bluuebunny/crossref_metadata_2025_split huggingface dataset:
Genomic perspective on the bacillus causing paratyphoid B fever
Authors: Hawkey Jane , Frézal Lise , Tran Dien Alicia , Zhukova Anna , Brown Derek , Chattaway Marie Anne , Simon Sandra , Izumiya Hidemasa , Fields Patricia I. , De Lappe Niall , Kaftyreva Lidia , Xu Xuebin , Isobe Junko , Clermont Dominique , Njamkepo Elisabeth , Akeda Yukihiro , Issenhuth-Jeanjean Sylvie , Makarova Mariia , Wang Yanan , Hunt Martin , Jenkins Brent M. , Ravel Magali , Guibert Véronique , Serre Estelle , Matveeva Zoya , Fabre Laëtitia , Cormican Martin , Yue Min , Zhu Baoli , Morita Masatomo , Iqbal Zamin , Silva Nodari Carolina , Pardos de la Gandara Maria , Weill François-Xavier 
Published: December 2024

AbstractParatyphoid B fever (PTB) is caused by an invasive lineage (phylogroup 1, PG1) of Salmonella enterica serotype Paratyphi B (SPB). However, little was known about the global population structure, geographic distribution, and evolution of this pathogen. Here, we report a whole-genome analysis of 568 historical and contemporary SPB PG1 isolates, obtained globally, between 1898 and 2021. We show that this pathogen existed in the 13th century, subsequently diversifying into 11 lineages and 38 genotypes with strong phylogeographic patterns. Following its discovery in 1896, it circulated across Europe until the 1970s, after which it was mostly reimported into Europe from South America, the Middle East, South Asia, and North Africa. Antimicrobial resistance recently emerged in various genotypes of SPB PG1, mostly through mutations of the quinolone-resistance-determining regions of gyrA and gyrB. This study provides an unprecedented insight into SPB PG1 and essential genomic tools for identifying and tracking this pathogen, thereby facilitating the global genomic surveillance of PTB.
Boron-induced transformation of ultrathin Au films into two-dimensional metallic nanostructures
Authors: Preobrajenski Alexei , Vinogradov Nikolay , Duncan David A. , Lee Tien-Lin , Tsitsvero Mikhail , Taketsugu Tetsuya , Lyalin Andrey 
Published: December 2024

AbstractThe synthesis of large, freestanding, single-atom-thick two-dimensional (2D) metallic materials remains challenging due to the isotropic nature of metallic bonding. Here, we present a bottom-up approach for fabricating macroscopically large, nearly freestanding 2D gold (Au) monolayers, consisting of nanostructured patches. By forming Au monolayers on an Ir(111) substrate and embedding boron (B) atoms at the Au/Ir interface, we achieve suspended monoatomic Au sheets with hexagonal structures and triangular nanoscale patterns. Alternative patterns of periodic nanodots are observed in Au bilayers on the B/Ir(111) substrate. Using scanning tunneling microscopy, X-ray spectroscopies, and theoretical calculations, we reveal the role of buried B species in forming the nanostructured Au layers. Changes in the Au monolayer’s band structure upon substrate decoupling indicate a transition from 3D to 2D metal bonding. The resulting Au films exhibit remarkable thermal stability, making them practical for studying the catalytic activity of 2D gold.
Automated discovery of experimental designs in super-resolution microscopy with XLuminA
Authors: Rodríguez Carla , Arlt Sören , Möckl Leonhard , Krenn Mario 
Published: December 2024

AbstractDriven by human ingenuity and creativity, the discovery of super-resolution techniques, which circumvent the classical diffraction limit of light, represent a leap in optical microscopy. However, the vast space encompassing all possible experimental configurations suggests that some powerful concepts and techniques might have not been discovered yet, and might never be with a human-driven direct design approach. Thus, AI-based exploration techniques could provide enormous benefit, by exploring this space in a fast, unbiased way. We introduce XLuminA, an open-source computational framework developed using JAX, a high-performance computing library in Python. XLuminA offers enhanced computational speed enabled by JAX’s accelerated linear algebra compiler (XLA), just-in-time compilation, and its seamlessly integrated automatic vectorization, automatic differentiation capabilities and GPU compatibility. XLuminA demonstrates a speed-up of 4 orders of magnitude compared to well-established numerical optimization methods. We showcase XLuminA’s potential by re-discovering three foundational experiments in advanced microscopy, and identifying an unseen experimental blueprint featuring sub-diffraction imaging capabilities. This work constitutes an important step in AI-driven scientific discovery of new concepts in optics and advanced microscopy.
Rationally designed laterally-condensed-catalysts deliver robust activity and selectivity for ethylene production in acetylene hydrogenation
Authors: Li Zehua , Öztuna Eylül , Skorupska Katarzyna , Vinogradova Olga V. , Jamshaid Afshan , Steigert Alexander , Rohner Christian , Dimitrakopoulou Maria , Prieto Mauricio J. , Kunkel Christian , Stredansky Matus , Kube Pierre , Götte Michael , Dudzinski Alexandra M. , Girgsdies Frank , Wrabetz Sabine , Frandsen Wiebke , Blume Raoul , Zeller Patrick , Muske Martin , Delgado Daniel , Jiang Shan , Schmidt Franz-Philipp , Köhler Tobias , Arztmann Manuela , Efimenko Anna , Frisch Johannes , Kokumai Tathiana M. , Garcia-Diez Raul , Bär Marcus , Hammud Adnan , Kröhnert Jutta , Trunschke Annette , Scheurer Christoph , Schmidt Thomas , Lunkenbein Thomas , Amkreutz Daniel , Kuhlenbeck Helmut , Bukas Vanessa J. , Knop-Gericke Axel , Schlatmann Rutger , Reuter Karsten , Cuenya Beatriz Roldan , Schlögl Robert 
Published: December 2024

AbstractFuture carbon management strategies require storage in elemental form, achievable through a sequence of CO2 hydrogenation reactions. Hydrogen is recycled from molecular intermediates by dehydrogenation, and side product acetylene selectively hydrogenated to ethylene. Existing Pd alloy catalysts for gas purification underperform in concentrated feeds, necessitating novel concepts. Atomistic simulations unveil superior selectivity of Pd:C solid solutions that optimize chemisorption energies and preclude sub-surface hydrides, verified here with model thin films. Multiple design criteria deduced from conventional catalysts facilitate synthesizing a self-repairing Pd:C system of a laterally condensed catalyst (LCC). A Pd layer prepared on a designated SiO2 buffer layer enables control of reactive interface, sub-surface volume and extended functional interface towards the buffer. Function and metric are supervised by operando micro-spectroscopy. This catalyst design shows, ethylene productivity >1 kmolC2H4/gPd/hour is reproducibly achieved and benchmarked against known catalysts. Photovoltaics deposition technologies enable scalability on real-world substrates saving active metal. A design-of-experiment approach demonstrates the improvement potential of the LCC approach.
Enhanced warming of European mountain permafrost in the early 21st century
Authors: Noetzli Jeannette , Isaksen Ketil , Barnett Jamie , Christiansen Hanne H. , Delaloye Reynald , Etzelmüller Bernd , Farinotti Daniel , Gallemann Thomas , Guglielmin Mauro , Hauck Christian , Hilbich Christin , Hoelzle Martin , Lambiel Christophe , Magnin Florence , Oliva Marc , Paro Luca , Pogliotti Paolo , Riedl Claudia , Schoeneich Philippe , Valt Mauro , Vieli Andreas , Phillips Marcia 
Published: December 2024

AbstractMountain permafrost, constituting 30% of the global permafrost area, is sensitive to climate change and strongly impacts mountain ecosystems and communities. This study examines 21st century permafrost warming in European mountains using decadal ground temperature data from sixty-four boreholes in the Alps, Scandinavia, Iceland, Sierra Nevada and Svalbard. During 2013–2022, warming rates at 10 metres depth exceed 1 °C dec−1 in cases, generally surpassing previous estimates because of accelerated warming and the use of a comprehensive data set. Substantial permafrost warming occurred at cold and ice-poor bedrock sites at high elevations and latitudes, at rates comparable to surface air temperature increase. In contrast, latent heat effects in ice-rich ground near 0 °C reduce warming rates and mask important changes of mountain permafrost substrates. The warming patterns observed are consistent across all sites, depths and time periods. For the coming decades, the propagation of permafrost warming to greater depths is largely predetermined already.
A shape-changing haptic navigation interface for vision impairment
Authors: Quinn Robert , Murtough Stephen , de Winton Henry , Ellis-Frew Brandon , Zane Sebastiano , De Sousa Jonathan , Kempapidis Theofilos , Gomes Renata S. M. , Spiers Adam J. 
Published: December 2024

AbstractIndividuals with visual impairment (VI) require aids such as white canes and guide dogs to navigate their environments. Modern localisation technologies have the capacity to transform the way individuals with VI navigate surroundings, but they have yet to do so. A critical barrier is the inability of human–machine interfaces to communicate precise navigation instructions non-visually. We present a shape changing haptic interface (Shape) that provides spatial guidance in two dimensions via bending of its body. Individuals with VI and sighted individuals were recruited to locate virtual targets in 3D space using Shape and vibration feedback (Vibration), and sighted individuals were also asked to visually locate targets. Throughout, device orientation and position were tracked in real-time using a virtual reality system. Individuals with VI located targets significantly faster and more efficiently using Shape, than with Vibration, and there were no significant differences in time or efficiency between Shape and natural vision. Moreover, participants scored Shape significantly more positively than Vibration in a Likert user experience survey, while no significant differences were observed between Shape and natural vision. Here, we provide compelling evidence for the application of a new shape-changing haptic interface as part of an effective future digital navigation system for individuals with VI.
Organoclay flocculation as a pathway to export carbon from the sea surface
Authors: Sharma Diksha , Menon Vignesh Gokuladas , Desai Manasi , Niu Danielle , Bates Eleanor , Kandel Annie , Zinser Erik R. , Fields David M. , O’Toole George A. , Sharma Mukul 
Published: December 2024

AbstractMarine microorganisms play a critical role in regulating atmospheric CO2 concentration via the biological carbon pump. Deposition of continental mineral dust on the sea surface increases carbon sequestration but the interaction between minerals and marine microorganisms is not well understood. We discovered that the interaction of clay minerals with dissolved organic matter and a γ-proteobacterium in seawater increases Transparent Exopolymer Particle (TEP) concentration, leading to organoclay floc formation. To explore this observation further, we conducted a microcosm experiment using surface seawater collected from the Spring 2023 phytoplankton bloom in the Gulf of Maine. Unfiltered (natural community) and filtered (200 μm and 3 μm) seawater was sprayed with clay (20 mg L− 1 and 60 mg L− 1) and incubated. All clay treatments led to a tenfold increase in TEP concentration. 16S rRNA gene amplicon sequence analyses of seawater and settled organoclay flocs showed the dominance of α-proteobacteria, γ-proteobacteria, and Bacteroidota. The initial seawater phytoplankton community was dominated by dinoflagellates followed by a haptophyte (Phaeocystis sp.) and diatoms. Following clay addition, dinoflagellate cell abundance declined sharply while diatom cell abundance increased. By analyzing organoclay flocs for 18S rRNA we confirmed that dinoflagellates were removed in the flocs. The clay amendment removed as much as 50% of phytoplankton organic carbon. We then explored the fate of organoclay flocs at the next trophic level by feeding clay and phytoplankton (Rhodomonas salina) to Calanus finmarchicus. The copepod ingested R. salina and organoclay flocs and egested denser fecal pellets with 1.8- to 3.6- fold higher sinking velocity compared to controls. Fecal pellet density enhancement could facilitate carbon sequestration through zooplankton diel vertical migration. These findings provide insights into how atmospheric dust-derived clay minerals interact with marine microorganisms to enhance the biological carbon pump, facilitating the burial of organic carbon at depths where it is less likely to exchange with the atmosphere.
Detoxification of hydrogen sulfide by synthetic heme model compounds
Authors: Nakagami Atsuki , Mao Qiyue , Horitani Masaki , Kodera Masahito , Kitagishi Hiroaki 
Published: December 2024

AbstractHydrogen sulfide is a lethal toxic gas that disrupts cellular respiration in the mitochondrial system. Currently, no antidote is available for the clinical treatment of hydrogen sulfide poisoning. In this study, we investigated the function of iron(III)porphyrin complexes as hydrogen sulfide scavengers in water and evaluated their potential use as therapeutic agents for hydrogen sulfide poisoning. The compounds, named met-hemoCD-P and met-hemoCD-I, are composed of iron(III)porphyrin complexed with per-methylated β-cyclodextrin dimers that contain a pyridine (met-hemoCD-P) or imidazole axial fifth ligand that is coordinated to Fe(III) (met-hemoCD-I). These compounds formed stable HS–Fe(III) complexes under physiological conditions, with binding constants of 1.2 × 105 and 2.5 × 106 M–1 for met-hemoCD-P and met-hemoCD-I, respectively. The binding constant of met-hemoCD-I was 10-times higher than that reported for native human met-hemoglobin at pH 7.4 and 25oC. Electron paramagnetic resonance (EPR) spectroscopy and H2S quantification assays revealed that after SH– was coordinated to met-hemoCD-I, it was efficiently converted to nontoxic sulfite and sulfate ions via homolytic cleavage of the HS–Fe(III) bond followed by aerobic oxidation. Mouse animal experiments revealed that the survival rate was significantly improved when NaSH-treated mice were injected with met-hemoCD-I. After the injection, mitochondrial CcO function in brain and heart tissues recovered, and met-hemoCD-I injected was excreted in the urine without chemical decomposition.
A simulated annealing algorithm for randomizing weighted networks
Authors: Milisav Filip , Bazinet Vincent , Betzel Richard F. , Misic Bratislav 
Published: December 2024

Abstract
Scientific discovery in connectomics relies on network null models. The prominence of network features is conventionally evaluated against null distributions estimated using randomized networks. Modern imaging technologies provide an increasingly rich array of biologically meaningful edge weights. Despite the prevalence of weighted graph analysis in connectomics, randomization models that only preserve binary node degree remain most widely used. Here we propose a simulated annealing procedure for generating randomized networks that preserve weighted degree (strength) sequences. We show that the procedure outperforms other rewiring algorithms and generalizes to multiple network formats, including directed and signed networks, as well as diverse real-world networks. Throughout, we use morphospace representation to assess the sampling behavior of the algorithm and the variability of the resulting ensemble. Finally, we show that accurate strength preservation yields different inferences about brain network organization. Collectively, this work provides a simple but powerful method to analyze richly detailed next-generation connectomics datasets.
PDGFRA is a conserved HAND2 effector during early cardiac development
Authors: Xu Yanli , Gehlot Rupal , Capon Samuel J. , Albu Marga , Gretz Jonas , Bloomekatz Joshua , Mattonet Kenny , Vucicevic Dubravka , Talyan Sweta , Kikhi Khrievono , Günther Stefan , Looso Mario , Firulli Beth A. , Sanda Miloslav , Firulli Anthony B. , Lacadie Scott Allen , Yelon Deborah , Stainier Didier Y. R. 
Published: December 2024

AbstractThe basic helix–loop–helix transcription factor HAND2 has multiple roles during vertebrate organogenesis, including cardiogenesis. However, much remains to be uncovered about its mechanism of action. Here, we show the generation of several hand2 mutant alleles in zebrafish and demonstrate that dimerization-deficient mutants display the null phenotype but DNA-binding-deficient mutants do not. Rescue experiments with Hand2 variants using a newly identified hand2 enhancer confirmed these observations. To identify Hand2 effectors critical for cardiogenesis, we analyzed the transcriptomes of hand2 loss- and gain-of-function embryonic cardiomyocytes and tested the function of eight candidate genes in vivo; pdgfra was most effective in rescuing myocardial migration in hand2 mutants. Accordingly, we identified a putative Hand2-binding region in the zebrafish pdgfra locus that is important for its expression. In addition, Hand2 loss- and gain-of-function experiments in mouse embryonic stem cell-derived cardiac cells decreased and increased Pdgfra expression, respectively. Altogether, these results further our mechanistic understanding of HAND2 function during early cardiogenesis.
Remote meta-selective C–H bromination of arenes using a recyclable Ru-based aminopropyl bifunctional PMO with robust imidazolium bridges
Authors: Moradi Hesamodin , Karimi Babak , Karimpour Touraj , Mastrorilli Piero , Todisco Stefano 
Published: December 2024

A new generation of robust aminopropyl-functionalized PMO-ILs, containing 35% imidazolium bridges, were utilized to immobilize an active and recyclable ruthenium catalyst for the selective meta-bromination of 2-aryl pyridines and other heterocycles.
LiTaO3‐ on‐YAG surface acoustic wave resonator with low TCF and spurious modes mitigation
Authors: Yantchev Ventsislav , Ji Yuancheng , Bolamiri Farshad Farahi , Guo Fei 
Published: December 2024

AbstractSurface acoustic wave (SAW) resonators employing LiTaO3 piezoelectric platelet on yttrium aluminium garnet (YAG) substrate are designed with a low temperature coefficient of frequency (TCF) and spurious modes suppression. Transverse modes in the structure are suppressed through the transducer topology, while the higher‐order plate‐guided modes are inherently suppressed by the YAG‐based device platform. Fabricated 1.7 GHz SAW resonator demonstrates significant suppression of the higher order spurious modes as compared to their counterpart on Si (100) base while retaining very low TCF and Q factor of about 2700. The maximum resonance‐to‐antiresonance (R‐aR) bandwidth is estimated to be 4.8%. YAG‐based SAW platform is an alternative to the classical Si‐based SAW platform in radio frequency filters in the lower GHz range, offering high performance and simplifying the stack topology by eliminating the need for additional charge trapping layers. Preliminary estimations show that YAG being commercially viable in photonics is scalable to 4″–6″ low‐cost wafers, required in the RF SAW industry.
Blind reconstruction of BCH codes based on candidate generator polynomial in random situation
Authors: Sharifian Mazraeh Mollaei Ali , Sharifian Mazraeh Mollaei Masoud 
Published: December 2024

AbstractA novel method for blind reconstruction of binary Bose–Chaudhuri–Hocquenghem codes is proposed. Compared to previously reported works, a new approach to find the goal generator polynomial is employed. First, using the feature that each codeword polynomial of a t‐error‐correcting Bose–Chaudhuri–Hocquenghem code has the same 2t consecutive roots over Galois field, a new set of candidate generator polynomials is introduced. Then, this set in a random situation to find the correct generator polynomial is investigated. Monte Carlo simulations demonstrate the superiority of the proposed reconstruction algorithm compared to the previous methods.
AR‐assisted surgery: Precision placement of patient specific hip implants based on 3D printed PSIs
Authors: Iribar‐Zabala Amaia , Fernández‐Fernández Tanya , Orozco‐Martínez Javier , Calvo‐Haro José , Pérez‐Mañanes Rubén , Aguilera‐Jiménez Elena , de Gregorio‐Bermejo Carla , Benito Rafael , Pose‐Díez‐de‐la‐Lastra Alicia , Beristain‐Iraola Andoni , Pascau Javier , García‐Sevilla Mónica 
Published: December 2024

AbstractPatient‐specific implant placement in the case of pelvic tumour resection is usually a complex procedure, where the planned optimal position of the prosthesis may differ from the final location. This discrepancy arises from incorrect or differently executed bone resection and improper final positioning of the prosthesis. In order to overcome such mismatch, a navigation solution is presented based on an augmented reality application for HoloLens 2 to assist the entire procedure. This involves placing patient‐specific instruments for tumour resection guidance in the supraacetabular, ischial and symphysial regions, performing the osteotomy and assisting within the adequate positioning of the implant. The supraacetabular patient‐specific instrument and the prosthesis included optical markers attached to them to be used as reference for surgical guidance. The proposed application and workflow were validated by two clinicians on six phantoms, designed and fabricated from different cadaver specimens. The accuracy of the solution was evaluated by comparing the final position after navigation with the position defined in the surgical plan. Preliminary assessment shows promising results for the guidance system, with positive clinician feedback.
An intelligent retrievable object‐tracking system with real‐time edge inference capability
Authors: Li Yujie , Wang Yifu , Ma Zihang , Wang Xinghe , Tan Benying , Ding Shuxue 
Published: December 2024

AbstractAn intelligent retrievable object‐tracking system assists users in quickly and accurately locating lost objects. However, challenges such as real‐time processing on edge devices, low image resolution, and small‐object detection significantly impact the accuracy and efficiency of video‐stream‐based systems, especially in indoor home environments. To overcome these limitations, a novel real‐time intelligent retrievable object‐tracking system is designed. The system incorporates a retrievable object‐tracking algorithm that combines DeepSORT and sliding window techniques to enhance tracking capabilities. Additionally, the YOLOv7‐small‐scale model is proposed for small‐object detection, integrating a specialized detection layer and the convolutional batch normalization LeakyReLU spatial‐depth convolution module to enhance feature capture for small objects. TensorRT and INT8 quantization are used for inference acceleration on edge devices, doubling the frames per second. Experiments on a Jetson Nano (4 GB) using YOLOv7‐small‐scale show an 8.9% improvement in recognition accuracy over YOLOv7‐tiny in video stream processing. This advancement significantly boosts the system's performance in efficiently and accurately locating lost objects in indoor home settings.