bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pathogen-driven CRISPR screens identify TREX1 as a regulator of DNA self-sensing during influenza virus infection
Authors: King Cason R. , Liu Yiping , Amato Katherine A. , Schaack Grace A. , Hu Tony , Smith Judith A , Mehle Andrew 
Published: February 2023

SummaryIntracellular pathogens interact with host factors, exploiting those that enhance replication while countering those that suppress it. Genetic screens have begun to define the host:pathogen interface and establish a mechanistic basis for host-directed therapies. Yet, limitations of current approaches leave large regions of this interface unexplored. To uncover host factors with pro-pathogen functions, we developed a novel fitness-based screen that queries factors important during the middle-to-late stages of infection. This was achieved by engineering influenza virus to direct the screen by programing dCas9 to modulate host gene expression. A genome-wide screen identified the cytoplasmic DNA exonuclease TREX1 as a potent pro-viral factor. TREX1 normally degrades cytoplasmic DNA to prevent inappropriate innate immune activation by self DNA. Our mechanistic studies revealed that this same process functions during influenza virus infection to enhance replication. Infection triggered release of mitochondrial DNA into the cytoplasm, activating antiviral signaling via cGAS and STING. TREX1 metabolized the mitochondrial DNA preventing its sensing. Collectively, these data show that self-DNA is deployed to amplify host innate sensing during RNA virus infection, a process tempered by TREX1. Moreover, they demonstrate the power and generality of pathogen driven fitness-based screens to pinpoint key host regulators of intracellular pathogens.
Genotypic and phenotypic evidence indicates the introduction of two distinct forms of a non-native species (Gekko gecko) to Florida, USA
Authors: Fieldsend Thomas W. , Rösler Herbert , Krysko Kenneth L. , Harman Madison E.A. , Mahony Stephen , Collins Timothy M. 
Published: February 2023

AbstractThe red-spotted tokay geckoGekko gecko(Linnaeus, 1758) is a widely distributed Asian gecko that has established outside of its native range in Florida, USA. This study used genotypic and phenotypic data to determine whether multiple, distinct forms of red-spotted tokay gecko are present in Florida, specifically the morphologically distinct “G. g. gecko” and “Form B”. Two discrete mitochondrial clades (ND2) were identified in Florida tokay geckos, the native range distributions of which were found to correspond closely with the native ranges ofG. g. gecko(the Malay Archipelago) and Form B (mainland Asia), respectively. Furthermore, each mitochondrial clade was non-randomly associated with a separate nuclear (RAG-1) clade, supporting the existence of two discrete genotypic lineages, representative ofG. g. geckoand Form B. Both lineages were detected in Florida, and population-level morphological structure was non-randomly associated with genotype, confirming a genotype-phenotype link. Multiple lines of evidence thus indicate the introduction of both forms of tokay gecko to Florida, where hybridisation likely also occurs. The link between morphological Form B and a unique genotypic lineage also indicates the existence of a tokay gecko taxon distinct from the recognised subspeciesG. g. azhariMertens, 1955 andG. g. gecko(Linnaeus, 1758).
HOPS-dependent lysosomal fusion controls Rab19 availability for ciliogenesis in polarized epithelial cells
Authors: Hoffman Huxley K. , Prekeris Rytis 
Published: February 2023

ABSTRACTPrimary cilia are sensory cellular organelles crucial for organ development and homeostasis. Ciliogenesis in polarized epithelial cells requires Rab19-mediated clearing of apical cortical actin to allow the cilium to grow from the apically-docked basal body into the extracellular space. Loss of the lysosomal membrane-tethering HOPS complex disrupts this actin-clearing and ciliogenesis, but it remains unclear how ciliary function of HOPS relates to its canonical function in regulating late endosome-lysosome fusion. Here, we show that disruption of HOPS-dependent lysosomal fusion indirectly impairs actin-clearing and ciliogenesis by disrupting the targeting of Rab19 to the basal body. We also find that Rab19 functions in endolysosomal cargo trafficking apart from its previously-identified role in ciliogenesis. In summary, we show that inhibition of lysosomal fusion abnormally accumulates Rab19 on late endosomes, thus depleting Rab19 from the basal body and thereby disrupting Rab19-mediated actin-clearing and ciliogenesis.Summary statementLoss of HOPS-mediated lysosomal fusion indirectly blocks apical actin clearing and ciliogenesis in polarized epithelia by trapping Rab19 on late endosomes and depleting Rab19 from the basal body.
Lack of neutralizing antibodies against the current circulating influenza viruses during the Omicron outbreak in Hong Kong
Authors: Liang Weiwen , Lv Huibin , Chen Chunke , Sun Yuanxin , Hui David S , Pun Mok Chris Ka 
Published: February 2023

AbstractWe report the seroprevalence to the circulating influenza A H1N1 and H3N2 viruses from plasma samples collected from 479 adults between 2021 and 2022. Our results show that there is lack of neutralizing antibodies to these viruses and highlight the importance of promoting influenza vaccination during the emerging of COVID-19.
Attentional capture by fearful faces requires consciousness and is modulated by task-relevancy: a dot-probe EEG study
Authors: Qiu Zeguo , Jiang Jiaqin , Becker Stefanie I. , Pegna Alan J. 
Published: February 2023

AbstractIn the current EEG study, we used a dot-probe task in conjunction with backward masking to examine the neural activity underlying awareness and spatial processing of fearful faces and the neural processes for subsequent cued spatial targets. We presented face images under different viewing conditions (subliminal and supraliminal) and manipulated the relation between a fearful face in the pair and a subsequent target. Through both mass univariate analysis and multivariate pattern analysis, we found that fearful faces can be processed to an extent where they attract spatial attention only when they are presented supraliminally and when they are task-relevant. The spatial attention capture by fearful faces also modulated the processing of subsequent lateralised targets that were spatially congruent with the fearful face, in both behavioural and neural data. There was no evidence for nonconscious processing of the fearful faces in the current paradigm. We conclude that spatial attentional capture by fearful faces requires visual awareness and it is modulated by top-down task demands.
Decoupling cell size homeostasis in diatoms from the geometrical constraints of the silica cell-wall
Authors: de Haan Diede , Ramos Nahuel-Hernan , Gal Assaf 
Published: February 2023

SummaryUnicellular organisms are known to exert tight control over their cell size. In the case of diatoms, abundant eukaryotic microalgae, the layout of the rigid silica cell wall imposes geometrical restrictions on cell size. A generally accepted theory states that the need to fit any new silica element into a previously formed structure causes a reduction in size with each vegetative division cycle, until cell size restoration is achieved by a switch to another life-cycle stage. Nevertheless, several reported exceptions cast doubt on the generality of this theory.Here, we monitored clonal cultures of the diatomStephanopyxis turrisfor up to two years, recording the sizes of thousands of cells, in order to follow the distribution of cell sizes in the population.Our results show that allS. turriscultures above a certain size threshold undergo a gradual size reduction, in accordance with the postulated geometrical driving force. However, once the cell size reaches a lower threshold, a constant size range is maintained by different cellular strategies.These observations suggest two distinct mechanisms to regulate the cell size of diatoms, reduction and homeostasis. The interplay between these mechanisms can explain the behavior of different diatoms species in various environments.
Micro- to nano-scale investigation of Precambrian metasediments: biogenicity and preservation in the 3.22 Ga Moodies Group (Barberton Greenstone Belt, S. Africa) and the 2.46 Ga Brockman Iron Formation (Hamersley Basin, W. Australia)
Authors: Bellon Hervé , Gieraltowski Jacek , Michaud François , Simon Gaëlle , Cerantola Stéphane , Homann Martin , Foster Ian , Ballet Pascal , Lalonde Stefan V. 
Published: February 2023

AbstractPrecambrian metasediments provide a unique archive for understanding Earth’s earliest biosphere, however traces of microbial life preserved in ancient rocks are often controversial. In this study we leveraged several micro- to nano-scale techniques to study filamentous structures previously reported in clastic sediments of the 3.22 Ga Moodies Group, Barberton Greenstone Belt, S. Africa. We performed petrographic, mineralogical, electron microprobe, confocal fluorescence and electron microscopy analyses of these structures in order to evaluate their biogenicity and syngenecity. We also examined drill core samples of deep-water iron formations from the 2.46 Ga Joffre member of the Brockman Iron Formation (Hamersley Basin, W. Australia) to better understand their potential biogenicity. In both cases, we aimed to resolve primary vs. secondary mineral assemblages and their relation to filamentous or sedimentary structures. In the Moodies Group samples, filamentous structures were resolved by confocal imaging and revealed to be crosscut by later metamorphic phases, highlighting their syngenetic nature. Three-dimensional imaging reveals that while the filamentous structures are not necessarily associated with grain boundaries (e.g., as organic coatings), they form both sheets and filaments, complicating their interpretation but not ruling out a biological origin. No organic microstructures appeared to be preserved in our Dales Gorge samples. We also examined the possible application of electron paramagnetic resonance spectroscopy (EPR) to carbonaceous matter in ancient silica-rich matrices, similar to Bourbin et al. (2013), using samples from the Brockman iron formation. While resonance associated with organic matter was largely unresolvable in the Brockman iron formation samples due to their low organic matter contents, large effects on the EPR spectra were apparent stemming from the presence of magnetic iron minerals, highlighting the need to carefully consider sample composition in EPR analyses targeting ancient organic matter. Collectively, this study highlights the added value of micro- to nano-scale techniques as applied to Precambrian metasediments containing traces of ancient life, for example in revealing the pre-metamorphic emplacement and three-dimensional structure of filaments in the Moodies Group, but also the potential drawbacks and pitfalls, such as the case of strong magnetic mineral interference in EPR analysis of organic matter in trace abundance in the Dales Gorge.
Ev-OSMOSE: An eco-genetic marine ecosystem model
Authors: Morell Alaia , Shin Yunne-Jai , Barrier Nicolas , Travers-Trolet Morgane , Ernande Bruno 
Published: February 2023

ABSTRACTIn the last decade, marine ecosystem models have been increasingly used to project interspecific biodiversity under various global change and management scenarios, considering ecological dynamics only. However, fish populations may also adapt to climate and fishing pressures, via evolutionary changes, leading to modifications in their life-history that could either mitigate or worsen, or even make irreversible, the impacts of these pressures. Building on the multispecies individual-based model Bioen-OSMOSE, an eco-evolutionary fish community model, Ev-Osmose, has been developed to account for evolutionary dynamics together with physiological and ecological dynamics in fish diversity projections. A gametic inheritance module describing the individuals’ genetic structure has been implemented. The genetic structure is defined by finite numbers of loci and alleles per locus that determine the genetic variability of growth, maturation and reproductive effort. Climate change and fishing activities will generate selection pressures on fish life-history traits that will respond through microevolution. This paper is an overview of the Ev-OSMOSE model. To illustrate the ability of the Ev-OSMOSE model to represent realistic fish community dynamics, genotypic and phenotypic traits’ mean and variance and consistent evolutionary patterns, we applied the model to the North Sea ecosystem. The simulated outputs are confronted to observed data of commercial catch, maturity ogives and length at age and to estimates of biomass for each modeled species. In addition to the evaluation of their mean value, the emerging traits’ variability is confronted to length-at-age and maturity data. To ensure the consistency of genetic inheritance and the resulting evolutionary patterns, we assessed the transmission of traits’ genotypic value across cohorts. Overall, the state of the modelled ecosystem was convincing at all these different biological levels. These results open perspectives for using Ev-OSMOSE in different marine regions to project the eco-evolutionary impact of various global change and management scenarios on different biological levels.
Regional assessment of male murine bone exposes spatial heterogeneity in osteocyte lacunar volume associated with intracortical canals and regulation by VEGF
Authors: Trend Jacob , Sharma Alisha , Michels Lysanne , Goggin Patricia , Schneider Philipp , Deinhardt Katrin , Clarkin Claire E 
Published: February 2023

AbstractThe porous bone cortex comprises an interconnected network of intracortical vascular canals and osteocyte lacunae, embedded within the bone mineral. Increases in cortical porosity reduce bone strength and increase fracture risk. To date, our understanding of mechanisms coupling the arrangements of the vascular: lacunar network in the bone cortex is poorly understood yet it could be key in establishing regulation of cortical porosity evident with age. Using synchrotron radiation-based computed tomography we develop automated tools to characterise the 3D spatial organisation and morphology of osteocyte lacunae, and the bone vasculature at the tibiofibular junction (TFJ), defining posterior, medial, lateral, and anterior regions in male C57BL/6 mice (n = 3). We also investigate the role of osteoblast-derived VEGF in regulating the 3D spatial arrangement by conditional disruption of VEGF in osteocalcin-expressing cells (OcnVEGFKO versus WT, n = 3). Regional lacunar phenotypes were assessed by 3D distance mapping of lacunar organisation surrounding the vascular compartments, including endosteal and periosteal surfaces, or intracortical canals. Surface-associated lacunae were indistinct in size across posterior, medial, lateral and anterior regions. However, lacunae associated with intracortical canals were significantly larger exclusively within the posterior region. In the absence of VEGF, the increased lacunar volume associated with posterior intracortical canals was lost. Our results suggest that the influence of intracortical canals on lacunar volumes is spatially regulated and sensitive to locally produced growth factors such as osteoblast-derived VEGF.
Shear-Mediated Platelet Microparticles Demonstrate Phenotypic Heterogeneity as to Morphology, Receptor Distribution, and Hemostatic Function
Authors: Roka-Moiia Yana , Ammann Kaitlyn , Miller-Gutierrez Samuel , Sheriff Jawaad , Bluestein Danny , Italiano Joseph E. , Flaumenhaft Robert C. , Slepian Marvin J. 
Published: February 2023

ABSTRACTObjectiveImplantable cardiovascular therapeutic devices (CTD) including stents, percutaneous heart valves and ventricular assist devices, while lifesaving, impart supraphysiologic shear stress to platelets resulting in thrombotic and bleeding device-related coagulopathy. We previously demonstrated that shear-mediated platelet dysfunction is associated with downregulation of platelet GPIb-IX-V and αIIbβ3 receptors via generation of platelet-derived microparticles (PDMPs). Here, we test the hypothesis that shear-generated PDMPs manifest phenotypical heterogeneity of their morphology and surface expression of platelet receptors, and modulate platelet hemostatic function.Approach and ResultsHuman gel-filtered platelets were exposed to continuous shear stress and sonication. Alterations of platelet morphology were visualized using transmission electron microscopy. Surface expression of platelet receptors and PDMP generation were quantified by flow cytometry. Thrombin generation was quantified spectrophotometrically, and platelet aggregation in plasma was measured by optical aggregometry. We demonstrate that platelet exposure to shear stress promotes notable alterations in platelet morphology and ejection of several distinctive types of PDMPs. Shear-mediated microvesiculation is associated with the differential remodeling of platelet receptors with PDMPs expressing significantly higher levels of both adhesion (αIIbβ3, GPIX, PECAM-1, P-selectin, and PSGL-1) and agonist-evoked receptors (P2Y12& PAR1). Shear-mediated PDMPs have a bidirectional effect on platelet hemostatic function, promoting thrombin generation and inhibiting platelet aggregation induced by collagen and ADP.ConclusionsShear-generated PDMPs demonstrate phenotypic heterogeneity as to morphologic features and defined patterns of surface receptor alteration, and impose a bidirectional effect on platelet hemostatic function. PDMP heterogeneity suggests that a range of mechanisms are operative in the microvesiculation process, contributing to CTD coagulopathy and posing opportunities for therapeutic manipulation.
A review on developing optimization techniques in civil engineering
Authors: Zaheer Qasim , Manzoor Mir Majaid , Ahamad Muhammad Jawad 
Published: February 2023

PurposeThe purpose of this article is to analyze the optimization process in depth, elaborating on the components of the entire process and the techniques used. Researchers have been drawn to the expanding trend of optimization since the turn of the century. The rate of research can be used to measure the progress and increase of this optimization procedure. This study is phenomenal to understand the optimization process and different algorithms in addition to their application by keeping in mind the current computational power that has increased the implementation for several engineering applications.Design/methodology/approachTwo-dimensional analysis has been carried out for the optimization process and its approaches to addressing optimization problems, i.e. computational power has increased the implementation. The first section focuses on a thorough examination of the optimization process, its objectives and the development of processes. Second, techniques of the optimization process have been evaluated, as well as some new ones that have emerged to overcome the above-mentioned problems.FindingsThis paper provided detailed knowledge of optimization, several approaches and their applications in civil engineering, i.e. structural, geotechnical, hydraulic, transportation and many more. This research provided tremendous emerging techniques, where the lack of exploratory studies is to be approached soon.Originality/valueOptimization processes have been studied for a very long time, in engineering, but the current computational power has increased the implementation for several engineering applications. Besides that, different techniques and their prediction modes often require high computational strength, such parameters can be mitigated with the use of different techniques to reduce computational cost and increase accuracy.
Key influence factors on the evacuation route selection for fire emergencies in urban underground complexes
Authors: Li Xiaojuan , Chang Ching-Ter , Zhu Yue-Yue , Li Lu-Lu 
Published: February 2023

PurposeThe development of urban underground complexes (UUCs) has great positive significance for improving urban safety. Therefore, it is necessary to identify the key factors of the people's behavior of evacuation route selection (BERS) for fire emergencies and UUCs’ development. This study aims to find out the factors affecting people's BERS in the evacuation process of UUCs.Design/methodology/approachThis study aims to find out the factors affecting people's BERS in the evacuation process of UUCs. To achieve this goal, the authors conducted a field experiment in F City. Furthermore, the people's BERS are obtained by using a structural equation model and compared with the field test results.FindingsThe authors found that the key factors for people's BERS are lighting conditions, route distance, flow direction guidance and indication. The results of this study contribute to the safety field by providing key factors for fire emergencies. It can also be used to improve fire safety management, evacuation strategies and assist in the development of intelligent evacuation systems.Originality/valueThe results of this study contribute to the safety field by providing key factors for fire emergencies. It can also be used to improve fire safety management, evacuation strategies and assist in the development of intelligent evacuation systems.
Energy analysis at the interface of piezo/thermoelastic half spaces
Authors: Gupta Vipin , Kumar Rajesh , Kumar Rajneesh , Barak M.S. 
Published: February 2023

Purpose
This paper aims to study the energy ratios of plane waves on an interface of nonlocal thermoelastic halfspace (NTS) and nonlocal orthotropic piezothermoelastic half-space (NOPS).

Design/methodology/approach
The memory-dependent derivatives (MDDs) approach with a hyperbolic two-temperature (HTT), three-phase lag theory is used here to study how the energy ratios change at the interface with the angle of incidence.

Findings
Plane waves that travel through NTS and hit the interface as a longitudinal wave, a thermal wave, or a transversal wave send four waves into the NOPS medium and three waves back into the NTS medium. The amplitude ratios of the different waves that are reflected and transmitted are used to calculate the energy ratios of the waves. It is observed that these ratios are affected by the HTT, nonlocal and MDD parameters.

Research limitations/implications
The energy ratios correspond to four distinct models; nonlocal HTT with memory, nonlocal HTT without memory, local HTT with memory and nonlocal classical-two-temperature with memory concerning the angle of incidence from 0 degree to 90 degree.

Practical implications
This model applies to several fields, including earthquake engineering, soil dynamics, high-energy particle physics, nuclear fusion, aeronautics and other fields where nonlocality, MDD and conductive temperature play an important role.

Originality/value
The authors produced the submitted document entirely on their initiative, with equal contributions from all of them.