processes such as signal transduction, enzyme catalysis, and molecular recognition. The relative free energies of conformations that contribute to these functional equilibria are evolved for the physiology of the organism. Despite the importance of these equilibria for understanding biological function and developing treatments for disease, the computational and experimental methods capable of quantifying them are limited to systems of modest size. Here, we demonstrate that AlphaFold2 contact distance distributions can approximate conformational Boltzmann distributions, which we evaluate through examination of the joint probability distributions of inter-residue contact distances along functionally relevant collective variables of several protein systems. Further, we show that contact distance probability distributions generated by AlphaFold2 are sensitive to points mutations thus AF2 can predict the structural effects of mutations in some systems. We anticipate that our approach will be a valuable tool to model the thermodynamics of conformational changes in large biomolecular systems.
Single Cell Transcriptomes, Lineage, and Differentiation of Functional Airway Microfold Cells
Authors: Surve Manalee V. , Lin Brian , Reedy Jennifer L. , Crossen Arianne J. , Xu Anthony , Klein Bruce S. , Vyas Jatin M. , Rajagopal Jayaraj 
Published: August 2023

ABSTRACTThe airway epithelium is frequently exposed to pathogens and allergens, but the cells that are responsible for sampling these inhaled environmental agents have not been fully defined. Thus, there is a critical void in our understanding of how luminal antigens are delivered to the immune cells that drive the appropriate immune defenses against environmental assaults. In this study, we report the first single cell transcriptomes of airway Microfold (M) cells, whose gut counterparts have long been known for their antigen sampling abilities. Given their very recent discovery in the lower respiratory airways, the mechanisms governing the differentiation and functions of airway M cells are largely unknown. Here, we shed light on the pathways of airway M cell differentiation, establish their lineage, and identify a functional M cell-specific endocytic receptor, the complement receptor 2 (CR2). Lastly, we demonstrate that airway M cells can endocytoseAspergillus fumigatusconidia in a CR2-dependent manner. Collectively, this work lays a foundation for deepening our understanding of lung mucosal immunology and the mechanisms that drive lung immunity and tolerance.
Conditional deletion ofCcl2in smooth muscle cells does not reduce early atherosclerosis in mice
Authors: Gunnersen Stine , Shim Jeong Tangkjær , Liu Fan , Tietge Uwe J.F. , Sørensen Charlotte Brandt , Bentzon Jacob Fog 
Published: August 2023

AbstractBackground and aimsC-C motif chemokine ligand 2 (CCL2) is a pro-inflammatory chemokine important for monocyte recruitment to the arterial wall and atherosclerotic plaques. Global knockout ofCcl2reduces plaque formation and macrophage content in mice, but the importance of different plaque cell types in mediating this effect has not been resolved. Smooth muscle cells (SMCs) can adopt a potentially pro-inflammatory function with expression of CCL2. The present study aimed to test the hypothesis that SMC-secreted CCL2 is involved in early atherogenesis in mice.MethodsSMC-restricted Cre recombinase was activated at 6 weeks of age in mice with homozygous floxed or wildtypeCcl2alleles. Separate experiments in mice lacking the Cre recombinase transgene were conducted to control for genetic background effects. Hypercholesterolemia and atherosclerosis were induced by a tail vein injection of recombinant adeno-associated virus (rAAV) encoding proprotein convertase subtilisin /kexin type 9 (PCSK9) and a high-fat diet for 12 weeks.ResultsUnexpectedly, mice with SMC-specificCcl2deletion developed higher levels of plasma cholesterol and larger atherosclerotic plaques with more macrophages compared with wild-type littermates. When total cholesterol levels were incorporated into the statistical analysis, none of the effects on plaque development between groups remained significant. Importantly, changes in plasma cholesterol and atherosclerosis remained in mice lacking Cre recombinase indicating that they were not caused by SMC-specific CCL2 deletion but by effects of the floxed allele or passenger genes.ConclusionsSMC-specific deficiency ofCcl2does not significantly affect plaque development in hypercholesterolemic mice.Bullet pointsSMCs express CCL2 in human plaques and upon inflammatory activation of a murine SMC line in vitro.Deletion of the Ccl2 gene in SMCs using Cre recombinase does not influence the size or composition of atherosclerotic plaque in mice.Only by conducting a control study in mice without Cre recombinase was an initially observed difference in atherosclerosis concluded to be a genetic background effect.
Habitat use of loggerhead (Caretta caretta) and green (Chelonia mydas) turtles in the Northwest Pacific Ocean, the northern limit of their distribution range
Authors: Kim Il-Hun , Park Il-Kook , Park Daesik , Kim Min-Seop , Cho In-Young , Yang Dongwoo , Han Dong-Jin , Cho Eunvit , Shim Won Joon , Hong Sang Hee , An Yong-Rock 
Published: August 2023

AbstractVerifying habitats, including the foraging and nesting areas for sea turtles, enables an understanding of their spatial ecology and successful planning of their conservation and management strategies. Recently, the observation frequency and bycatch of loggerhead (Caretta caretta) and green (Chelonia mydas) turtles have increased in the northern limit of their distribution range, in the northern part of the East China Sea and East Sea (Sea of Japan). We conducted satellite tracking to investigate the habitat use of seven loggerhead and eight green turtles from June 2016 to August 2022 in this area, where little is known about their spatial ecology. We applied a 50 percent volume contour method to determine their main foraging areas and analyzed 6 environmental variables to characterize their habitats. Loggerhead turtles mainly stayed in and used the East China Sea as a foraging area during the tracking period, while two individuals among them also used the East Sea as a seasonal foraging area. Most green turtles also used the East China Sea as a foraging area, near South Korea and Japan, with one individual among them using the southern part of the East Sea as a seasonal foraging area. Notably, one green turtle traveled to Hainan Island in the South China Sea, a historical nesting area. Our results showed that the two sea turtle species included the East Sea as a seasonal foraging area, possibly owing to the abundance of food sources available, despite its relatively lower sea temperature. Considering that loggerhead and green sea turtles were observed using the northern part of the East China Sea and East Sea more frequently than previously known and that the sea temperature gradually increases due to climate change, conservation and management activities are required for sea turtles in these areas.
S-PLM: Structure-aware Protein Language Model via Contrastive Learning between Sequence and Structure
Authors: Wang Duolin , Pourmirzaei Mahdi , Abbas Usman L , Zeng Shuai , Manshour Negin , Esmaili Farzaneh , Poudel Biplab , Jiang Yuexu , Shao Qing , Chen Jin , Xu Dong 
Published: August 2023

AbstractProteins play an essential role in various biological and engineering processes. Large protein language models (PLMs) present excellent potential to reshape protein research by accelerating the determination of protein function and the design of proteins with the desired functions. The prediction and design capacity of PLMs relies on the representation gained from the protein sequences. However, the lack of crucial 3D structure information in most PLMs restricts the prediction capacity of PLMs in various applications, especially those heavily dependent on 3D structures. To address this issue, we introduce S-PLM, a 3D structure-aware PLM that utilizes multi-view contrastive learning to align the sequence and 3D structure of a protein in a coordinated latent space. S-PLM applies Swin-Transformer on AlphaFold-predicted protein structures to embed the structural information and fuses it into sequence-based embedding from ESM2. Additionally, we provide a library of lightweight tuning tools to adapt S-PLM for diverse protein property prediction tasks. Our results demonstrate S-PLM’s superior performance over sequence-only PLMs on all protein clustering and classification tasks, achieving competitiveness comparable to state-of-the-art methods requiring both sequence and structure inputs. S-PLM and its lightweight tuning tools are available athttps://github.com/duolinwang/S-PLM/.
Fungal-bacteria interactions provide shelter for bacteria in Caesarean section scar diverticulum
Authors: Chen Peigen , Chen Haicheng , Liu Ziyu , Pan Xinyi , Liu Qianru , Yang Xing 
Published: August 2023

AbstractCaesarean section scar diverticulum (CSD) is a significant cause of infertility among women who have previously had a Caesarean section, primarily due to persistent inflammatory exudation associated with this condition. Even though abnormal bacterial composition is identified as a critical factor leading to this chronic inflammation, clinical data suggests that a long-term cure is often unattainable with antibiotic treatment alone. In our study, we employed metagenomic analysis and mass spectrometry techniques to investigate the fungal composition in CSD and its interaction with bacteria. We discovered that local fungal abnormalities in CSD can disrupt the stability of the bacterial population and the entire microbial community by altering bacterial abundance via specific metabolites. For instance,Lachnellula suecicareduces the abundance of severalLactobacillus spp., such asLactobacillus jensenii, by diminishing the production of metabolites likeGoyaglycoside AandJanthitrem E. Concurrently,Clavispora lusitaniaeandOphiocordyceps australiscan synergistically impact the abundance ofLactobacillus spp. by modulating metabolite abundance. Our findings underscore that abnormal fungal composition and activity are key drivers of local bacterial dysbiosis in CSD.
TheArabidopsisSR45 splicing factor bridges the splicing machinery and the exon-exon junction complex
Authors: Fanara Steven , Schloesser Marie , Joris Marine , De Franco Simona , Vandevenne Marylène , Kerff Frédéric , Hanikenne Marc , Motte Patrick 
Published: August 2023

AbstractThe Arabidopsis splicing factor serine/arginine-rich 45 (SR45) contributes to several biological processes. Thesr45-1loss-of-function mutant exhibits delayed root development, late flowering, unusual numbers of floral organs, shorter siliques with decreased seed sets, narrower leaves and petals, and altered metal distribution. SR45 bears a unique RNA recognition motif (RRM) flanked by one serine/arginine-rich (RS) domain on both sides. Here, we studied the function of each of SR45 domains by examining their involvement in: (i) the spatial distribution of SR45, (ii) the establishment of a protein-protein interaction network including spliceosomal and exon-exon junction complex (EJC) components, and (iii) the RNA binding specificity. We report that the endogenousSR45promoter is active during vegetative and reproductive growth, and that the SR45 protein localizes in the nucleus. We demonstrate that the C-terminal arginine/serine-rich domain is a determinant of nuclear localization. We show that the SR45 RNA recognition motif (RRM) domain specifically binds purine-rich RNA motifs via three residues (H101, H141, Y143), and is also involved in protein-protein interactions. We further show that SR45 bridges both mRNA splicing and surveillance machineries as a partner of EJC core components and peripheral factors, which requires phosphoresidues likely phosphorylated by kinases from both CLK and SRPK families. Our findings provide insights into the contribution of each SR45 domain to both spliceosome and EJC assemblies.HighlightThe contribution of the Arabidopsis SR45 splicing factor individual domains to its nuclear localization, ability to contactin plantanovel protein partners and specifically bind RNA motifs was examined.
CryoEM reveals the structure of an archaeal pilus involved in twitching motility
Authors: Gaines Matthew C. , Sivabalasarma Shamphavi , Isupov Michail N. , Haque Risat Ul , McLaren Mathew , Hanus Cyril , Gold Vicki A.M. , Albers Sonja-Verena , Daum Bertram 
Published: August 2023

AbstractAmongst the major archaeal filament types, several have been shown to closely resemble bacterial homologues of the Type IV pili (T4P). WithinSulfolobales,member species encode for three types of T4P, namely the archaellum, the UV-inducible pilus (Uvp) and the archaeal adhesive pilus (Aap). Whereas the archaellum functions primarily in swimming motility, and the Uvp in UV-induced cell aggregation and DNA-exchange, the Aap plays an important role in adhesion and twitching motility. All previously solved Aap appear to have almost identical helical structures. Here, we present a cryoEM structure of the Aap of the archaeal model organismSulfolobus acidocaldarius.We identify the component subunit as AapB and find that while its structure follows the canonical T4P blueprint, it adopts three distinct conformations within the pilus. The tri-conformer Aap structure that we describe challenges our current understanding of pilus structure and sheds new light on the principles of twitching motility.
Biomechanical comparison of plate materials and designs for subcondylar fracture fixation: Anin silicoassessment
Authors: Gupta Anoushka , Dutta Abir , Dutta Kaushik , Mukherjee Kaushik 
Published: August 2023

AbstractThe fixation of common mandibular subcondylar fractures is associated with a high complication rate, and the decision of a suitable plate design and material still remains a challenge. Computational models have been developed and verified for understanding mandibular fracture fixation, but most of the investigation has been limited to a simplified model, single force and evaluation of plate-only designs. Using finite elements, we analysed the fracture stability with five materials - Nitinol, Magnesium alloys, two types of Titanium alloys (Ti-6Al-4V and Ti-29Nb-13Ta-4.6Zr) and Stainless Steel 316L, for four types of fixation plate designs. The soft tissues such as periodontal ligament, were included and molar clenching tasks were considered for accurately mimicking the physiological mastication cycle. The maximum principal tensile strain in the mandible was found to be decreasing with an increase in stiffness for most of the cases, except for the trapezoid and strut plates. We attribute the differences between trapezoid/strut and double mini/lambda to the presence of an additional screw near the sigmoid notch in the proximal segment in case of double mini and lambda plates. As the mandible reconstructed with double mini plates had the least interfragmentary gap, the double mini plate was deemed as the most suitable design. The results such as a lower von Mises stress in plates (compared to yield strength) indicated that the anchorage provided by titanium alloys (Ti-6Al-4V and TNTZ) is sufficient for load bearing.
Two distinct mechanisms of Plexin A function inDrosophilaoptic lobe lamination and morphogenesis
Authors: Bustillo Maria E. , Douthit Jessica , Astigarraga Sergio , Treisman Jessica E. 
Published: August 2023

AbstractVisual circuit development is characterized by subdivision of neuropils into layers that house distinct sets of synaptic connections. We find that in theDrosophilamedulla, this layered organization depends on the axon guidance regulator Plexin A. Inplexin Anull mutants, synaptic layers of the medulla neuropil and arborizations of individual neurons are wider and less distinct than in controls. Analysis of Semaphorin function indicates that Semaphorin 1a, provided by cells that include Tm5 neurons, is the primary partner for Plexin A in medulla lamination. Removal of the cytoplasmic domain of endogenous Plexin A does not disrupt the formation of medulla layers; however, both null and cytoplasmic domain deletion mutations ofplexin Aresult in an altered overall shape of the medulla neuropil. These data suggest that Plexin A acts as a receptor to mediate morphogenesis of the medulla neuropil, and as a ligand for Semaphorin 1a to subdivide it into layers. Its two independent functions illustrate how a few guidance molecules can organize complex brain structures by each playing multiple roles.Summary statementThe axon guidance molecule Plexin A has two functions inDrosophilamedulla development; morphogenesis of the neuropil requires its cytoplasmic domain, but establishing synaptic layers through Semaphorin 1a does not.
What’s on the menu? How celebrity chef brands create happiness
Authors: Rodrigues Paula , Brochado Ana , Sousa Ana , Borges Ana Pinto , Barbosa Isabel 
Published: August 2023

PurposeThis study aims, first, to understand consumers’ perception of chefs as human brands (i.e. study one). Second, tests were run to assess the validity of a new conceptual model of the relationships between the factors of chef image, luxury restaurant image, both images’ congruity and consumers’ hedonic and novelty experiences and happiness and well-being (i.e. study two).Design/methodology/approachThe first qualitative study involved using Leximancer software to analyse the data drawn from 43 interviews with luxury restaurant clients. In the second quantitative study, 993 valid survey questionnaires were collected, and the proposed model was tested using structural equation modelling.FindingsThe results reveal that consumers perceive chefs as human brands and the associated narratives include both performance- and popularity-based characteristics. The findings support the conclusion that individuals give great importance to chefs’ image and the congruence between chefs and their restaurant’s image. In addition, luxury restaurant image only affects novelty experiences, and both hedonic and novelty experiences have a positive effect on customers’ happiness and well-being.Research limitations/implicationsThis research focused on Portuguese luxury restaurants. The consumers’ happiness and well-being needs to be replaced by other outcomes to confirm if the model produces consistent results.Practical implicationsThe results should help luxury restaurant managers understand more fully which pull factors are valued by their clients and which aspects contribute the most to their pleasure and welfare.Originality/valueThis study adds to the extant literature by exploring consumers’ perceptions of chefs as human brands and the role these chefs’ image play in customers’ luxury restaurant experiences and perceived happiness and well-being.
Bridging the theory-practice gap: a critical reflection on information and communication technology research
Authors: Law Rob , Lei Soey Sut Ieng , Zhang Ke , Lau Arthur 
Published: August 2023

Purpose
Through critically reflecting on existing research on information and communication technology (ICT) in hospitality, the purpose of this study is to propose recommendations for future research to further narrow the theory-practice gap.

Design/methodology/approach
Personal experiences along with evidence from the literature provide a foundation for discussion, which is further enriched by integrating industry practitioners’ points of view.

Findings
Single-perspective and technology adoption studies have dominated ICT research in the hospitality literature. Technology effectiveness has often been measured indirectly. Oversimplifying technological issues has limited the generalizability of research findings.

Research limitations/implications
Future studies are suggested to go beyond examining technology adoption, embrace multi-perspective approaches and incorporate a wider range of situational and contextual factors.

Originality/value
Through a unique perspective, this study highlights the limitations of previous ICT research in the hospitality literature and provides suggestions for future research to better meet the needs of practitioners. The arguments presented are not purely from an academic standpoint, as they have been endorsed by senior industry executives.
Adoption of the Internet of Things in higher education: opportunities and challenges
Authors: Fernández-Batanero José M. , Montenegro-Rueda Marta , Fernández-Cerero José , López Menéses Eloy 
Published: August 2023

Purpose
The purpose of this study is to determine the characteristics of the studies in terms of country, participant profile and methodology, as well as to determine what the Internet of Things (IoT) is currently contributing to higher education.

Design/methodology/approach
The study was developed following the methodology supported by the Preferred Reporting Items for Systematic Reviews and Meta-Analyses statement and the PICOS strategy, retrieving scientific literature from Web of Science, Scopus, ERIC and Google Scholar. Of the 237 studies that the search yielded, 11 were included.

Findings
The results showed that among the opportunities offered by IoT is that it not only brings the introduction of information and communication technology into the classroom, but also enhances student interest, thus, improving the quality of teaching in higher education. On the other hand, one of the challenges it faces is the attitude of teachers towards its adoption, as well as the level of digital competence of teachers.

Originality/value
This study presents how higher education institutions are including the IoT in their educational activities. The IoT refers to a network of digital interconnectivity between devices, people and the internet itself that enables the exchange of data between them, allowing key information about the use and performance of devices and objects to be captured to detect patterns, make recommendations, improve efficiency and create better user experiences.