bluuebunny/crossref_metadata_2025_split huggingface dataset:
ForestForward: visualizing and accessing integrated world forest data from the last fifty years
Authors: Tejada-Gutierrez Eva Luz , Mateo-Fornés Jordi , Solsona Francesc , Alves Rui 
Published: December 2024

AbstractDATABASE URL:https://forestforward.udl.catMitigating the effects of environmental exploitation on forests requires robust data analysis tools to inform sustainable management strategies and enhance ecosystem resilience. Access to extensive, integrated plant biodiversity data, spanning decades, is essential for this purpose. However, such data is often fragmented across diverse datasets with varying standards, posing two key challenges: first, integrating these datasets into a unified, well-structured data warehouse, and second, handling the vast volume of data using big data technologies to analyze and monitor the temporal evolution of ecosystems. To address these challenges, we developed and used an ETL (Extract, Transform, Load) protocol that curated and integrates 4,482 forestry datasets from around the world, dating back to the 18th century, into a 100GB data warehouse containing over 172 million records sourced from the GBIF (Global Biodiversity Information Facility) repository. We implemented Python scripts and a NoSQL MongoDB database to streamline and automate the ETL process, using the data warehouse to create the ForestForward web platform. ForestForward is a free, user-friendly application developed using the Django framework, which enables users to consult, download, and visualize the curated data. The platform allows users to explore data layers by year and observe the temporal evolution of ecosystems through visual representations.
Sense of control buffers against stress
Authors: Fielder Jennifer C. , Shi Jinyu , McGlade Daniel , Huys Quentin J.M. , Steinbeis Nikolaus 
Published: December 2024

AbstractStress is one of the most pervasive causes of mental ill-health across the lifespan. Subjective dimensions of stress perception, such as perceived control, are especially potent in shaping stress responses. While the impact of reduced or no control over stress is well understood, much less is known about whether heightened feelings of control buffer against the negative impact of later stress. We designed a novel paradigm with excellent psychometric properties to sensitively capture and induce different states of subjective control. Across two studies with a total of 768 neurotypical adults, we show a robust association between sense of control and stress as well as symptoms of mental ill-health. More importantly, in a subsample of 295 participants we show that compared to a neutral control group, inducing a heightened state of subjective control buffers against the impact of later stress. These findings demonstrate a causal role for a heightened sense of control in mitigating the negative impact of stressful experiences and spell out important directions for future preventative interventions.
The interplay between executive functions and updating predictive representations
Authors: Pedraza Felipe , Vékony Teodóra , Farkas Bence C. , Haesebaert Frederic , Phelipon Romane , Mihalecz Imola , Janacsek Karolina , Tillmann Barbara , Anders Royce , Plancher Gaën , Nemeth Dezso 
Published: December 2024

AbstractModifying habits, particularly unwanted behaviors, is often challenging. Cognitive research has focused on understanding the mechanisms underlying habit formation and how habits can be rewired. A key mechanism is statistical learning, the continuous, implicit extraction of probabilistic patterns from the environment, which forms the basis of predictive processing. However, the interplay between executive functions (EF) and the rewiring – or updating – of these probabilistic representations remains largely unexplored. To address this gap, we conducted an experiment consisting of four sessions: 1) Learning Phase – acquisition of probabilistic representations, 2) Rewiring Phase – updating these probabilistic representations, 3) Retrieval Phase – accessing learned representations, and 4) EF assessment, targeting five key aspects: attentional control, inhibition, working memory, flexibility, and verbal fluency. We focused on the relationship between these EF measures and the updating of previously acquired knowledge using an interindividual differences approach. Our results revealed a positive relationship between rewiring and inhibition, suggesting that better inhibitory control may facilitate the adaptive restructuring of probabilistic predictive representations. Conversely, a negative relationship was identified between rewiring and semantic fluency, implying that certain underlying aspects of verbal fluency tasks, such as access to long-term memory representations, may hinder the updating process. We interpret this relationship through the lens of competitive memory network models. Our findings indicate that the rewiring of implicit probabilistic representations is a multifaceted cognitive process requiring both the suppression of proactive interference from prior knowledge through cognitive inhibition and a strong reliance on model-free functioning.
Experimental BTV-3 and BTV-8 infection ofCulicoides sonorensisbiting midges
Authors: Zeiske Sophie , Sick Franziska , Kampen Helge , Hoffmann Bernd , Beer Martin , Wernike Kerstin 
Published: December 2024

AbstractBTV-3 emerged in the Netherlands in 2023 and spread rapidly to neighboring countries. Compared to the BTV-8 outbreak in 2006, the course of the BTV-3 epizootic is more severe. Experimental infection of laboratory-rearedCulicoides sonorensismidges showed a slightly higher replication rate of BTV-3 than of BTV-8.One sentence summary lineWe experimentally infected laboratory-rearedCulicoides sonorensisbiting midges with bluetongue virus (BTV) serotypes 3 and 8 using virus-containing blood meal and found slightly higher replication rates of BTV-3.
Investigating the quaternary structure of a homomultimeric catechol 1,2-dioxygenase: An integrative structural biology study
Authors: Almeida-Juarez Arisbeth Guadalupe , Chodankar Shirish , Pardo-López Liliana , Zavala-Padilla Guadalupe , Rudiño-Piñera Enrique 
Published: December 2024

AbstractThe structural analysis of catechol 1,2 dioxygenase fromStutzerimonas frequensGOM2, SfC12DO, was conducted using various structural techniques. SEC-SAXS experiments revealed that SfC12DO, after lyophilization and reconstitution processes, can form multiple enzymatically active oligomers, including dimers, tetramers, and octamers. These findings differ from previous studies, which reported active dimers in homologous counterparts with available crystallographic structures, or trimers observed exclusively in solution for SfsC12DO and its homologous isoA C12DO fromAcinetobacter radioresistensunder low ionic strength conditions. In some cases, tetramers were also reported, such as for theRodococcus erythropolisC12DO. The combined results of Small-Angle X-ray Scattering, Dynamic Light Scattering, and Transmission Electron Microscopy experiments provided additional insights into these active oligomers’ shape and molecular organization in an aqueous solution. These results highlight the oligomeric structural plasticity of SfC12DO, proving that it can exist in different oligomeric forms depending on the physicochemical characteristics of the solutions in which the experiments were performed. Remarkably, regardless of its oligomeric state, SfC12DO maintains its enzymatic activity even after prior lyophilization. All these characteristics make SfC12DO a very promising candidate for extensive bioremediation applications in polluted soils or waters.
The Impact of Instrumental Music on Dual-task Interference in a Simulated Driving Environment
Authors: Khadiv Elahe , Sahlabadi Ali Salehi , Hashemirad Reza , Namdari Mahshid , Abbaszadeh Mojtaba 
Published: December 2024

AbstractNumerous drivers engage in both listening to music and undertaking secondary tasks while driving. Secondary tasks have been shown to have a negative impact on driving performance. However, the effect of music on driving performance can vary, either improving or impairing it. Nevertheless, the influence of background music on dual-task interference remains uncertain. In this study, we aimed to investigate the impact of instrumental background music on dual-task performance within a simulated driving environment. Twenty-four participants performed a color-discrimination task followed by a driving lane-change task. The results indicated that music enhanced accuracy in the lane-change task without a corresponding increase in reaction time (RT), both in single- and dual-task conditions. Additionally, when the time gap between the two tasks was 600 ms, RT for the lane-change task decreased with high music tempo. However, RT for the lane-change task did not exhibit any changes in response to music tempo when the onset time between the two tasks was short (100 ms), as well as in the single-task condition. Notably, participants’ perceived workload did not significantly differ across the various task conditions. These findings emphasize the potential of background music to improve dual-task performance, particularly when considering the temporal gap between tasks.
Mitophagosomes induced during EV-D68 infection promote viral nonlytic release
Authors: Jassey Alagie , Paudel Bimal , Wagner Michael A. , Pollack Noah , Cheng I-Ting , Godoy-Ruiz Raquel , Weber David J. , Jackson William T. 
Published: December 2024

AbstractEnterovirus-D68 (EV-D68) is a plus-strand RNA virus that primarily causes infant respiratory infections. In rare pediatric cases, infection with EV-D68 has been associated with acute flaccid myelitis, a polio-like paralytic disease. We have previously demonstrated that EV-D68 induces nonselective autophagy for its benefit. Here, we demonstrate that EV-D68 induces mitophagy, the specific autophagic degradation of mitochondria. EV-D68 infection induces mitophagosome formation and several hallmarks of mitophagy, including mitochondrial fragmentation, mitochondrial membrane potential loss, and Parkin translocation to the mitochondria were observed in EV-D68 infected cells. The 3C protease of EV-D68 cleaves the mitochondrial fusion protein, mitofusin-2, near the C-terminal HR2 domain to induce mitochondrial fragmentation, and these fragmented mitochondria colocalized with double-stranded RNA (dsRNA), which labels viral RNA replication sites after peak viral RNA replication. Depleting components of mitophagy signaling specifically reduced EV-D68 release without impacting viral intracellular titers. Our results suggest that whereas the machinery of macroautophagy supports various stages of enterovirus replication, including viral genomic RNA replication and capsid maturation, mitophagy is the specific form of autophagy that regulates the nonlytic release of enteroviruses from cells.SignificanceEV-D68 is a respiratory pathogen and a significant cause of acute respiratory illness in infants, against which no prophylactic vaccines or antivirals exist. We have previously shown that EV-D68, like other enteroviruses, triggers and benefits from nonselective autophagy. However, it was unclear whether the virus induces selective autophagy. Here, we demonstrate that EV-D68 infection induces mitophagy and uses mitophagosomes to traffic virions to the surface of cells for nonlytic release. Our findings suggest that mitophagy may constitute the specific form of autophagy that facilitates the autophagosome-mediated nonlytic release of enteroviruses from infected cells and that targeting mitophagy could be an effective strategy to impede EV-D68 nonlytic release.
Seeing speech: neural mechanisms of cued speech perception in prelingually deaf and hearing users
Authors: Sarré Annahita , Cohen Laurent 
Published: December 2024

AbstractFor many deaf people, lip-reading plays a major role in verbal communication. However, lip movements are by nature ambiguous, so that lip reading does not allow for a full understanding of speech. The resulting language access difficulties may have serious consequences on language, cognitive and social development. Cued speech (CS) was developed to eliminate this ambiguity by complementing lip-reading with hand gestures, giving access to the entire phonological content of speech through the visual modality alone. Despite its proven efficiency for improving linguistic and communicative abilities, the mechanisms of CS perception remain largely unknown. The goal of the present study is to delineate the brain regions involved in cued speech perception and identify their role in visual and language-related processes.Three matched groups of participants were scanned during two fMRI experiments: Prelingually deaf users of cued speech, hearing users of cued speech, and naive hearing controls. In Experiment 1, we presented videos of silent CS sentences, isolated lip movements, isolated gestures, plus CS sentences with speech sounds and meaningless CS sentences. In Experiment 2, we presented pictures of faces, bodies, written words, tools, and houses in order to understand the contribution of category-specific visual regions to CS perception.We delineated a number of mostly left-hemisphere brain regions involved in CS perception. We first found that language areas were activated in all groups by both silent CS sentences and isolated lip movements, and by gestures in deaf participants only. Despite overlapping activations when perceiving CS, several findings differentiated experts from novices. As such, CS expertise was associated with a leftward functional lateralization of the lateral occipital cortex, possibly driven by the expert identification of hand gestures. The Visual Word Form Area, which supports the interface between vision and language during reading, did not contribute to CS perception. Moreover, the integration of lip movements and gestures took place in a temporal language-related region in deaf users, and in movement-related regions in hearing users, reflecting their different profile of expertise in CS comprehension and production. Finally, we observed a strong involvement of the Dorsal Attentional Network in hearing users of CS, and identified the neural correlates of the variability in individual proficiency.Cued speech constitutes a novel pathway for accessing core language processes, halfway between speech perception and reading. The current study provides a delineation of the common and specific brain structures supporting those different modalities of language input, paving the way for further research.
Drip irrigation suppresses methane emissions by reshaping the rhizosphere microbiomes in rice
Authors: Lau Kenny J.X. , Ma Ali , Chen Bin , Shibu Thankaraj Salammal Maria , Ramachandran Srinivasan , Naqvi Naweed I. 
Published: December 2024

ABSTRACTThe rhizosphere microbiomes of rice plants consist of a complex consortium of methanogens, methanotrophs, nitrogen- and/or sulphur-assimilating microorganisms. Controlled irrigation has been purported to be the cultivation method of choice over continuous flooding as it reduces water usage and aerates the soil to minimize the emission of the potent greenhouse gases. However, a systemic understanding of the assembly and function of microbiota in the rhizosphere under drip and flood irrigation remains unclear. Here, we report a significant reduction in methane emissions in drip irrigation compared to flooded paddies. Genotypic or varietal differences did not influence such increased methane emissions from flooded soil cultivation of rice. Using metagenomic sequencing and computational analyses, we provide a deeper understanding of how drip irrigation or continuous flooding affect the root-associated microbiomes in rice. Rhizosphere soil from two different rice varieties, Huanghuazhan and Temasek rice, grown under drip or flood conditions in a greenhouse was collected 2 months post-transplantation for metagenomic analysis. Our results reveal that drip irrigation favours microbes involved in the nitrifying-denitrifying processes while continuous flooding enriches for methanotrophs and methanogenic archaea. Syntrophic microbial clusters associated with methanogenesis were significantly reduced in drip irrigation. We identified several keystone taxa in the co-occurrence network models related to methanogenic and methanotrophic activities, as well as beneficial microbes from the soil rhizosphere, andActinomycetesfrom floodwater. Lastly, oxygen availability and redox potential were identified as key drivers that reshape rhizosphere microbiota leading to the functional differences observed between the two irrigation regimes.
Heterogeneous, temporally consistent, and plastic brain development after preterm birth
Authors: Thalhammer Melissa , Seidlitz Jakob , Neubauer Antonia , Menegaux Aurore , Schmitz-Koep Benita , Di Biase Maria A. , Schulz Julia , Dorfschmidt Lena , Bethlehem Richard A. I. , Alexander-Bloch Aaron , Adamson Chris , Ball Gareth , Zimmer Claus , Daamen Marcel , Boecker Henning , Bartmann Peter , Wolke Dieter , Hedderich Dennis M. , Sorg Christian 
Published: December 2024

AbstractThe current view of neurodevelopment after preterm birth presents a strong paradox: diverse neurocognitive outcomes suggest heterogeneous neurodevelopment, yet numerous brain imaging studies focusing on average dysmaturation imply largely uniform aberrations across individuals1. Here we show both, spatially heterogeneous individual brain abnormality patterns (IBAPs) but with consistent underlying biological mechanisms of injury and plasticity. Using cross-sectional structural magnetic resonance imaging data from preterm neonates and longitudinal data from preterm children and adults in a normative reference framework2, we demonstrate that brain development after preterm birth is highly heterogeneous in both severity and patterns of deviations. Individual brain abnormalities were also consistent for their extent and location along the life course, associated with glial cell underpinnings, and plastic for influences of the early social environment. Thus, IBAPs of preterm birth are spatially heterogenous, temporally consistent for extent, spatial location, and cellular underpinnings, and plastic for social-environmental impacts. Our findings extend conventional views of preterm neurodevelopment, revealing a nuanced landscape of individual variation, with consistent commonalities between subjects. This integrated perspective of preterm neurodevelopment implies more targeted theranostic intervention strategies, specifically integrating brain charts2and imaging at birth, as well as social interventions during early development3.
Assessing target genes for homing suppression gene drive
Authors: Xu Xuejiao , Fang Jialing , Chen Jingheng , Yang Jie , Yang Xiaozhen , Hou Shibo , Sun Weitang , Champer Jackson 
Published: December 2024

AbstractGene drives are engineered alleles that bias their own inheritance in offspring, enabling the spread of specific traits throughout a population. Targeting female fertility genes in a gene drive can be an efficient strategy for population suppression. In this study, we investigated nine female fertility genes inDrosophila melanogasterusing CRISPR-based homing gene drives. Employing a multiplexed gRNA approach to prevent formation of functional resistance alleles, we aimed to maintain high drive conversion efficiency with low fitness costs in female drive carriers. Drive efficiency was assessed in individual crosses and had varied performance across different target genes. Notably, drives targeting theoctopamine β2 receptor(oct) andstall(stl) genes exhibited the highest drive conversion rates and were further tested in cages. A drive targetingstlsuccessfully suppressed a cage population with a high release frequency, though suppression failed in another replicate cage with lower initial release frequency. Fitness costs in female drive carriers were observed in test cages, impacting the overall efficiency of population suppression. Further tests on the fertility of these lines using individual crosses indicated that some fitness costs were possibly due to the maternal deposition of Cas9 combined with new gRNA expression, which would only occur in progeny of drive males when testing split drives with separate Cas9 (when mimicking cages with complete drives) but not for complete drive systems. This could enable success in complete drives with higher maternal Cas9 deposition, even if cage experiments in split drives fail. Our findings underscore the potential and challenges of assessing gene drives for population control, providing valuable insights for optimizing and testing suppression gene drive designs.
RNA-mediated MYC multimerization suppresses innate immune signaling
Authors: Uhl Leonie , Aziba Amel , Löbbert Sinah , Russell Timothy , Kannan Toshitha , Valanju Omkar R. , Schülein-Völk Christina , de Martines Tim , Montesinos Francisco , Bolz Michael , Cossa Giacomo , Endres Theresa , Solvie Daniel , Krenz Bastian , Maric Hans M. , Papadopoulos Dimitrios , Vos Seychelle M. , Eilers Martin 
Published: December 2024

AbstractIn response to perturbed transcription elongation, the MYC oncoprotein multimerizes and undergoes a phase transition; the underlying mechanisms and their function are unknown. Here, we show that MYC re-localizes from its canonical location on DNA to RNA in response to the accumulation of intronic RNA. MYC binds RNA directly, which enhances its multimerization. MYC multimers concentrate the nuclear exosome, a 3’-5’ RNA exonuclease, and its targeting complexes around double-stranded RNA and R-loops, and promote exosome recruitment to R-loops. RNA binding of MYC suppresses activation of the innate immune kinase TBK1. Upon MYC depletion, intron-derived dsRNAs, including RNA derived from repetitive elements and small nucleolar RNAs, accumulate on TLR3, a pattern recognition receptor that activates TBK1. In MYC-depleted cells, TLR3-bound snoRNAs carry aberrant 3’-ends, indicating defective exosomal processing. Our data show that the phase transition of MYC is a RNA-driven stress response that suppresses the accumulation of immunogenic RNAs.
Disruption of LEDGF/p75-directed integration derepresses antisense transcription of the HIV-1 genome
Authors: Tedbury Philip R. , Mahboubi Darius , Puray-Chavez Maritza , Shah Raven , Ukah Obiaara B. , Wahoski Claudia C. , Fadel Hind J. , Poeschla Eric M. , Gao Xinlin , McFadden William M. , Gaitanidou Maria , Kesesidis Nikolaos , Kirby Karen A. , Vanderford Thomas H. , Kvaratskhelia Mamuka , Achuthan Vasudevan , Behrens Ryan T. , Engelman Alan N. , Sarafianos Stefan G. 
Published: December 2024

AbstractDisruption of HIV-1 Integrase (IN) interactions with the host-factor Lens Epithelium-Derived Growth Factor (LEDGF)/p75 leads to decreased, random integration, increased latent infection, and described here, accumulation of HIV-1 antisense RNA (asRNA). asRNA increase was observed following interruptions of IN-LEDGF/p75 interactions either through pharmacologic perturbations of IN-LEDGF/p75 by treatment with allosteric HIV-1 integrase inhibitors (ALLINIs) or in cell lines with LEDGF genetic knockout. Additionally, by impairing Tat-dependent HIV transcription, asRNA abundance markedly increases. Illumina sequencing characterization of asRNA transcripts in primary T cells infected in the presence of ALLINIs showed that most initiate from within the HIV-1. Overall, loss of IN-LEDGF/p75 interactions increase asRNA abundance. Understanding the relationship between ALLINIs, integration sites, asRNA, and latency could aid in future therapeutic strategies.