bluuebunny/crossref_metadata_2025_split huggingface dataset:
Circadian oscillation of perireceptor events influence olfactory sensitivity in diurnal and nocturnal mosquitoes
Authors: De Tanwee Das , Pelletier Julien , Gupta Satyajeet , Kona Madhavinadha Prasad , Singh Om P. , Dixit Rajnikant , Ignell Rickard , Karmodiya Krishanpal 
Published: October 2023

AbstractOlfaction and circadian rhythm gate different behaviors in mosquitoes that are important for their capacity to transmit disease. However, the mechanisms of odor detection, and the circadian-guided changes in olfactory sensitivity across different mosquito species, remain largely unexplored. To this end, we performed a circadian-dependent RNA-sequencing study of the peripheral olfactory- and brain tissues of femaleAnopheles culicifaciesandAedes aegyptimosquitoes. Data analysis revealed a significant upregulation of genes encoding: (a) odorant binding proteins (OBPs), required for transportation of odorant molecules towards the olfactory receptors, and (b) xenobiotic-metabolizing enzymes (XMEs) during the day time inAedes aegyptiand during the dusk-transition phase inAnopheles culicifacies. While XMEs primarily function in the elimination of toxic xenobiotics, concurrent elevation of XMEs and OBPs are hypothesized to act cumulatively to regulate perireceptor events and odorant sensitivity. Electroantennographic analysis with bothAnopheles gambiaeandAedes aegyptiagainst diverse behaviorally relevant odorants, combined with XMEs inhibitors and RNA interference, establish the proof-of-concept that XMEs function in perireceptor events during odorant detection and influence the odorant sensitivity in mosquitoes. Additionally, the RNA-sequencing and RNAi-mediated knockdown data revealed that daily temporal modulation of neuronal serine proteases may facilitate the consolidation of the brain function, and influence the odor detection process in both diurnal and nocturnal mosquitoes. These findings provide the impetus to further explore the species-specific rhythmic expression pattern of the neuro-olfactory encoded molecular factors, which could pave the way to develop and implement successful mosquito control methods.Graphical AbstractHighlightsCircadian oscillation of perireceptor proteins possibly influences time-of-day dependent change olfactory sensitivity in diurnal and nocturnal mosquitoesDiurnal and nocturnal mosquitoes depict distinct dynamic change in perireceptor proteinsInhibition of cytochrome P450 gene minimizes antennal response to different odorantsNeuronal serine protease may consolidate brain function and odor detection
ThepanC-encoded pantothenate synthetase to tackle carbapenem-resistant OprDPseudomonas aeruginosamutant revealed through Tn-Seq
Authors: Van Maele Cléophée , Caboche Ségolène , Moutel Marin , Bonnomet Arnaud , Moussalih Sophie , Luczka Emilie , Jacquier Hervé , Muggeo Anaëlle , Guillard Thomas 
Published: October 2023

AbstractFor the World Health Organization, carbapenem-resistantPseudomonas aeruginosa is a critical priority for which new antimicrobial drugs are needed. Consequently, understanding the underlying mechanisms of resistant bacteria infection will enable the identification of new therapeutic targets. Loss of the OprD porin is the main determinant of resistance to the last resort carbapenem antibiotics and has been described to enhance fitnessin vivoand virulence. Transposon sequencing is a high-throughput sequencing technique that makes it possible to identify essential genes (EGs) that may turn out to be therapeutic targets. However, such a strategy has not yet been used for OprD-deficientP. aeruginosa. In this study, we identified the EGs specific to PA14 OprD mutant for LB growth and we established a list of 30 EGs among these, we highlighted thepanCgene encoding pantothenate synthetase as a promising target. Using CRISPRi, we confirmed that silencingpanCreduced LB growth, and decreasedsigXexpression, whose overexpression is associated with membrane fluidity, as well as the expression of genes involved in the fatty acid synthesis (FAS). Taking into account the weakness of PA14 OprD mutant due to an altered membrane consecutive to a decrease in unsaturated FAS in the absence ofpanC,we showed that silencingpanCextended the destruction time of 16HBE airway cells. Overall, our findings highlighted the anti-virulence potential ofpanCinhibition and shed new light on its inhibition as a target for treating carbapenem-resistant OprD-defective PA lung infections.
Diurnal rhythmicity of fecal microbiota and metabolite profiles in the first year of life: a randomized controlled interventional trial with infant formula
Authors: Heppner Nina , Reitmeier Sandra , Heddes Marjolein , Merino Michael Vig , Schwartz Leon , Dietrich Alexander , List Markus , Gigl Michael , Meng Chen , Omer Hélène , Kleigrewe Karin , Schirmer Melanie , van der Veen Daan R , Kiessling Silke , Haller Dirk 
Published: October 2023

SummaryMicrobiota assembly in the infant gut is influenced by time and duration of dietary exposure to breast-milk, infant formula and solid foods. In this randomized controlled intervention study, longitudinal sampling of infant stool (n=998) showed similar development of fecal bacterial communities (16S rRNA/shallow metagenomics sequencing) between formula- and breast-fed infants during the first year of life (N=210). Infant formula supplemented with galacto-oligosaccharides (GOS) was most efficient to sustain high levels of bifidobacteria compared to formula containingB. longumandB. breveor placebo. In addition to primary endpoints, metabolite and bacterial profiling revealed 24-hour oscillations and data integration identified circadian networks. Rhythmicity in bacterial diversity, specific taxa and functional pathways increased with age and was strongest following breast-feeding and GOS-supplementation. Circadian rhythms in dominant taxa were discoveredex-vivoin a chemostat model. Hence, microbiota rhythmicity develops early in life, likely via bacterial intrinsic clock mechanism and is affected by diet.
FVIII interacts with cell surface to regulate endothelial cell functionality
Authors: Olgasi Cristina , Cucci Alessia , Molineris Ivan , Assanelli Simone , Anselmi Francesca , Borsotti Chiara , Sgromo Chiara , Lauria Andrea , Merlin Simone , Walker Gillian , Capasso Paola , Oliviero Salvatore , Follenzi Antonia 
Published: October 2023

AbstractHaemophilia A (HA) is a rare bleeding disorder caused by factor 8 (F8) mutations. Clinical manifestations are spontaneous bleedings that primarily consist of hemarthrosis and intracranial haemorrhages. To date, the impairment of vessel stability in HA patients and the correlation between FVIII and endothelial functionality is poorly understood.Here we show that FVIII plays a role in endothelial cell functionality. Blood Outgrowth endothelial cells (BOECs) knockout generated by CRISPR/Cas9, HA BOECs and HA iPSCs-derived ECs showed alteration of vessel-formation, endothelial cell migration, and vessel permeability. Importantly, the impaired EC phenotype was rescued by treatment with recombinant human FVIII or by lentiviral vector (LV) expressing FVIII. The FVIII function on endothelium was confirmed in vivo in a mouse model of severe HA which showed that an altered angiogenesis and vesselpermeability could be treated by exogenous FVIII. BOECstranscriptomic profiles revealed that FVIIIregulates the expression of endothelial basement membrane and extracellular matrix genes. Furthermore, exogenous expression of Nidogen2, identified as a FVIII regulated gene, restored the extracellular matrix integrity and EC functionality of HA ECs. In conclusion, FVIII is not only a coagulation factor but also an endothelial cell autocrine factor which promotes vessel stability.
A three-node Turing gene circuit forms periodic spatial patterns in bacteria
Authors: Tica J , Oliver Huidobro M , Zhu T , Wachter GKA , Pazuki RH , Tonello E , Siebert H , Stumpf MPH , Endres RG , Isalan M 
Published: October 2023

SummaryTuring patterns1are well-known self-organising systems that can form spots, stripes, or labyrinths. They represent a major theory of patterning in tissue organisation, due to their remarkable similarity to some natural patterns, such as skin pigmentation in zebrafish2, digit spacing3,4, and many others. The involvement of Turing patterns in biology has been debated because of their stringent fine-tuning requirements, where patterns only occur within a small subset of parameters5,6. This has complicated the engineering of a synthetic gene circuit for Turing patterns from first principles, even though natural genetic Turing networks have been successfully identified4,7. Here, we engineered a synthetic genetic reaction-diffusion system where three nodes interact according to a non-classical Turing network with improved parametric robustness6. The system was optimised inE. coliand reproducibly generated stationary, periodic, concentric stripe patterns in growing colonies. The patterns were successfully reproduced with a partial differential equation model, in a parameter regime obtained by fitting to experimental data. Our synthetic Turing system can contribute to novel nanotechnologies, such as patterned biomaterial deposition8,9, and provide insights into developmental patterning programs10.
Neuroinflammation in post-acute sequelae of COVID-19 (PASC) as assessed by [11C]PBR28 PET correlates with vascular disease measures
Authors: VanElzakker Michael B. , Bues Hannah F. , Brusaferri Ludovica , Kim Minhae , Saadi Deena , Ratai Eva-Maria , Dougherty Darin D. , Loggia Marco L. 
Published: October 2023

ABSTRACTThe COVID-19 pandemic caused by SARS-CoV-2 has triggered a consequential public health crisis of post-acute sequelae of COVID-19 (PASC), sometimes referred to as long COVID. The mechanisms of the heterogeneous persistent symptoms and signs that comprise PASC are under investigation, and several studies have pointed to the central nervous and vascular systems as being potential sites of dysfunction. In the current study, we recruited individuals with PASC with diverse symptoms, and examined the relationship between neuroinflammation and circulating markers of vascular dysfunction. We used [11C]PBR28 PET neuroimaging, a marker of neuroinflammation, to compare 12 PASC individuals versus 43 normative healthy controls. We found significantly increased neuroinflammation in PASC versus controls across a wide swath of brain regions including midcingulate and anterior cingulate cortex, corpus callosum, thalamus, basal ganglia, and at the boundaries of ventricles. We also collected and analyzed peripheral blood plasma from the PASC individuals and found significant positive correlations between neuroinflammation and several circulating analytes related to vascular dysfunction. These results suggest that an interaction between neuroinflammation and vascular health may contribute to common symptoms of PASC.
Trait Reward Sensitivity Modulates Connectivity with the Temporoparietal Junction and Anterior Insula during Strategic Decision Making
Authors: Sazhin Daniel , Wyngaarden James B. , Dennison Jeff B. , Zaff Ori , Fareri Dominic , McCloskey Michael S. , Alloy Lauren B. , Jarcho Johanna M. , Smith David V. 
Published: October 2023

AbstractMany decisions happen in social contexts such as negotiations, yet little is understood about how people balance fairness versus selfishness. Past investigations found that activation in brain areas involved in executive function and reward processing was associated with people offering less with no threat of rejection from their partner, compared to offering more when there was a threat of rejection. However, it remains unclear how trait reward sensitivity may modulate activation and connectivity patterns in these situations. To address this gap, we used task-based fMRI to examine the relation between reward sensitivity and the neural correlates of bargaining choices. Participants (N = 54) completed the Sensitivity to Punishment (SP)/Sensitivity to Reward (SR) Questionnaire and the Behavioral Inhibition System/Behavioral Activation System scales. Participants performed the Ultimatum and Dictator Games as proposers and exhibited strategic decisions by being fair when there was a threat of rejection, but being selfish when there was not a threat of rejection. We found that strategic decisions evoked activation in the Inferior Frontal Gyrus (IFG) and the Anterior Insula (AI). Next, we found elevated IFG connectivity with the Temporoparietal junction (TPJ) during strategic decisions. Finally, we explored whether trait reward sensitivity modulated brain responses while making strategic decisions. We found that people who scored lower in reward sensitivity made less strategic choices when they exhibited higher AI-Angular Gyrus connectivity. Taken together, our results demonstrate how trait reward sensitivity modulates neural responses to strategic decisions, potentially underscoring the importance of this factor within social and decision neuroscience.
A tripartite chemogenetic fluorescent reporter for imaging ternary protein interactions
Authors: Bottone Sara , Broch Fanny , Brion Aurélien , Hajji Lina El , Benaissa Hela , Gautier Arnaud 
Published: October 2023

ABSTRACTMost cellular processes are carried out by multiprotein assemblies. Although various molecular tools exist to visualize binary protein interactions in live cells, the visualization of multiprotein complexes remains a challenge. Here, we report the engineering of a complementation-based approach allowing one to visualize the interaction of three proteins through effective proximity-induced complementation of three fragments of pFAST, a chemogenetic fluorescent reporter that binds and stabilizes the fluorescent state of fluorogenic chromophores (so-called fluorogens). This tripartite-split-pFAST allowed the observation of dynamic ternary protein interactions in the cytosol, at the plasma membrane and at the junction of multiple organelles, opening great prospects to study the role and function of multiprotein complexes in live cells and in various biologically relevant contexts.
Tumor-wide RNA splicing aberrations generate immunogenic public neoantigens
Authors: Kwok Darwin W. , Stevers Nicholas O. , Nejo Takahide , Chen Lee H. , Etxeberria Inaki , Jung Jangham , Okada Kaori , Cove Maggie Colton , Lakshmanachetty Senthilnath , Gallus Marco , Barpanda Abhilash , Hong Chibo , Chan Gary K.L. , Wu Samuel H. , Ramos Emilio , Yamamichi Akane , Liu Jerry , Watchmaker Payal , Ogino Hirokazu , Saijo Atsuro , Du Aidan , Grishanina Nadia , Woo James , Diaz Aaron , Chang Susan M. , Phillips Joanna J. , Wiita Arun P. , Klebanoff Christopher A. , Costello Joseph F. , Okada Hideho 
Published: October 2023

SummaryT-cell-mediated immunotherapies are limited by the extent to which cancer-specific antigens are homogenously expressed throughout a tumor. We reasoned that recurrent splicing aberrations in cancer represent a potential source of tumor-wide and public neoantigens, and to test this possibility, we developed a novel pipeline for identifying neojunctions expressed uniformly within a tumor across diverse cancer types. Our analyses revealed multiple neojunctions that recur across patients and either exhibited intratumor heterogeneity or, in some cases, were tumor-wide. We identified CD8+ T-cell clones specific for neoantigens derived from tumor-wide and conserved neojunctions inGNASandRPL22, respectively. TCR-engineered CD8+T-cells targeting these mutations conferred neoantigen-specific tumor cell eradication. Furthermore, we revealed that cancer-specific dysregulation in splicing factor expression leads to recurrent neojunction expression. Together, these data reveal that a subset of neojunctions are both intratumorally conserved and public, providing the molecular basis for novel T-cell-based immunotherapies that address intratumoral heterogeneity.
TBK1 is ubiquitinated by TRIM5α to assemble mitophagy machinery
Authors: Saha Bhaskar , Olsvik Hallvard , Williams Geneva L , Oh Seeun , Evjen Gry , Sjøttem Eva , Mandell Michael A 
Published: October 2023

SUMMARYUbiquitination of mitochondrial proteins provides a basis for the downstream recruitment of mitophagy machinery, yet whether ubiquitination of the machinery itself contributes to mitophagy is unknown. Here, we show that K63-linked polyubiquitination of the key mitophagy regulator TBK1 is essential for its mitophagy functions. This modification is catalyzed by the ubiquitin ligase TRIM5α. Mitochondrial damage triggers TRIM5α’s auto-ubiquitination and its interaction with ubiquitin-binding autophagy adaptors including NDP52, optineurin, and NBR1. Autophagy adaptors, along with TRIM27, enable TRIM5α to engage with TBK1. TRIM5α with intact ubiquitination function is required for the proper accumulation of active TBK1 on damaged mitochondria in Parkin-dependent and Parkin-independent mitophagy pathways. Additionally, we show that TRIM5α can directly recruit autophagy initiation machinery to damaged mitochondria. Our data support a model in which TRIM5α provides a self-amplifying, mitochondria-localized, ubiquitin-based, assembly platform for TBK1 and mitophagy adaptors that is ultimately required to recruit the core autophagy machinery.
Impact of gene selection criteria on transcriptomic ontology-based point of departure estimates
Authors: Black Michael B. , Efremenko Alina Y. , Rasim Barutcu A. , McMullen Patrick D. 
Published: October 2023

AbstractApical effects are typically associated with changes in gene expression, which allows for the use of short- term in life transcriptomic studies to derive biologically relevant points of departure (POD). These methods offer cost savings over conventional toxicology assessments and can derive data from very short-term studies where apical effects may not yet be present. When there is limited or insufficient data for a conventional POD assessment, a transcriptomic screen could provide valuable data for deriving a cellular bioactivity POD for chemical screening and hazard assessment. We used existing transcriptomic data from published 5-day rat in vivo kidney and liver exposures to examine the effect of differential gene expression metrics for the selection of genes used for ontology pathway-based POD derivation. Williams Trend Test (WTT) indicate no gene expression dose-response in 6 instances and ANOVA in one, while DESeq2 detected differentially expressed genes in all instances. The three statistical metrics produced consistent POD values. One chemical (PFOA in liver) showed ontology enrichment indicative of a cytotoxic response at the highest dose, emphasizing the effect which too high a dose can have on the derivation of POD values if such response is not accounted for. Whether the choice of a gene selection metric combining both a statistical significance criterion as well as a minimum magnitude of change threshold affects the sensitivity of POD values depends on the specifics of the dose- response. Existing alternative and complementary analyses could be utilized with existing analyses pipelines to better inform analytical decisions when using transcriptomics and BMD for point of departure determinations.
Video-Microscopy-Based Automated Trajectory Determination for High-Velocity, Densely Clustered, Indistinguishable Objects Moving in A Directed Force Field
Authors: Tyson Christopher , Gaire Santosh , Pegg Ian , Sarkar Abhijit 
Published: October 2023

AbstractWe present a method for tracking densely clustered, high-velocity, indistinguishable objects being spawned at a high rate and moving in a directed force field using only object centroids as inputs and no other image information. The algorithm places minimal restrictions on the velocities or accelerations of the objects being tracked and uses a methodology based on a scoring function and a back-tracking refinement process. This combination leads to successful tracking of hundreds of particles in challenging environments even when the displacement of the individual objects at successive times approaches the separation between neighboring objects in any one frame. We note that these cases can be particularly difficult to handle by existing methods. The performance of the algorithm is methodically examined by comparison to simulated trajectories which vary the temporal and spatial densities, velocities, and accelerations of the objects in motion, as well as the signal-to-noise ratio. Also, we demonstrate its capability by analyzing data from experiments with superparamagnetic microspheres moving in an inhomogeneous magnetic field in aqueous buffer at room temperature. Our method should be widely applicable since trajectory determination problems are ubiquitous in video microscopy applications in biology, materials science, physics, and engineering.
Knowledge sharing in the era of Covid-19: a bibliometric analysis using scopus and web-of-science (WoS)
Authors: Pandey Jayesh , Majumdarr Shubh , Farooq Rayees , Gupta Santushti , Bose Pallav 
Published: October 2023

PurposeThis study aims to conduct a bibliometric analysis of knowledge sharing during COVID-19 and highlight prominent contributors, diverse trends and themes followed with provisions of future research avenues.Design/methodology/approachThe study through scientific procedures and rationales for systematic literature reviews framework analyses 148 peer-reviewed journal publications and conference proceedings indexed in Scopus and WoS databases from 2020 to 2022. It uses general statistics and diverse bibliometric techniques, including co-occurrence analysis for trend and cluster identification in the literature.FindingsThe findings reveal an exponential annual growth rate of 150% in the domain, highlighting the global research focus. With regards to domain contribution, theJournal of Knowledge Managementand China leads with ten publications in their respective categories. The co-occurrence analysis further highlights four diverse clusters in the domain, which are further discussed in detail. The study highlights significant contributions from developed economies, thus providing scope for future research from developing or transitioning economies in the Middle East, Central Asia or Africa. The study concludes by presenting the elementary role of knowledge sharing in response to external crises.Originality/valueThe interest in the knowledge sharing domain has grown exponentially during the COVID-19 pandemic. This research is the first bibliometric analysis with comprehensive and rigorous analytic techniques to unearth critical developments and insights for a holistic understanding.
Zakat al-mustaghallat for Malaysian landlords of residential properties
Authors: Amin Hanudin , Shaikh Imran Mehboob 
Published: October 2023

Purpose
This study aims to examine the zakat al-mustaghallat acceptance index (ZAMAi) through the examination of its predictors identified in this work, including attitude, social influence, self-efficacy, amount of information and Islamic altruism, at best.

Design/methodology/approach
Drawing from the attitude-social influence-self efficacy model, this study evaluated the effects of these factors on ZAMAi using an empirical investigation surveying 184 respondents who were identified as the owners of residential properties in Malaysia.

Findings
In the core model, this study found significant outcomes for the effects of attitude, social influence, self-efficacy, amount of information and Islamic altruism, along with the demographic items tested. For post hoc analysis, this study found two significant outcomes drawn from the role of attitude as a mediating variable in this study.

Research limitations/implications
The results obtained from this study should be used with caution owing to its limited applicability and the constraints of subjects and variables in the framework developed.

Practical implications
The results obtained can become a yardstick to gauge the success of zakat al-mustaghallat acceptance in Malaysia.

Originality/value
This study introduced new measures of ZAMAi, where Malaysian landlords are brought into play.