bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dimensions of wisdom perception across twelve countries on five continents
Authors: Rudnev M. , Barrett H. C. , Buckwalter W. , Machery E. , Stich S. , Barr K. , Bencherifa A. , Clancy R. F. , Crone D. L. , Deguchi Y. , Fabiano E. , Fodeman A. D. , Guennoun B. , Halamová J. , Hashimoto T. , Homan J. , Kanovský M. , Karasawa K. , Kim H. , Kiper J. , Lee M. , Liu X. , Mitova V. , Nair R. B. , Pantovic L. , Porter B. , Quintanilla P. , Reijer J. , Romero P. P. , Singh P. , Tber S. , Wilkenfeld D. A. , Yi L. , Grossmann I. 
Published: August 2024

AbstractWisdom is the hallmark of social judgment, but how people across cultures recognize wisdom remains unclear—distinct philosophical traditions suggest different views of wisdom’s cardinal features. We explore perception of wise minds across 16 socio-economically and culturally diverse convenience samples from 12 countries. Participants assessed wisdom exemplars, non-exemplars, and themselves on 19 socio-cognitive characteristics, subsequently rating targets’ wisdom, knowledge, and understanding. Analyses reveal two positively related dimensions—Reflective Orientation and Socio-Emotional Awareness. These dimensions are consistent across the studied cultural regions and interact when informing wisdom ratings: wisest targets—as perceived by participants—score high on both dimensions, whereas the least wise are not reflective but moderately socio-emotional. Additionally, individuals view themselves as less reflective but more socio-emotionally aware than most wisdom exemplars. Our findings expand folk psychology and social judgment research beyond the Global North, showing how individuals perceive desirable cognitive and socio-emotional qualities, and contribute to an understanding of mind perception.
Suppressing torsional buckling in auxetic meta-shells
Authors: Ghorbani Aref , Mirzaali Mohammad J. , Roebroek Tobias , Coulais Corentin , Bonn Daniel , van der Linden Erik , Habibi Mehdi 
Published: August 2024

AbstractTake a thin cylindrical shell and twist it; it will buckle immediately. Such unavoidable torsional buckling can lead to systemic failure, for example by disrupting the blood flow through arteries. In this study, we prevent this torsional buckling instability using a combination of auxeticity and orthotropy in cylindrical metamaterial shells with a holey pattern. When the principal axes of the orthotropic meta-shell are relatively aligned with that of the compressive component of the applied stress during twisting, the meta-shell uniformly shrinks in the radial direction as a result of a local buckling instability. This shrinkage coincides with a softening-stiffening transition that leads to ordered stacking of unit cells along the compressive component of the applied stress. These transitions due to local instabilities circumvent the usual torsional instability even under a large twist angle. This study highlights the potential of tailoring anisotropy and programming instabilities in metamaterials, with potential applications in designing mechanical elements for soft robotics, biomechanics or fluidics. As an example of such applications, we demonstrate soft torsional compressor for generating pulsatile flows through a torsion release mechanism.
Community use of oral antibiotics transiently reprofiles the intestinal microbiome in young Bangladeshi children
Authors: Baldi Andrew , Braat Sabine , Imrul Hasan Mohammed , Bennett Cavan , Barrios Marilou , Jones Naomi , Moir-Meyer Gemma , Abdul Azeez Imadh , Wilcox Stephen , Saiful Alam Bhuiyan Mohammad , Ataide Ricardo , Clucas Danielle , Harrison Leonard C. , Arifeen Shams El , Bowden Rory , Biggs Beverley-Ann , Jex Aaron , Pasricha Sant-Rayn 
Published: August 2024

AbstractAntibiotics may alter the gut microbiome, and this is one of the mechanisms by which antimicrobial resistance may be promoted. Suboptimal antimicrobial stewardship in Asia has been linked to antimicrobial resistance. We aim to examine the relationship between oral antibiotic use and composition and antimicrobial resistance in the gut microbiome in 1093 Bangladeshi infants. We leverage a trial of 8-month-old infants in rural Bangladesh: 61% of children were cumulatively exposed to antibiotics (most commonly cephalosporins and macrolides) over the 12-month study period, including 47% in the first 3 months of the study, usually for fever or respiratory infection. 16S rRNA amplicon sequencing in 11-month-old infants reveals that alpha diversity of the intestinal microbiome is reduced in children who received antibiotics within the previous 7 days; these samples also exhibit enrichment for Enterococcus and Escherichia/Shigella genera. No effect is seen in children who received antibiotics earlier. Using shotgun metagenomics, overall abundance of antimicrobial resistance genes declines over time. Enrichment for an Enterococcus-related antimicrobial resistance gene is observed in children receiving antibiotics within the previous 7 days, but not earlier. Presence of antimicrobial resistance genes is correlated to microbiome composition. In Bangladeshi children, community use of antibiotics transiently reprofiles the gut microbiome.
Selective excitation of vibrations in a single molecule
Authors: Luo Yang , Sheng Shaoxiang , Pisarra Michele , Martin-Jimenez Alberto , Martin Fernando , Kern Klaus , Garg Manish 
Published: August 2024

AbstractThe capability to excite, probe, and manipulate vibrational modes is essential for understanding and controlling chemical reactions at the molecular level. Recent advancements in tip-enhanced Raman spectroscopies have enabled the probing of vibrational fingerprints in a single molecule with Ångström-scale spatial resolution. However, achieving controllable excitation of specific vibrational modes in individual molecules remains challenging. Here, we demonstrate the selective excitation and probing of vibrational modes in single deprotonated phthalocyanine molecules utilizing resonance Raman spectroscopy in a scanning tunneling microscope. Selective excitation is achieved by finely tuning the excitation wavelength of the laser to be resonant with the vibronic transitions between the molecular ground electronic state and the vibrational levels in the excited electronic state, resulting in the state-selective enhancement of the resonance Raman signal. Our approach contributes to setting the stage for steering chemical transformations in molecules on surfaces by selective excitation of molecular vibrations.
Inefficient nitrogen transport to the lower mantle by sediment subduction
Authors: Huang Weihua , Yang Yan , Li Yuan , Xu Zheng , Yang Shuiyuan , Guo Shengbin , Xia Qunke 
Published: August 2024

AbstractThe fate of sedimentary nitrogen during subduction is essential for understanding the origin of nitrogen in the deep Earth. Here we study the behavior of nitrogen in slab sediments during the phengite to K-hollandite transition at 10–12 GPa and 800–1100 °C. Phengite stability is extended by 1–3 GPa in the nitrogen (NH4+)-bearing system. The phengite-fluid partition coefficient of nitrogen is 0.031 at 10 GPa, and K-hollandite-fluid partition coefficients of nitrogen range from 0.008 to 0.064, showing a positive dependence on pressure but a negative dependence on temperature. The nitrogen partitioning data suggest that K-hollandite can only preserve ~43% and ~26% of the nitrogen from phengite during the phengite to K-hollandite transition along the cold and warm slab geotherms, respectively. Combined with the slab sedimentary nitrogen influx, we find that a maximum of ~1.5 × 108 kg/y of nitrogen, representing ~20% of the initial sedimentary nitrogen influx, could be transported by K-hollandite to the lower mantle. We conclude that slab sediments may have contributed less than 15% of the lower mantle nitrogen, most of which is probably of primordial origin.
Associations between gut microbiota and incident fractures in the FINRISK cohort
Authors: Grahnemo Louise , Kambur Oleg , Lahti Leo , Jousilahti Pekka , Niiranen Teemu , Knight Rob , Salomaa Veikko , Havulinna Aki S. , Ohlsson Claes 
Published: August 2024

AbstractThe gut microbiota (GM) can regulate bone mass, but its association with incident fractures is unknown. We used Cox regression models to determine whether the GM composition is associated with incident fractures in the large FINRISK 2002 cohort (n = 7043, 1092 incident fracture cases, median follow-up time 18 years) with information on GM composition and functionality from shotgun metagenome sequencing. Higher alpha diversity was associated with decreased fracture risk (hazard ratio [HR] 0.92 per standard deviation increase in Shannon index, 95% confidence interval 0.87–0.96). For beta diversity, the first principal component was associated with fracture risk (Aitchison distance, HR 0.90, 0.85–0.96). In predefined phyla analyses, we observed that the relative abundance of Proteobacteria was associated with increased fracture risk (HR 1.14, 1.07–1.20), while the relative abundance of Tenericutes was associated with decreased fracture risk (HR 0.90, 0.85–0.96). Explorative sub-analyses within the Proteobacteria phylum showed that higher relative abundance of Gammaproteobacteria was associated with increased fracture risk. Functionality analyses showed that pathways related to amino acid metabolism and lipopolysaccharide biosynthesis associated with fracture risk. The relative abundance of Proteobacteria correlated with pathways for amino acid metabolism, while the relative abundance of Tenericutes correlated with pathways for butyrate synthesis. In conclusion, the overall GM composition was associated with incident fractures. The relative abundance of Proteobacteria, especially Gammaproteobacteria, was associated with increased fracture risk, while the relative abundance of Tenericutes was associated with decreased fracture risk. Functionality analyses demonstrated that pathways known to regulate bone health may underlie these associations.
Physics and chemistry from parsimonious representations: image analysis via invariant variational autoencoders
Authors: Valleti Mani , Ziatdinov Maxim , Liu Yongtao , Kalinin Sergei V. 
Published: August 2024

AbstractElectron, optical, and scanning probe microscopy methods are generating ever increasing volume of image data containing information on atomic and mesoscale structures and functionalities. This necessitates the development of the machine learning methods for discovery of physical and chemical phenomena from the data, such as manifestations of symmetry breaking phenomena in electron and scanning tunneling microscopy images, or variability of the nanoparticles. Variational autoencoders (VAEs) are emerging as a powerful paradigm for the unsupervised data analysis, allowing to disentangle the factors of variability and discover optimal parsimonious representation. Here, we summarize recent developments in VAEs, covering the basic principles and intuition behind the VAEs. The invariant VAEs are introduced as an approach to accommodate scale and translation invariances present in imaging data and separate known factors of variations from the ones to be discovered. We further describe the opportunities enabled by the control over VAE architecture, including conditional, semi-supervised, and joint VAEs. Several case studies of VAE applications for toy models and experimental datasets in Scanning Transmission Electron Microscopy are discussed, emphasizing the deep connection between VAE and basic physical principles. Python codes and datasets discussed in this article are available at https://github.com/saimani5/VAE-tutorials and can be used by researchers as an application guide when applying these to their own datasets.
A Scottish provenance for the Altar Stone of Stonehenge
Authors: Clarke Anthony J. I. , Kirkland Christopher L. , Bevins Richard E. , Pearce Nick J. G. , Glorie Stijn , Ixer Rob A. 
Published: August 2024

AbstractUnderstanding the provenance of megaliths used in the Neolithic stone circle at Stonehenge, southern England, gives insight into the culture and connectivity of prehistoric Britain. The source of the Altar Stone, the central recumbent sandstone megalith, has remained unknown, with recent work discounting an Anglo-Welsh Basin origin1,2. Here we present the age and chemistry of detrital zircon, apatite and rutile grains from within fragments of the Altar Stone. The detrital zircon load largely comprises Mesoproterozoic and Archaean sources, whereas rutile and apatite are dominated by a mid-Ordovician source. The ages of these grains indicate derivation from an ultimate Laurentian crystalline source region that was overprinted by Grampian (around 460 million years ago) magmatism. Detrital age comparisons to sedimentary packages throughout Britain and Ireland reveal a remarkable similarity to the Old Red Sandstone of the Orcadian Basin in northeast Scotland. Such a provenance implies that the Altar Stone, a 6 tonne shaped block, was sourced at least 750 km from its current location. The difficulty of long-distance overland transport of such massive cargo from Scotland, navigating topographic barriers, suggests that it was transported by sea. Such routing demonstrates a high level of societal organization with intra-Britain transport during the Neolithic period.
Precision spectroscopy on 9Be overcomes limitations from nuclear structure
Authors: Dickopf Stefan , Sikora Bastian , Kaiser Annabelle , Müller Marius , Ulmer Stefan , Yerokhin Vladimir A. , Harman Zoltán , Keitel Christoph H. , Mooser Andreas , Blaum Klaus 
Published: August 2024

AbstractMany powerful tests of the standard model of particle physics and searches for new physics with precision atomic spectroscopy are hindered by our lack of knowledge of nuclear properties. Ideally, these properties may be derived from precise measurements of the most sensitive and theoretically best-understood observables, often found in hydrogen-like systems. Although these measurements are abundant for the electric properties of nuclei, they are scarce for the magnetic properties, and precise experimental results are limited to the lightest of nuclei1–4. Here we focus on 9Be, which offers the unique possibility to use comparisons between different charge states available for high-precision spectroscopy in Penning traps to test theoretical calculations typically obscured by nuclear structure. In particular, we perform high-precision spectroscopy of the 1s hyperfine and Zeeman structure in hydrogen-like 9Be3+. We determine the effective Zemach radius with an uncertainty of 500 ppm, and the bare nuclear magnetic moment with an uncertainty of 0.6 parts per billion— uncertainties unmatched beyond hydrogen. Moreover, we compare our measurements with the measurements conducted on the three-electron charge state 9Be+ (ref. 5), which enables testing the calculation of multi-electron diamagnetic shielding effects of the nuclear magnetic moment at the parts per billion level. Furthermore, we test the quantum electrodynamics methods used for the calculation of the hyperfine splitting. Our results serve as a crucial benchmark for transferring high-precision results of nuclear magnetic properties across different electronic configurations.
Twist-assisted all-antiferromagnetic tunnel junction in the atomic limit
Authors: Chen Yuliang , Samanta Kartik , Shahed Naafis A. , Zhang Haojie , Fang Chi , Ernst Arthur , Tsymbal Evgeny Y. , Parkin Stuart S. P. 
Published: August 2024

AbstractAntiferromagnetic spintronics1,2 shows great potential for high-density and ultrafast information devices. Magnetic tunnel junctions (MTJs), a key spintronic memory component that are typically formed from ferromagnetic materials, have seen rapid developments very recently using antiferromagnetic materials3,4. Here we demonstrate a twisting strategy for constructing all-antiferromagnetic tunnel junctions down to the atomic limit. By twisting two bilayers of CrSBr, a 2D antiferromagnet (AFM), a more than 700% nonvolatile tunnelling magnetoresistance (TMR) ratio is shown at zero field (ZF) with the entire twisted stack acting as the tunnel barrier. This is determined by twisting two CrSBr monolayers for which the TMR is shown to be derived from accumulative coherent tunnelling across the individual CrSBr monolayers. The dependence of the TMR on the twist angle is calculated from the electron-parallel momentum-dependent decay across the twisted monolayers. This is in excellent agreement with our experiments that consider twist angles that vary from 0° to 90°. Moreover, we also find that the temperature dependence of the TMR is, surprisingly, much weaker for the twisted as compared with the untwisted junctions, making the twisted junctions even more attractive for applications. Our work shows that it is possible to push nonvolatile magnetic information storage to the atomically thin limit.
Recognition and control of neutrophil extracellular trap formation by MICL
Authors: Malamud Mariano , Whitehead Lauren , McIntosh Alasdair , Colella Fabio , Roelofs Anke J. , Kusakabe Takato , Dambuza Ivy M. , Phillips-Brookes Annie , Salazar Fabián , Perez Federico , Shoesmith Romey , Zakrzewski Przemyslaw , Sey Emily A. , Rodrigues Cecilia , Morvay Petruta L. , Redelinghuys Pierre , Bedekovic Tina , Fernandes Maria J. G. , Almizraq Ruqayyah , Branch Donald R. , Amulic Borko , Harvey Jamie , Stewart Diane , Yuecel Raif , Reid Delyth M. , McConnachie Alex , Pickering Matthew C. , Botto Marina , Iliev Iliyan D. , McInnes Iain B. , De Bari Cosimo , Willment Janet A. , Brown Gordon D. 
Published: August 2024

AbstractRegulation of neutrophil activation is critical for disease control. Neutrophil extracellular traps (NETs), which are web-like structures composed of DNA and neutrophil-derived proteins, are formed following pro-inflammatory signals; however, if this process is uncontrolled, NETs contribute to disease pathogenesis, exacerbating inflammation and host tissue damage1,2. Here we show that myeloid inhibitory C-type lectin-like (MICL), an inhibitory C-type lectin receptor, directly recognizes DNA in NETs; this interaction is vital to regulate neutrophil activation. Loss or inhibition of MICL functionality leads to uncontrolled NET formation through the ROS–PAD4 pathway and the development of an auto-inflammatory feedback loop. We show that in the context of rheumatoid arthritis, such dysregulation leads to exacerbated pathology in both mouse models and in human patients, where autoantibodies to MICL inhibit key functions of this receptor. Of note, we also detect similarly inhibitory anti-MICL autoantibodies in patients with other diseases linked to aberrant NET formation, including lupus and severe COVID-19. By contrast, dysregulation of NET release is protective during systemic infection with the fungal pathogen Aspergillus fumigatus. Together, we show that the recognition of NETs by MICL represents a fundamental autoregulatory pathway that controls neutrophil activity and NET formation.
Growth of complete ammonia oxidizers on guanidine
Authors: Palatinszky Marton , Herbold Craig W. , Sedlacek Christopher J. , Pühringer Dominic , Kitzinger Katharina , Giguere Andrew T. , Wasmund Kenneth , Nielsen Per H. , Dueholm Morten K. D. , Jehmlich Nico , Gruseck Richard , Legin Anton , Kostan Julius , Krasnici Nesrete , Schreiner Claudia , Palmetzhofer Johanna , Hofmann Thilo , Zumstein Michael , Djinović-Carugo Kristina , Daims Holger , Wagner Michael 
Published: August 2024

AbstractGuanidine is a chemically stable nitrogen compound that is excreted in human urine and is widely used in manufacturing of plastics, as a flame retardant and as a component of propellants, and is well known as a protein denaturant in biochemistry1–3. Guanidine occurs widely in nature and is used by several microorganisms as a nitrogen source, but microorganisms growing on guanidine as the only substrate have not yet been identified. Here we show that the complete ammonia oxidizer (comammox) Nitrospira inopinata and probably most other comammox microorganisms can grow on guanidine as the sole source of energy, reductant and nitrogen. Proteomics, enzyme kinetics and the crystal structure of a N. inopinata guanidinase homologue demonstrated that it is a bona fide guanidinase. Incubation experiments with comammox-containing agricultural soil and wastewater treatment plant microbiomes suggested that guanidine serves as substrate for nitrification in the environment. The identification of guanidine as a growth substrate for comammox shows an unexpected niche of these globally important nitrifiers and offers opportunities for their isolation.
Rapid discovery of monoclonal antibodies by microfluidics-enabled FACS of single pathogen-specific antibody-secreting cells
Authors: Fischer Katrin , Lulla Aleksei , So Tsz Y. , Pereyra-Gerber Pehuén , Raybould Matthew I. J. , Kohler Timo N. , Yam-Puc Juan Carlos , Kaminski Tomasz S. , Hughes Robert , Pyeatt Gwendolyn L. , Leiss-Maier Florian , Brear Paul , Matheson Nicholas J. , Deane Charlotte M. , Hyvönen Marko , Thaventhiran James E. D. , Hollfelder Florian 
Published: August 2024

AbstractMonoclonal antibodies are increasingly used to prevent and treat viral infections and are pivotal in pandemic response efforts. Antibody-secreting cells (ASCs; plasma cells and plasmablasts) are an excellent source of high-affinity antibodies with therapeutic potential. Current methods to study antigen-specific ASCs either have low throughput, require expensive and labor-intensive screening or are technically demanding and therefore not widely accessible. Here we present a straightforward technology for the rapid discovery of monoclonal antibodies from ASCs. Our approach combines microfluidic encapsulation of single cells into an antibody capture hydrogel with antigen bait sorting by conventional flow cytometry. With our technology, we screened millions of mouse and human ASCs and obtained monoclonal antibodies against severe acute respiratory syndrome coronavirus 2 with high affinity (<1 pM) and neutralizing capacity (<100 ng ml−1) in 2 weeks with a high hit rate (>85% of characterized antibodies bound the target). By facilitating access to the underexplored ASC compartment, the approach enables efficient antibody discovery and immunological studies into the generation of protective antibodies.
Induction of trained immunity in broiler chickens following delivery of oligodeoxynucleotide containing CpG motifs to protect against Escherichia coli septicemia
Authors: Subhasinghe Iresha , Ahmed Khawaja Ashfaque , Ayalew Lisanework E. , Gautam Hemlata , Popowich Shelly , Matsuyama-Kato Ayumi , Chow-Lockerbie Betty , Tikoo Suresh K. , Griebel Philip , Gomis Susantha 
Published: August 2024

AbstractOligodeoxynucleotides containing CpG motifs (CpG-ODN) can promote antimicrobial immunity in chickens by enriching immune compartments and activating immune cells. Innate memory, or trained immunity, has been demonstrated in humans and mice, featuring the absence of specificity to the initial stimulus and subsequently cross-protection against pathogens. We hypothesize that CpG-ODN can induce trained immunity in chickens. We delivered single or multiple administrations of CpG-ODN to birds and mitochondrial oxidative phosphorylation (OXPHOS) and glycolysis of peripheral blood mononuclear cells were quantified using Seahorse XFp. Next, chickens were administered with CpG-ODN twice at 1 and 4 day of age and challenged with Escherichia coli at 27 days of age. The CpG-ODN administered groups had significantly higher mitochondrial OXPHOS until 21 days of age while cellular glycolysis gradually declined by 14 days of age. The group administered with CpG-ODN twice at 1 and 4 days of age had significantly higher survival, lower clinical score and bacterial load following challenge with E. coli at 27 d of age. This study demonstrated the induction of trained immunity in broiler chickens following administration of CpG-ODN twice during the first 4 days of age to protect birds against E. coli septicemia at 27 days of age.