bluuebunny/crossref_metadata_2025_split huggingface dataset:
Smoking changes adaptive immunity with persistent effects
Authors: Saint-André Violaine , Charbit Bruno , Biton Anne , Rouilly Vincent , Possémé Céline , Bertrand Anthony , Rotival Maxime , Bergstedt Jacob , Patin Etienne , Albert Matthew L. , Quintana-Murci Lluis , Duffy Darragh ,   The Milieu Intérieur Consortium, Abel Laurent , Alcover Andres , Aschard Hugues , Bousso Philippe , Bourke Nollaig , Brodin Petter , Bruhns Pierre , Cerf-Bensussan Nadine , Cumano Ana , D’Enfert Christophe , Demangel Caroline , Deriano Ludovic , Dillies Marie-Agnès , Santo James Di , Eberl Gérard , Enninga Jost , Fellay Jacques , Gomperts-Boneca Ivo , Hasan Milena , Hedestam Gunilla Karlsson , Hercberg Serge , Ingersoll Molly A. , Lantz Olivier , Kenny Rose Anne , Ménager Mickaël , Michel Frédérique , Mouquet Hugo , O’Farrelly Cliona , Rausell Antonio , Rieux-Laucat Frédéric , Rogge Lars , Fontes Magnus , Sakuntabhai Anavaj , Schwartz Olivier , Schwikowski Benno , Shorte Spencer , Tangy Frédéric , Toubert Antoine , Touvier Mathilde , Ungeheuer Marie-Noëlle , Zimmer Christophe 
Published: February 2024

AbstractIndividuals differ widely in their immune responses, with age, sex and genetic factors having major roles in this inherent variability1–6. However, the variables that drive such differences in cytokine secretion—a crucial component of the host response to immune challenges—remain poorly defined. Here we investigated 136 variables and identified smoking, cytomegalovirus latent infection and body mass index as major contributors to variability in cytokine response, with effects of comparable magnitudes with age, sex and genetics. We find that smoking influences both innate and adaptive immune responses. Notably, its effect on innate responses is quickly lost after smoking cessation and is specifically associated with plasma levels of CEACAM6, whereas its effect on adaptive responses persists long after individuals quit smoking and is associated with epigenetic memory. This is supported by the association of the past smoking effect on cytokine responses with DNA methylation at specific signal trans-activators and regulators of metabolism. Our findings identify three novel variables associated with cytokine secretion variability and reveal roles for smoking in the short- and long-term regulation of immune responses. These results have potential clinical implications for the risk of developing infections, cancers or autoimmune diseases.
Room-temperature quantum optomechanics using an ultralow noise cavity
Authors: Huang Guanhao , Beccari Alberto , Engelsen Nils J. , Kippenberg Tobias J. 
Published: February 2024

AbstractAt room temperature, mechanical motion driven by the quantum backaction of light has been observed only in pioneering experiments in which an optical restoring force controls the oscillator stiffness1,2. For solid-state mechanical resonators in which oscillations are controlled by the material rigidity, the observation of these effects has been hindered by low mechanical quality factors, optical cavity frequency fluctuations3, thermal intermodulation noise4,5 and photothermal instabilities. Here we overcome these challenges with a phononic-engineered membrane-in-the-middle system. By using phononic-crystal-patterned cavity mirrors, we reduce the cavity frequency noise by more than 700-fold. In this ultralow noise cavity, we insert a membrane resonator with high thermal conductance and a quality factor (Q) of 180 million, engineered using recently developed soft-clamping techniques6,7. These advances enable the operation of the system within a factor of 2.5 of the Heisenberg limit for displacement sensing8, leading to the squeezing of the probe laser by 1.09(1) dB below the vacuum fluctuations. Moreover, the long thermal decoherence time of the membrane oscillator (30 vibrational periods) enables us to prepare conditional displaced thermal states of motion with an occupation of 0.97(2) phonons using a multimode Kalman filter. Our work extends the quantum control of solid-state macroscopic oscillators to room temperature.
Genetic determinants of micronucleus formation in vivo
Authors: Adams D. J. , Barlas B. , McIntyre R. E. , Salguero I. , van der Weyden L. , Barros A. , Vicente J. R. , Karimpour N. , Haider A. , Ranzani M. , Turner G. , Thompson N. A. , Harle V. , Olvera-León R. , Robles-Espinoza C. D. , Speak A. O. , Geisler N. , Weninger W. J. , Geyer S. H. , Hewinson J. , Karp N. A. ,   The Sanger Mouse Genetics Project, Tudor Catherine L. , Green Angela L. , Mazzeo Cecilia Icoresi , Siragher Emma , Lillistone Charlotte , Gleeson Diane , Sethi Debarati , Bayzetinova Tanya , Burvill Jonathan , Habib Bishoy , Weavers Lauren , Maswood Ryea , Miklejewska Evelina , Woods Michael , Grau Evelyn , Newman Stuart , Sinclair Caroline , Brown Ellen , Doe Brendan , Galli Antonella , Ramirez-Solis Ramiro , Ryder Edward , Steel Karen , Bradley Allan , Skarnes William C. , Adams David J. , Lafont David , Vancollie Valerie E. , McLaren Robbie S. B. , Hughes-Hallett Lena , Rowley Christine , Sanderson Emma , Tuck Elizabeth , Dabrowska Monika , Griffiths Mark , Gannon David , Cockle Nicola , Kirton Andrea , Bottomley Joanna , Ingle Catherine , Lelliott Chris , White Jacqueline K. , Fu B. , Yang F. , Kozik Z. , Choudhary J. , Yu L. , van Ruiten M. S. , Rowland B. D. , Lelliott C. J. , del Castillo Velasco-Herrera M. , Verstraten R. , Bruckner L. , Henssen A. G. , Rooimans M. A. , de Lange J. , Mohun T. J. , Arends M. J. , Kentistou K. A. , Coelho P. A. , Zhao Y. , Zecchini H. , Perry J. R. B. , Jackson S. P. , Balmus G. 
Published: February 2024

AbstractGenomic instability arising from defective responses to DNA damage1 or mitotic chromosomal imbalances2 can lead to the sequestration of DNA in aberrant extranuclear structures called micronuclei (MN). Although MN are a hallmark of ageing and diseases associated with genomic instability, the catalogue of genetic players that regulate the generation of MN remains to be determined. Here we analyse 997 mouse mutant lines, revealing 145 genes whose loss significantly increases (n = 71) or decreases (n = 74) MN formation, including many genes whose orthologues are linked to human disease. We found that mice null for Dscc1, which showed the most significant increase in MN, also displayed a range of phenotypes characteristic of patients with cohesinopathy disorders. After validating the DSCC1-associated MN instability phenotype in human cells, we used genome-wide CRISPR–Cas9 screening to define synthetic lethal and synthetic rescue interactors. We found that the loss of SIRT1 can rescue phenotypes associated with DSCC1 loss in a manner paralleling restoration of protein acetylation of SMC3. Our study reveals factors involved in maintaining genomic stability and shows how this information can be used to identify mechanisms that are relevant to human disease biology1.
Influence of pump laser fluence on ultrafast myoglobin structural dynamics
Authors: Barends Thomas R. M. , Gorel Alexander , Bhattacharyya Swarnendu , Schirò Giorgio , Bacellar Camila , Cirelli Claudio , Colletier Jacques-Philippe , Foucar Lutz , Grünbein Marie Luise , Hartmann Elisabeth , Hilpert Mario , Holton James M. , Johnson Philip J. M. , Kloos Marco , Knopp Gregor , Marekha Bogdan , Nass Karol , Nass Kovacs Gabriela , Ozerov Dmitry , Stricker Miriam , Weik Martin , Doak R. Bruce , Shoeman Robert L. , Milne Christopher J. , Huix-Rotllant Miquel , Cammarata Marco , Schlichting Ilme 
Published: February 2024

AbstractHigh-intensity femtosecond pulses from an X-ray free-electron laser enable pump–probe experiments for the investigation of electronic and nuclear changes during light-induced reactions. On timescales ranging from femtoseconds to milliseconds and for a variety of biological systems, time-resolved serial femtosecond crystallography (TR-SFX) has provided detailed structural data for light-induced isomerization, breakage or formation of chemical bonds and electron transfer1,2. However, all ultrafast TR-SFX studies to date have employed such high pump laser energies that nominally several photons were absorbed per chromophore3–17. As multiphoton absorption may force the protein response into non-physiological pathways, it is of great concern18,19whether this experimental approach20allows valid conclusions to be drawn vis-à-vis biologically relevant single-photon-induced reactions18,19. Here we describe ultrafast pump–probe SFX experiments on the photodissociation of carboxymyoglobin, showing that different pump laser fluences yield markedly different results. In particular, the dynamics of structural changes and observed indicators of the mechanistically important coherent oscillations of the Fe–CO bond distance (predicted by recent quantum wavepacket dynamics21) are seen to depend strongly on pump laser energy, in line with quantum chemical analysis. Our results confirm both the feasibility and necessity of performing ultrafast TR-SFX pump–probe experiments in the linear photoexcitation regime. We consider this to be a starting point for reassessing both the design and the interpretation of ultrafast TR-SFX pump–probe experiments20such that mechanistically relevant insight emerges.
A new family of bacterial ribosome hibernation factors
Authors: Helena-Bueno Karla , Rybak Mariia Yu. , Ekemezie Chinenye L. , Sullivan Rudi , Brown Charlotte R. , Dingwall Charlotte , Baslé Arnaud , Schneider Claudia , Connolly James P. R. , Blaza James N. , Csörgő Bálint , Moynihan Patrick J. , Gagnon Matthieu G. , Hill Chris H. , Melnikov Sergey V. 
Published: February 2024

AbstractTo conserve energy during starvation and stress, many organisms use hibernation factor proteins to inhibit protein synthesis and protect their ribosomes from damage1,2. In bacteria, two families of hibernation factors have been described, but the low conservation of these proteins and the huge diversity of species, habitats and environmental stressors have confounded their discovery3–6. Here, by combining cryogenic electron microscopy, genetics and biochemistry, we identify Balon, a new hibernation factor in the cold-adapted bacterium Psychrobacter urativorans. We show that Balon is a distant homologue of the archaeo-eukaryotic translation factor aeRF1 and is found in 20% of representative bacteria. During cold shock or stationary phase, Balon occupies the ribosomal A site in both vacant and actively translating ribosomes in complex with EF-Tu, highlighting an unexpected role for EF-Tu in the cellular stress response. Unlike typical A-site substrates, Balon binds to ribosomes in an mRNA-independent manner, initiating a new mode of ribosome hibernation that can commence while ribosomes are still engaged in protein synthesis. Our work suggests that Balon–EF-Tu-regulated ribosome hibernation is a ubiquitous bacterial stress-response mechanism, and we demonstrate that putative Balon homologues in Mycobacteria bind to ribosomes in a similar fashion. This finding calls for a revision of the current model of ribosome hibernation inferred from common model organisms and holds numerous implications for how we understand and study ribosome hibernation.
A model of human neural networks reveals NPTX2 pathology in ALS and FTLD
Authors: Hruska-Plochan Marian , Wiersma Vera I. , Betz Katharina M. , Mallona Izaskun , Ronchi Silvia , Maniecka Zuzanna , Hock Eva-Maria , Tantardini Elena , Laferriere Florent , Sahadevan Sonu , Hoop Vanessa , Delvendahl Igor , Pérez-Berlanga Manuela , Gatta Beatrice , Panatta Martina , van der Bourg Alexander , Bohaciakova Dasa , Sharma Puneet , De Vos Laura , Frontzek Karl , Aguzzi Adriano , Lashley Tammaryn , Robinson Mark D. , Karayannis Theofanis , Mueller Martin , Hierlemann Andreas , Polymenidou Magdalini 
Published: February 2024

AbstractHuman cellular models of neurodegeneration require reproducibility and longevity, which is necessary for simulating age-dependent diseases. Such systems are particularly needed for TDP-43 proteinopathies1, which involve human-specific mechanisms2–5 that cannot be directly studied in animal models. Here, to explore the emergence and consequences of TDP-43 pathologies, we generated induced pluripotent stem cell-derived, colony morphology neural stem cells (iCoMoNSCs) via manual selection of neural precursors6. Single-cell transcriptomics and comparison to independent neural stem cells7 showed that iCoMoNSCs are uniquely homogenous and self-renewing. Differentiated iCoMoNSCs formed a self-organized multicellular system consisting of synaptically connected and electrophysiologically active neurons, which matured into long-lived functional networks (which we designate iNets). Neuronal and glial maturation in iNets was similar to that of cortical organoids8. Overexpression of wild-type TDP-43 in a minority of neurons within iNets led to progressive fragmentation and aggregation of the protein, resulting in a partial loss of function and neurotoxicity. Single-cell transcriptomics revealed a novel set of misregulated RNA targets in TDP-43-overexpressing neurons and in patients with TDP-43 proteinopathies exhibiting a loss of nuclear TDP-43. The strongest misregulated target encoded the synaptic protein NPTX2, the levels of which are controlled by TDP-43 binding on its 3′ untranslated region. When NPTX2 was overexpressed in iNets, it exhibited neurotoxicity, whereas correcting NPTX2 misregulation partially rescued neurons from TDP-43-induced neurodegeneration. Notably, NPTX2 was consistently misaccumulated in neurons from patients with amyotrophic lateral sclerosis and frontotemporal lobar degeneration with TDP-43 pathology. Our work directly links TDP-43 misregulation and NPTX2 accumulation, thereby revealing a TDP-43-dependent pathway of neurotoxicity.
Autonomous transposons tune their sequences to ensure somatic suppression
Authors: Ilık İbrahim Avşar , Glažar Petar , Tse Kevin , Brändl Björn , Meierhofer David , Müller Franz-Josef , Smith Zachary D. , Aktaş Tuğçe 
Published: February 2024

AbstractTransposable elements (TEs) are a major constituent of human genes, occupying approximately half of the intronic space. During pre-messenger RNA synthesis, intronic TEs are transcribed along with their host genes but rarely contribute to the final mRNA product because they are spliced out together with the intron and rapidly degraded. Paradoxically, TEs are an abundant source of RNA-processing signals through which they can create new introns1, and also functional2 or non-functional chimeric transcripts3. The rarity of these events implies the existence of a resilient splicing code that is able to suppress TE exonization without compromising host pre-mRNA processing. Here we show that SAFB proteins protect genome integrity by preventing retrotransposition of L1 elements while maintaining splicing integrity, via prevention of the exonization of previously integrated TEs. This unique dual role is possible because of L1’s conserved adenosine-rich coding sequences that are bound by SAFB proteins. The suppressive activity of SAFB extends to tissue-specific, giant protein-coding cassette exons, nested genes and Tigger DNA transposons. Moreover, SAFB also suppresses LTR/ERV elements in species in which they are still active, such as mice and flies. A significant subset of splicing events suppressed by SAFB in somatic cells are activated in the testis, coinciding with low SAFB expression in postmeiotic spermatids. Reminiscent of the division of labour between innate and adaptive immune systems that fight external pathogens, our results uncover SAFB proteins as an RNA-based, pattern-guided, non-adaptive defence system against TEs in the soma, complementing the RNA-based, adaptive Piwi-interacting RNA pathway of the germline.
Rainforest transformation reallocates energy from green to brown food webs
Authors: Potapov Anton M. , Drescher Jochen , Darras Kevin , Wenzel Arne , Janotta Noah , Nazarreta Rizky , Kasmiatun  , Laurent Valentine , Mawan Amanda , Utari Endah H. , Pollierer Melanie M. , Rembold Katja , Widyastuti Rahayu , Buchori Damayanti , Hidayat Purnama , Turner Edgar , Grass Ingo , Westphal Catrin , Tscharntke Teja , Scheu Stefan 
Published: February 2024

AbstractTerrestrial animal biodiversity is increasingly being lost because of land-use change1,2. However, functional and energetic consequences aboveground and belowground and across trophic levels in megadiverse tropical ecosystems remain largely unknown. To fill this gap, we assessed changes in energy fluxes across ‘green’ aboveground (canopy arthropods and birds) and ‘brown’ belowground (soil arthropods and earthworms) animal food webs in tropical rainforests and plantations in Sumatra, Indonesia. Our results showed that most of the energy in rainforests is channelled to the belowground animal food web. Oil palm and rubber plantations had similar or, in the case of rubber agroforest, higher total animal energy fluxes compared to rainforest but the key energetic nodes were distinctly different: in rainforest more than 90% of the total animal energy flux was channelled by arthropods in soil and canopy, whereas in plantations more than 50% of the energy was allocated to annelids (earthworms). Land-use change led to a consistent decline in multitrophic energy flux aboveground, whereas belowground food webs responded with reduced energy flux to higher trophic levels, down to −90%, and with shifts from slow (fungal) to fast (bacterial) energy channels and from faeces production towards consumption of soil organic matter. This coincides with previously reported soil carbon stock depletion3. Here we show that well-documented animal biodiversity declines with tropical land-use change4–6 are associated with vast energetic and functional restructuring in food webs across aboveground and belowground ecosystem compartments.
Visuo-frontal interactions during social learning in freely moving macaques
Authors: Franch Melissa , Yellapantula Sudha , Parajuli Arun , Kharas Natasha , Wright Anthony , Aazhang Behnaam , Dragoi Valentin 
Published: February 2024

AbstractSocial interactions represent a ubiquitous aspect of our everyday life that we acquire by interpreting and responding to visual cues from conspecifics1. However, despite the general acceptance of this view, how visual information is used to guide the decision to cooperate is unknown. Here, we wirelessly recorded the spiking activity of populations of neurons in the visual and prefrontal cortex in conjunction with wireless recordings of oculomotor events while freely moving macaques engaged in social cooperation. As animals learned to cooperate, visual and executive areas refined the representation of social variables, such as the conspecific or reward, by distributing socially relevant information among neurons in each area. Decoding population activity showed that viewing social cues influences the decision to cooperate. Learning social events increased coordinated spiking between visual and prefrontal cortical neurons, which was associated with improved accuracy of neural populations to encode social cues and the decision to cooperate. These results indicate that the visual-frontal cortical network prioritizes relevant sensory information to facilitate learning social interactions while freely moving macaques interact in a naturalistic environment.
Seismic landslide susceptibility assessment using principal component analysis and support vector machine
Authors: Xu Ziyao , Che Ailan , Zhou Hanxu 
Published: February 2024

AbstractSeismic landslides are dangerous natural hazards that can cause immense damage to human lives and property. Susceptibility assessment of earthquake-triggered landslides provides the scientific basis and theoretical foundation for disaster emergency management in engineering projects. However, landslide susceptibility assessment requires a massive amount of historical landslide data. Evidence of past landslide activities may be lost due to changes in geographical conditions and human factors over time. The lack of landslide data poses difficulties in assessing landslide susceptibility. The aim of this study is to establish a generalized seismic landslide susceptibility assessment model for applying it to the Dayong highway in the Chenghai area, where earthquakes occur frequently but with a lack of landslide data. The landslide data used comes from the 2014 Ludian Ms (Surface wave magnitude) 6.5 earthquake in a region with geographical conditions similar to those in the Chenghai area. The influencing factors considered include elevation, slope, slope aspect, distance to streams, distance to faults, geology, terrain wetness index, normalized difference vegetation index, epicenter distance and peak ground acceleration. The frequency ratio method is used to eliminate influencing factors with poor statistical dispersion of landslides. Principal component analysis (PCA) is utilized to reduce the dimensionality of landslide conditioning factors and to improve the transferability of the assessment model to different regions. A support vector machine model is used to establish the susceptibility assessment model. The results show that the accuracy of the PCA–SVM model reaches 93.6%. The landslide susceptibility of the Chenghai area is classified into 5 classes, with the “Very high” landslide susceptibility class accounting for 0.63%. The 13-km section in the middle of the Dayong highway, which accounts for 8.9%, is identified as the high-risk area most obviously impacted by seismic landslides. This study provides a new approach for seismic landslide susceptibility assessment in areas lacking in landslide inventory data.
Assessing respiratory epidemic potential in French hospitals through collection of close contact data (April–June 2020)
Authors: Shirreff George , Huynh Bich-Tram , Duval Audrey , Pereira Lara Cristina , Annane Djillali , Dinh Aurélien , Lambotte Olivier , Bulifon Sophie , Guichardon Magali , Beaune Sebastien , Toubiana Julie , Kermorvant-Duchemin Elsa , Chéron Gerard , Cordel Hugues , Argaud Laurent , Douplat Marion , Abraham Paul , Tazarourte Karim , Martin-Gaujard Géraldine , Vanhems Philippe , Hilliquin Delphine , Nguyen Duc , Chelius Guillaume , Fraboulet Antoine ,   EMAE-MESuRS Working Group on Nosocomial SARS-CoV-2 Modelling, Temime Laura , Opatowski Lulla , Guillemot Didier 
Published: February 2024

AbstractThe transmission risk of SARS-CoV-2 within hospitals can exceed that in the general community because of more frequent close proximity interactions (CPIs). However, epidemic risk across wards is still poorly described. We measured CPIs directly using wearable sensors given to all present in a clinical ward over a 36-h period, across 15 wards in three hospitals in April-June 2020. Data were collected from 2114 participants and combined with a simple transmission model describing the arrival of a single index case to the ward to estimate the risk of an outbreak. Estimated epidemic risk ranged four-fold, from 0.12 secondary infections per day in an adult emergency to 0.49 per day in general paediatrics. The risk presented by an index case in a patient varied 20-fold across wards. Using simulation, we assessed the potential impact on outbreak risk of targeting the most connected individuals for prevention. We found that targeting those with the highest cumulative contact hours was most impactful (20% reduction for 5% of the population targeted), and on average resources were better spent targeting patients. This study reveals patterns of interactions between individuals in hospital during a pandemic and opens new routes for research into airborne nosocomial risk.