bluuebunny/crossref_metadata_2025_split huggingface dataset:
First detection ofIxodiphagus hookeri(Hymenoptera: Encyrtidae) inIxodes ricinusticks (Acari: Ixodidae) from multiple locations of Hungary
Authors: Tóth Adrienn Gréta , Farkas Róbert , Gyurkovszky Mónika , Krikó Eszter , Solymosi Norbert 
Published: September 2022

ABSTRACTThe parasiotid wasp,Ixodiphagus hookeri(Hymenoptera: Encyrtidae) is the natural enemy of a wide range of hard and soft tick species. While these encyrtid wasps are supposed to be distributed worldwide, only few studies report about its actual appearance patterns around the globe. Within a shotgun sequencing based metagenome analysis, the occurrence ofI. hookeriwas screened at multipleIxodes ricinus(Acari: Ixodidae) tick sampling points of Hungary, to contribute to the assessment of the appearance patterns of the parasitoid wasps in Central Europe. To our knowledge, the first report of the species in Hungary and the description of the southernmostI. hookeriassociated geoposition in Central Europe took place within our study.I. hookeriinfestedI. ricinusnymphs were detected at five sampling points of Hungary. The results show that the exact distribution range ofI. hookeriis still barely studied. At the same time, unprecedented public health issues being brought by climate change might require steps towards the exploitation of the tick biocontrol potential or ecological bioindicator role of the parasitoid wasp in the future.
Striatal ups or downs? Neural correlates of monetary reward anticipation, cue reactivity and their interaction in alcohol use disorder and gambling disorder
Authors: van Timmeren Tim , van Holst Ruth J. , Goudriaan Anna E. 
Published: September 2022

ABSTRACTStriatal dysfunction is a key characteristic of addictive disorders, but neuroimaging studies have reported conflicting findings. An integrative model of addiction points to the presence or absence of addiction-related cues as an explanation for striatal hypo-or hyperactivations, respectively, but has never been directly tested. Here, we developed a novel paradigm to investigate striatal activation during monetary reward anticipation in the presence versus absence of addiction-related pictures using functional MRI. Across two studies, we compared 46 alcohol use disorder (AUD) patients with 30 matched healthy controls; and 24 gambling disorder (GD) patients with 22 matched healthy controls. During monetary reward anticipation, hypoactivation of the reward system was seen in AUD individuals compared to HCs. Additionally, a behavioral interaction was seen where gambling cues made participants, across groups, respond faster for bigger, but slower for smaller rewards. However, no striatal differences were seen between the participants with AUD or GD and their matched controls. In sum, these findings suggest that striatal dysfunction is a key but heterogeneous mechanism within both AUD and GD and indicates an important but complex role for addiction-related cues in explaining striatal dysfunction in addiction.
Design principles for selective polarization of PAR proteins by cortical flows
Authors: Illukkumbura Rukshala , Hirani Nisha , Borrego-Pinto Joana , Bland Tom , Ng KangBo , Hubatsch Lars , McQuade Jessica , Endres Robert G. , Goehring Nathan W. 
Published: September 2022

AbstractClustering of membrane-associated molecules is thought to promote interactions with the actomyosin cortex, enabling size-dependent transport by actin flows. Consistent with this model, in the C. elegans zygote, anterior segregation of the polarity protein PAR-3 requires oligomerization. However, through direct assessment of advection of PAR proteins, we not only find no links between PAR-3 advection and oligomer size, but also observe efficient advection of both anterior and posterior PAR proteins. Consequently, differential cortex engagement cannot account for selective size-dependent PAR protein transport. Instead, combining experiment and theory we demonstrate that segregation efficiency of PAR proteins by cortical flow is determined by the stability of membrane association, which is enhanced by clustering and specifies persistence of transport. Indeed, stabilizing membrane association was sufficient to invert polarity of a normally posterior PAR protein. Our data therefore indicate that advection of membrane-associated proteins is more pervasive than anticipated and thus cells must tune membrane association dynamics to achieve differential transport by cortical flows.
Reconstitution of a minimal ESX-5 type VII secretion system suggests a role for PPE proteins in outer membrane transport of proteins
Authors: Bunduc C. M. , Ding Y. , Kuijl C. , Marlovits T. C. , Bitter W. , Houben E.N.G. 
Published: September 2022

AbstractMycobacteria utilize type VII secretion systems (T7SSs) to secrete proteins across their highly hydrophobic and diderm cell envelope. Pathogenic mycobacteria have up to five different T7SSs, called ESX-1 to ESX-5, which are crucial for growth and virulence. Here, we use a functionally reconstituted ESX-5 system in the avirulent speciesMycobacterium smegmatisthat lacks ESX-5, to define the role of eachesx-5gene in system functionality. By creating an array of gene deletions and assessing protein levels of components and membrane complex assembly, we observed that only the five components of the inner membrane complex are required for its assembly. However, in addition to these five core components, active secretion also depends on both the Esx and PE/PPE substrates. Tagging the PPE substrates followed by subcellular fractionation, surface labeling and membrane extraction showed that these proteins localize to the mycobacterial outer membrane. This indicates that they could play a role in secretion across this enigmatic outer barrier. These results provide a first full overview of the role of eachesx-5gene in T7SS functionality.
Glucose oxidation and nutrients availability drive neural crest development
Authors: Nekooie-Marnany Nioosha , Fodil Redouane , Féréol Sophie , Depp Marine , Motterlini Roberto , Foresti Roberta , Duband Jean-Loup , Dufour Sylvie 
Published: September 2022

ABSTRACTBioenergetic metabolism is a key regulator of cellular function and signaling activity but the exact roles of nutrient utilization and energy production in embryonic development remain unknown. Here we investigated the metabolic pathways and deciphered the role of carbon metabolism required for the development of neural crest cells (NCC), a migratory stem cell population of the vertebrate embryo. We uncovered that glucose oxidation constitutes the prominent metabolic signature of trunk NCC and supports their delamination, migration, and proliferation. Additionally, we found that glycolysis, mitochondrial respiration and the pentose phosphate pathway are all mobilized downstream of glucose uptake. These metabolic pathways do not support specific cellular processes but cooperate and are integrated to accomplish epithelium-to-mesenchyme transition, adhesion, locomotion and proliferation. Moreover, using different nutrient supplies (glucose vs. pyruvate) we show that glucose is crucial to modulate NCC migration and adaptation to environmental stiffness, control NCC stemness and drive their fate decisions through regulation of specific gene expression. Our data establish that NCC development is instructed by metabolic cues that mobilize defined metabolic pathways cooperating together in response to nutrient availability.SUMMARY STATEMENTHere we show that neural crest cell migration and fate decisions rely primarily on glucose oxidation for energy production and mobilize multiple cooperating metabolic pathways for their biosynthetic needs and execution of gene programs.
Sleep spindle maturation enhances slow oscillation-spindle coupling
Authors: Joechner Ann-Kathrin , Hahn Michael A. , Gruber Georg , Hoedlmoser Kerstin , Werkle-Bergner Markus 
Published: September 2022

AbstractThe synchronization of canonical fast sleep spindle activity (12.5-16 Hz) precisely during the slow oscillation up peak is considered an essential feature of adult non-rapid eye movement sleep. However, there is little knowledge on how this well-known coalescence between slow oscillations and sleep spindles develops. Leveraging individualized detection of single events, we first provide a detailed cross-sectional characterization of age-specific patterns of slow and fast sleep spindles, slow oscillations, and their coupling in children aged 5 to 6, 8 to 11, and 14 to 18 years. Critically, based on this, we then investigated how spindle and slow oscillation maturity substantiate age differences in their precise orchestration. While the predominant type of fast spindles was development-specific in that it was still nested in a frequency range below the canonical fast spindle range for the majority of children, the well-known slow oscillation-spindle coupling pattern was evident for sleep spindles in the canonical (adult-like) fast spindle range in all three age groups – but notably less precise in children. To corroborate these findings, we linked personalized measures of fast spindle maturity, which indicate the similarity between the prevailing development-specific and adult-like fast spindles, and slow oscillation maturity, which reflects the extent to which slow oscillations show frontal dominance, with individual slow oscillation-spindle coupling patterns. Importantly, we found that fast spindle maturity was uniquely associated with enhanced slow oscillation-spindle coupling strength and precision. Taken together, our results suggest that the increasing ability to generate canonical fast sleep spindles actuates precise slow oscillation-spindle coupling patterns across child and adolescent development.
Self-generated brain-wide spiking cascades govern replay dynamics in the hippocampus
Authors: Yang Yifan , Leopold David A. , Duyn Jeff H. , Liu Xiao 
Published: September 2022

AbstractDuring states of behavioral quiescence, neurons in the hippocampus replay sequences of spiking activity experienced in earlier behavioral episodes. While such replay sequences are hypothesized to serve learning and memory by facilitating synaptic consolidation, their generative mechanisms remain poorly understood. Increasing evidence suggests that they might be generated internally, or at least strongly constrained by internal circuit dynamics. Recent work demonstrated that, across the forebrain, approximately 70% of neurons participate in a pattern of sequential spiking cascades during rest. Like hippocampal replay sequences, these brain-wide spiking cascades occur together with high-frequency hippocampal ripples and therefore may share a common generative mechanism. Here we systematically investigated the relationship between replay activity and sequential spiking cascades by analyzing a database of intracortical electrocortical recordings in mice. For neuronal subpopulations in the hippocampus and visual cortex, we assessed spiking sequences elicited during video viewing as well as potential replay events during subsequent periods of rest. We found that replay events were unique to hippocampal time-sensitive neurons and occurred together with spiking cascades throughout the forebrain. Furthermore, forward and time-reversed replay sequences were associated with different types of spiking cascades. Overall, these findings indicate that hippocampal replay events are generated and structured according to resting state circuit dynamics manifest across a large portion of the brain.
Graph pangenome reveals functional, evolutionary, and phenotypic significance of human nonreference sequences
Authors: Wu Zhikun , Li Tong , Jiang Zehang , Zheng Jingjing , Liu Yun , Liu Yizhi , Xie Zhi 
Published: September 2022

AbstractThousands of DNA sequences in global populations are not present in the human reference genome, named nonreference sequence (NRS). Long-read sequencing (LRS) technologies enable better discovery of NRS with large length, particularly in repetitive regions. Here, wede novoassembled 539 genomes in five genetically divergent human populations sequenced by LRS technology and identified 5.1 million NRSs. These NRSs were merged into 45,284 nonredundant NRSs, of which 66.2% were novel. 78.5% of NRSs were repeat sequences, such as VNTR and STR. 38.7% of NRSs were common in the five populations, 35.6% were population specific, while 21.3% were ancestral and present in nonhuman primates. 144 NRS hotspots spanned 141 Mb of the human genome and many NRSs contained known functional domains or intersected with coding genes. Based on graph-based pangenome, we detected 565 transcript expression quantitative trait loci on NRSs, of which 467 were novel. We also detected 39 NRS candidates for adaptive selection within the human population related to the language system and diabetes. GWAS revealed 14 NRSs significantly associated with eight phenotypes, such as anaemia. Furthermore, we identified 154 NRSs in strong linkage disequilibrium with 258 phenotype-associated SNPs in the GWAS catalogue. Our work expands the landscape of human NRS and provides novel insights into functions of NRS to facilitate evolutionary and biomedical research.
SE(3) Equivalent Graph Attention Network as an Energy-Based Model for Protein Side Chain Conformation
Authors: Liu Deqin , Chen Sheng , Zheng Shuangjia , Zhang Sen , Yang Yuedong 
Published: September 2022

AbstractProtein design energy functions have been developed over decades by leveraging physical forces approximation and knowledge-derived features. However, manual feature engineering and parameter tuning might suffer from knowledge bias. Learning potential energy functions fully from crystal structure data is promising to automatically discover unknown or high-order features that contribute to the protein’s energy. Here we proposed a graph attention network as an energy-based model for protein conformation, namely GraphEBM. GraphEBM is equivariant to the SE(3) group transformation, which is the important principle of modern machine learning for molecules-related tasks. GraphEBM was benchmarked on the rotamer recovery task and outperformed both Rosetta and the state-of-the-art deep learning based methods. Furthermore, GraphEBM also yielded promising results on combinatorial side chain optimization, improving 22.2% χ1 rotamer recovery to the PULCHRA method on average.
New structures of Class II Fructose-1,6-Bisphosphatase from Francisella tularensis suggest a novel catalytic mechanism for the entire Class
Authors: Selezneva Anna I. , Harding Luke N. M. , Gutka Hiten J. , Movahedzadeh Farahnaz , Abad-Zapatero Celerino 
Published: September 2022

AbstractClass II Fructose-1,6-bisphosphatases (FBPaseII) (EC: 3.1.3.11) are highly conserved essential enzymes in the gluconeogenic pathway of microorganisms. Previous crystallographic studies of FBPasesII provided insights into various inactivated states of enzymes from different species. Presented here is the first crystal structure of FBPaseII in an active state, solved for the enzyme from Francisella tularensis (FtFBPaseII), containing native metal cofactor Mn2+ and complexed with catalytic product fructose-6-phosphate (F6P). Another crystal structure of the same enzyme complex is presented in inactivated state due to the structural changes introduced by crystal packing. Analysis of the interatomic distances among the substrate, product and divalent metal cations in the enzyme catalytic centers led to a revision of the catalytic mechanism suggested previously for class II FBPases. Instead of a metal cofactor for the stabilization of the transition state of the leaving phosphate group, we propose that the positive dipole of the neighboring α-helix backbone (G88-T89-T90-I91-T92-S93-K94) is responsible for retaining the cleaved phosphate. The revised catalytic mechanism involves a nucleophilic attack by a reactive water coordinated by both the T89 hydroxyl and a second water molecule coordinated directly by Mn2+. Additionally, a crystal structure of Mycobacterium tuberculosis FBPaseII (MtFBPaseII), containing the substrate fructose-1,6-bisphosphate (F1,6BP) bound, is presented in support of a novel catalytic mechanism for this class of enzymes.
Contributing Factors to Dietary Quality and Food Security in Low-Income Households with Children in the United States: A Scoping Review
Authors: Keown Denise Mc , Graves Lisa , McGowan Bethany , Eicher-Miller Heather A. 
Published: September 2022

AbstractBackgroundLow income and food insecure households are at risk of poor dietary quality and food insecurity. Especially in childhood, consuming a nutritionally adequate diet is an essential driver of health, growth, and development. Prior research has shown many household-level factors can present challenges to support the nutritional needs of the members of low income and food insecure households.ObjectiveThe aim of the scoping review is to identify the contributing factors to dietary quality and food security in U.S. households of school-aged children and synthesize the evidence.MethodsThe scoping review was conducted following the Preferred Reporting Items for Systematic Reviews and Meta-Analysis Protocols Extension for Scoping Reviews (PRISMA-ScR) using search terms addressing food insecurity, low-income and dietary behaviors in the database PubMed (NCBI). Screening by 3 independent reviewers at the title, abstract, and full study phases identified forty-three studies included in the review.ResultsThe studies addressed six themes: parental behaviors, child/adolescent behaviors, food procurement behaviors, food preparation behaviors, and psychosocial factors. Most studies were cross-sectional (n = 40, 93%) and focused on parental behaviors (n = 24, 56%), followed by food procurement behaviors, and food preparation behaviors.ConclusionThe findings can be used to inform the development of future nutritional education interventions aimed at improving the dietary quality and food security in households with children. The themes identified were interrelated and suggest that providing parents with education on the following topics: 1) the importance of modeling positive eating behaviors in the home, 2) approaches to support and encourage positive feeding practices with their children, and 3) practical strategies to overcome barriers to purchasing and preparing foods of high nutrient quality. For example, delivering educational sessions on meal selection and preparation and improving nutritional knowledge hold promise to improve dietary quality among food insecure and low-income households.
Inference of core needle biopsy whole slide images requiring definitive therapy for prostate cancer
Authors: Tsuneki Masayuki , Abe Makoto , Ichihara Shin , Kanavati Fahdi 
Published: September 2022

AbstractProstate cancer is often a slowly progressive indolent disease. Unnecessary treatments from overdiagnosis are a significant concern, particularly low-grade disease. Active surveillance has being considered as a risk management strategy to avoid potential side effects by unnecessary radical treatment. In 2016, American Society of Clinical Oncology (ASCO) endorsed the Cancer Care Ontario (CCO) Clinical Practice Guideline on active surveillance for the management of localized prostate cancer. Based on this guideline, we developed a deep learning model to classify prostate adenocarcinoma into indolent (applicable for active surveillance) and aggressive (necessary for definitive therapy) on core needle biopsy whole slide images (WSIs). In this study, we trained deep learning models using a combination of transfer, weakly supervised, and fully supervised learning approaches using a dataset of core needle biopsy WSIs (n=1300). We evaluated the models on a test set (n=645), achieving ROC-AUCs 0.846 (indolent) and 0.980 (aggressive). The results demonstrate the promising potential of deployment in a practical prostate adenocarcinoma histopathological diagnostic workflow system.
Divergence in bacterial ecology is reflected by difference in population genetic structure, phage-predator load and host range
Authors: Cahier Karine , Piel Damien , Barcia-Cruz Rubén , Goudenège David , Wegner K. Mathias , Monot Marc , Romalde Jesús L , Roux Frédérique Le 
Published: September 2022

ABSTRACTPhages depend on their bacterial host to replicate, but how habitat, density and diversity of the host population drive phage ecology is not well understood. Here, we addressed this question by comparing two populations of marine bacteria and their phages collected during a time series sampling in an oyster farm.Vibrio crassostreaereproduces more specifically in oysters. This population is genetically structured into clades of near clonal strains favoring infection by closely related phages and leading to a modular structure of the phage-bacterial infection network.Vibrio chagasii, on the other hand, blooms in the water column from where it can colonize oysters via filter-feeding. We found higher phage predation pressure onV. chagasiithat did not result from a broader host range of the phages but rather from a greater burst size generating more infectious particles in the environment. We showed that contrasting patterns of genetic diversity for host and phage lead to different infection network architectures. We also provided evidence that a bloom of phages generates epigenetic and genetic variability that can be selected to counteract host defense systems.
A qualitative study of food choice behaviors among college students with food allergies in the US
Authors: Lee Yee Ming , Sozen Erol , Wen Han 
Published: September 2022

PurposeThis study explored how food allergies have affected food-related behaviors and quality of life of college students with food allergies and identified factors influencing food choice decisions among this group of individuals.Design/methodology/approachOne-on-one interviews were conducted with 26 college students with self-reported or clinically diagnosed food allergies, recruited from two universities located in the southern region of the United States. The participants were asked a series of questions based on a semi-structured discussion guide. Each interview lasted about 30 min; all interviews were audio-recorded and transcribed verbatim. The transcriptions were coded independently by three researchers, and themes were identified.FindingsFood allergies affected the participants' food-related behaviors, including eating, food preparation and shopping, as well as some aspects of their quality of life. Individual factors, such as mood, other diseases, cultural background and sensory properties, also influenced food choices. Friends and families were the two most important social influencers of food choices. Regarding physical environmental factors, cost, convenience, value and variety were considered important in selecting food. However, the participants' food choices were less influenced by food advertisements and social media. Additionally, experiences and complex cuisines were also key factors in making food choices.Research limitations/implicationsTheoretically, this qualitative study applied a food choice decision framework in the context of college students with food allergies. Practical recommendations are provided, particularly to campus dining facilities, to fulfill the needs of college students with food allergies.Originality/valueThis study advanced the understanding of the complexity of food choice decision-making among college students with food allergies. A path diagram specific to food choice among college students with food allergies was developed based on the results of this study. This study also highlighted that food allergy management would involve various behavioral changes and revealed that the food choices are influenced by a wide range of factors.