bluuebunny/crossref_metadata_2025_split huggingface dataset:
Covalent penicillin-protein conjugates elicit anti-drug antibodies that are clonally and functionally restricted
Authors: Deimel Lachlan P. , Moynié Lucile , Sun Guoxuan , Lewis Viliyana , Turner Abigail , Buchanan Charles J. , Burnap Sean A. , Kutuzov Mikhail , Kobras Carolin M. , Demyanenko Yana , Mohammed Shabaz , Stracy Mathew , Struwe Weston B. , Baldwin Andrew J. , Naismith James , Davis Benjamin G. , Sattentau Quentin J. 
Published: August 2024

AbstractMany archetypal and emerging classes of small-molecule therapeutics form covalent protein adducts. In vivo, both the resulting conjugates and their off-target side-conjugates have the potential to elicit antibodies, with implications for allergy and drug sequestration. Although β-lactam antibiotics are a drug class long associated with these immunological phenomena, the molecular underpinnings of off-target drug-protein conjugation and consequent drug-specific immune responses remain incomplete. Here, using the classical β-lactam penicillin G (PenG), we probe the B and T cell determinants of drug-specific IgG responses to such conjugates in mice. Deep B cell clonotyping reveals a dominant murine clonal antibody class encompassing phylogenetically-related IGHV1, IGHV5 and IGHV10 subgroup gene segments. Protein NMR and x-ray structural analyses reveal that these drive structurally convergent binding modes in adduct-specific antibody clones. Their common primary recognition mechanisms of the penicillin side-chain moiety (phenylacetamide in PenG)—regardless of CDRH3 length—limits cross-reactivity against other β-lactam antibiotics. This immunogenetics-guided discovery of the limited binding solutions available to antibodies against side products of an archetypal covalent inhibitor now suggests future potential strategies for the ‘germline-guided reverse engineering’ of such drugs away from unwanted immune responses.
Antibody gene features associated with binding and functional activity in malaria vaccine-derived human mAbs
Authors: Coelho Camila H. , Marquez Susanna , Nguemwo Tentokam Bergeline C. , Berhe Anne D. , Miura Kazutoyo , Rao Vishal N. , Long Carole A. , Doumbo Ogobara K. , Sagara Issaka , Healy Sara , Kleinstein Steven H. , Duffy Patrick E. 
Published: August 2024

AbstractThe impact of adjuvants on malaria vaccine-induced antibody repertoire is poorly understood. Here, we characterize the impact of two adjuvants, Alhydrogel® and AS01, on antibody clonotype diversity, binding and function, post malaria vaccination. We expressed 132 recombinant anti-Pfs230D1 human monoclonal antibodies (mAbs) from participants immunized with malaria transmission-blocking vaccine Pfs230D1, formulated with either Alhydrogel® or AS01. Anti-Pfs230D1 mAbs generated by Alhydrogel® formulation showed higher binding frequency to Pfs230D1 compared to AS01 formulation, although the frequency of functional mAbs was similar between adjuvant groups. Overall, the AS01 formulation induced anti-Pfs230D1 functional antibodies from a broader array of germline sequences versus the Alhydrogel® formulation. All mAbs using IGHV1-69 gene from the Alhydrogel® cohort bound to recombinant Pfs230D1, but did not block parasite transmission to mosquitoes, similar to the IGHV1-69 mAbs isolated from the AS01 cohort. These findings may help inform vaccine design and adjuvant selection for immunization with Plasmodium antigens.
Dynamic clade transitions and the influence of vaccination on the spatiotemporal circulation of SARS-CoV-2 variants
Authors: Banho Cecília Artico , de Carvalho Marques Beatriz , Sacchetto Lívia , Lima Ana Karoline Sepedro , Parra Maisa Carla Pereira , Lima Alex Ranieri Jeronimo , Ribeiro Gabriela , Martins Antonio Jorge , Barros Claudia Renata dos Santos , Elias Maria Carolina , Sampaio Sandra Coccuzzo , Slavov Svetoslav Nanev , Rodrigues Evandra Strazza , Santos Elaine Vieira , Covas Dimas Tadeu , Kashima Simone , Brassaloti Ricardo Augusto , Petry Bruna , Clemente Luan Gaspar , Coutinho Luiz Lehmann , Assato Patricia Akemi , da Silva da Costa Felipe Allan , Grotto Rejane Maria Tommasini , Poleti Mirele Daiana , Lesbon Jessika Cristina Chagas , Mattos Elisangela Chicaroni , Fukumasu Heidge , Giovanetti Marta , Alcantara Luiz Carlos Junior , Souza-Neto Jayme A. , Rahal Paula , Araújo João Pessoa , Spilki Fernando Rosado , Althouse Benjamin M. , Vasilakis Nikos , Nogueira Maurício Lacerda 
Published: August 2024

AbstractSince 2021, the emergence of variants of concern (VOC) has led Brazil to experience record numbers of in COVID-19 cases and deaths. The expanded spread of the SARS-CoV-2 combined with a low vaccination rate has contributed to the emergence of new mutations that may enhance viral fitness, leading to the persistence of the disease. Due to limitations in the real-time genomic monitoring of new variants in some Brazilian states, we aimed to investigate whether genomic surveillance, coupled with epidemiological data and SARS-CoV-2 variants spatiotemporal spread in a smaller region, can reflect the pandemic progression at a national level. Our findings revealed three SARS-CoV-2 variant replacements from 2021 to early 2022, corresponding to the introduction and increase in the frequency of Gamma, Delta, and Omicron variants, as indicated by peaks of the Effective Reproductive Number (Reff). These distinct clade replacements triggered two waves of COVID-19 cases, influenced by the increasing vaccine uptake over time. Our results indicated that the effectiveness of vaccination in preventing new cases during the Delta and Omicron circulations was six and eleven times higher, respectively, than during the period when Gamma was predominant, and it was highly efficient in reducing the number of deaths. Furthermore, we demonstrated that genomic monitoring at a local level can reflect the national trends in the spread and evolution of SARS-CoV-2.
Marine Fish Movement: home range sizes for commercially relevant species
Authors: Bradley Darcy , Caughman Alicia M. , Fogg Sandra A. , Cabral Reniel B. , Mayorga Juan , Goodell Whitney , Millage Katherine D. , White Timothy D. 
Published: August 2024

AbstractEstimates of home range sizes for marine fishes are essential for designing and assessing the effects of spatial wildlife conservation policies and management interventions. However, in situ studies of marine species movement are challenging and often expensive, resulting in a paucity of data on the home range size of the vast majority of marine fishes. Here, we develop a set of new datasets, which we have collectively named Marine Fish Movement, that synthesises published empirically evaluated home ranges reported for adult marine fishes that interact with fisheries and leverage these data to estimate home range sizes for unstudied species. The empirical data contain estimated home range sizes (km2) for 193 species across 63 family groups from 179 studies published between 1971 and 2022. We use a random forest regression model to estimate home range sizes (km2) for 664 fished marine species currently lacking home range estimates. Marine Fish Movement can inform spatial interventions including the design and management of marine protected areas and dynamic fisheries management to meet sustainability goals.
Datasets of traits of zodariid spiders (Araneae: Zodariidae)
Authors: Pekár Stano 
Published: August 2024

AbstractSpecies traits are essential for inferences on ecology and the evolution of organisms. Spiders are the most abundant and diversified terrestrial predators, playing an important role in a range of ecosystem services. Here, I present datasetse on all traits of zodariid spiders, which are known to be free-living ground-dwellers occurring on all continents (except Antarctica) with the highest species diversity in Australia. I collated the data from published resources. The datasets includes nearly 100 000 trait records on all (90) genera and almost all species (1249) of the family. The majority of the 88 traits collected are morphometric, followed by those relating to ecology, reproduction, and physiology. Morphometric traits were available for the majority of species. Other trait classes were only available for some species. I provide a standardized classification of selected categorical traits (habitat, microhabitat, retreat type, circadian activity, prey, primary defensive, and predators). This is the first complete database of traits of a whole spider family, which is available through the World Spider Trait database.
Skin exposure to soil microbiota elicits changes in cell-mediated immunity to pneumococcal vaccine
Authors: Roslund Marja I. , Nurminen Noora , Oikarinen Sami , Puhakka Riikka , Grönroos Mira , Puustinen Leena , Kummola Laura , Parajuli Anirudra , Cinek Ondřej , Laitinen Olli H. , Hyöty Heikki , Sinkkonen Aki 
Published: August 2024

AbstractA resilient immune system is characterized by its capacity to respond appropriately to challenges, such as infections, and it is crucial in vaccine response. Here we report a paired randomized intervention-control trial in which we evaluated the effect of microbially rich soil on immune resilience and pneumococcal vaccine response. Twenty-five age and sex matched pairs of volunteers were randomized to intervention and control groups. The intervention group rubbed hands three times a day in microbially rich soil until participants received a pneumococcal vaccine on day 14. Vaccine response, skin and gut bacteriome and blood cytokine levels were analyzed on days 0, 14 and 35. Peripheral blood mononuclear cells (PBMCs) were stimulated with vaccine components and autoclaved soil for cytokine production. Commensal bacterial community shifted only in the intervention group during the 14-day intervention period. When PBMCs collected on day 14 before the vaccination were stimulated with the vaccine components, IFN-y production increased in the intervention but not in the control group. On day 35, vaccination induced a robust antibody response in both groups. In parallel, gut bacterial community was associated with TGF-β plasma levels and TGF-β decrease in plasma was lower in the intervention group. The results indicate that exposure to microbially rich soil can modulate the cell-mediated immunity to components in pneumococcal vaccine.
Controlling wind turbine tower vibration under external force by applying control systems combination
Authors: Amer Y. A. , EL-Sayed A. T. , Agwa M. M. 
Published: August 2024

AbstractThe global focus has recently shifted away from fuel-based power sources, and one of the most important projects for energy production is wind energy. To maintain low costs, the current research examines the problem of vibrations affecting wind turbine towers’ performance (WTTs). In particular, the tower, resulting from excessive vibrations, can negatively affect a structure’s power output and service life, as it can cause fatigue. Therefore, we conducted numerical tests on various types of controlled systems. Our tests revealed that combining a new technique cubic negative velocity control (CNVC) and linear negative acceleration control (LNAC) was the most effective and cost-efficient option for vibration damping. This solution was derived by using an approximation method for the averaging technique. The external force is an important component of a nonlinear dynamic system and can be characterized by two-degree-of-freedom (2-DOF) differential coupled equations. After implementing the control measures, we conducted a numerical analysis of the vibration values before and after the operation. Stability is studied numerically. The numerical and approximate solutions were confirmed through the frequency response equation and time history with fourth-order Runge–Kutta (RK-4). Finally, we investigated the effect of parameters and compared our results with those of previously published studies.
UAV propeller fault diagnosis using deep learning of non-traditional χ2-selected Taguchi method-tested Lempel–Ziv complexity and Teager–Kaiser energy features
Authors: Al-Haddad Luttfi A. , Giernacki Wojciech , Basem Ali , Khan Zeashan Hameed , Jaber Alaa Abdulhady , Al-Haddad Sinan A. 
Published: August 2024

AbstractFault detection and isolation in unmanned aerial vehicle (UAV) propellers are critical for operational safety and efficiency. Most existing fault diagnosis techniques rely basically on traditional statistical-based methods that necessitate better approaches. This study explores the application of untraditional feature extraction methodologies, namely Permutation Entropy (PE), Lempel–Ziv Complexity (LZC), and Teager–Kaiser Energy Operator (TKEO), on the PADRE dataset, which encapsulates various rotor fault configurations. The extracted features were subjected to a Chi-Square (χ2) feature selection process to identify the most significant features for input into a Deep Neural Network. The Taguchi method was utilized to test the performance of the recorded features, correspondingly. Performance metrics, including Accuracy, F1-Score, Precision, and Recall, were employed to evaluate the model’s effectiveness before and after the feature selection. The achieved accuracy has increased by 0.9% when compared with results utilizing traditional statistical methods. Comparative analysis with prior research reveals that the proposed untraditional features surpass traditional methods in diagnosing UAV propeller faults. It resulted in improved performance metrics with Accuracy, F1-Score, Precision, and Recall reaching 99.6%, 99.5%, 99.5%, and 99.5%, respectively. The results suggest promising directions for future research in UAV maintenance and safety protocols.
Tectonic structures of the Dome Fuji region, East Antarctica, based on new magnetic data
Authors: Guy Alexandra , Eagles Graeme , Eisen Olaf 
Published: August 2024

AbstractThe Oldest Ice Reconnaissance (OIR) airborne geophysical survey in East Antarctica was flown over approximately 170,000 km2 of the Dome Fuji region in 2016/17. The survey’s results support new insights into the subglacial geology and its meaning for the tectonic histories of the supercontinents Rodinia and Gondwana. The new magnetic and radar-derived bed topography data are integrated with previously acquired magnetic and gravity data, allowing the mapping of crustal domains within and beyond the survey’s limits. The magnetic data reveal three distinct domains within the survey region, delineated by N–S oriented boundaries, partly aligned with gravity domains following upward continuation transformations for both datasets. Additionally, four primary sets of magnetic lineaments were identified, exhibiting correlations with topographic and gravity patterns. These correlations indicate the continuation of the Tonian Oceanic Arc Super Terrane (TOAST) southward of its previously known southern limit. Moreover, an E–W-trending magnetic anomaly, the Elbert magnetic anomaly, suggests the suture between the recently-proposed subglacial Valkyrie craton and the TOAST. Furthermore, the analysis reveals a broad scale shear zone, named here the OIR shear zone, which formed as a result of oblique collision of the Ruker and Valkyrie cratons during the amalgamation of Gondwana.
Phenotypic diversity and population structure of Pecan (Carya illinoinensis) collections reveals geographic patterns
Authors: Wang Xinwang , Stein Larry , Black Mark , Kubenka Keith , Randall Jennifer , Ding Chen 
Published: August 2024

AbstractPecan (Carya illinoinensis) is an economically important nut crop known for its genetic diversity and adaptability to various climates. Understanding the growth variability, phenological traits, and population structure of pecan populations is crucial for breeding programs and conservation. In this study, plant growth and phenological traits were evaluated over three consecutive seasons (2015–2017) for 550 genotypes from 26 provenances. Significant variations in plant height, stem diameter, and budbreak were observed among provenances, with Southern provenances exhibiting faster growth and earlier budbreak compared to Northern provenances. Population structure analysis using SNP markers revealed eight distinct subpopulations, reflecting genetic differentiation among provenances. Notably, Southern Mexico collections formed two separate clusters, while Western collections, such as 'Allen 3', 'Allen 4', and 'Riverside', were distinguished from others. 'Burkett' and 'Apache' were grouped together due to their shared maternal parentage. Principal component analysis and phylogenetic tree analysis further supported subpopulation differentiation. Genetic differentiation among the 26 populations was evident, with six clusters highly in agreement with the subpopulations identified by STRUCTURE and fastSTRUCTURE. Principal components analysis (PCA) revealed distinct groups, corresponding to subpopulations identified by genetic analysis. Discriminant analysis of PCA (DAPC) based on provenance origin further supported the genetic structure, with clear separation of provenances into distinct clusters. These findings provide valuable insights into the genetic diversity and growth patterns of pecan populations. Understanding the genetic basis of phenological traits and population structure is essential for selecting superior cultivars adapted to diverse environments. The identified subpopulations can guide breeding efforts to develop resilient rootstocks and contribute to the sustainable management of pecan genetic resources. Overall, this study enhances our understanding of pecan genetic diversity and informs conservation and breeding strategies for the long-term viability of pecan cultivation.
Individual mangrove trees provide alternative reef fish habitat on backreefs
Authors: von Hammerstein Hannah , Fett Theresa-Marie , Ferse Sebastian C. A. , Helfer Véronique , Kininmonth Stuart , Bejarano Sonia 
Published: August 2024

AbstractMangrove trees occur in a variety of geomorphic and sedimentary settings. Yet, studies investigating their role as habitat providers often focus on the most common biophysical types, such as deltaic, estuarine, open coast or lagoonal mangroves on soft sediments, disregarding less typical environments. Here, we investigated the influence of individual mangrove trees growing on a consolidated backreef system (Laucala Bay, Fiji) on habitat use by reef fishes. Combining field surveys and an experiment, we quantified the extent to which reef mangrove trees serve as habitat for solitary or shoaling reef fishes. Using mangrove tree mimics, we disentangled effects attributable to the physical structure of trees from those related to their bio-chemical properties. We found that fish numbers were 3.7 times higher within close proximity to the mangrove trees than at control sites and correlated significantly with root system perimeter. The roots of larger trees sheltered aggregations of juveniles and adults at incoming and high tides. Mangrove trees and mimics attracted fishes alike. We show that mangrove trees on backreefs provide habitat for shoaling and adult reef fishes in addition to serving as nursery areas, an ecosystem service otherwise lacking on backreef areas with low structural complexity.
Disparities in clinical studies of AI enabled applications from a global perspective
Authors: Yang Rui , Nair Sabarinath Vinod , Ke Yuhe , D’Agostino Danny , Liu Mingxuan , Ning Yilin , Liu Nan 
Published: August 2024

AbstractArtificial intelligence (AI) has been extensively researched in medicine, but its practical application remains limited. Meanwhile, there are various disparities in existing AI-enabled clinical studies, which pose a challenge to global health equity. In this study, we conducted an in-depth analysis of the geo-economic distribution of 159 AI-enabled clinical studies, as well as the gender disparities among these studies. We aim to reveal these disparities from a global literature perspective, thus highlighting the need for equitable access to medical AI technologies.
Universal-neural-network-potential molecular dynamics for lithium metal and garnet-type solid electrolyte interface
Authors: Iwasaki Rinon , Tanibata Naoto , Takeda Hayami , Nakayama Masanobu 
Published: August 2024

AbstractAll-solid-state Li-metal batteries can conceivably improve the safety and extend the driving ranges of electric vehicles. In this regard, the garnet-type solid electrolyte Li7La3Zr2O12 (LLZ) has garnered considerable attention because of its high Li-ion conductivity and nonreactivity towards molten Li metal. Here, we perform molecular dynamics (MD) simulations using a universal neural network potential (UNNP) to analyse the Li-ion exchange at the LLZ/Li interface at the atomic scale. The UNNP-MD calculations show that Li ions traverse the LLZ/Li interface and that excess Li ions relative to the stoichiometric composition accumulate in an approximately 1 nm-thick zone near the LLZ phase interface, signifying the formation of a space-charge layer. Electronic structural analysis of the UNNP-MD-derived configuration, performed using density functional theory calculations, reveals band bending near the LLZ phase interface and the simultaneous suppression of Li metal reduction. These findings can help expedite the development of rationally designed all-solid-state Li-metal batteries.
Type II collagen scaffolds for tissue engineering
Authors: Hu Xu , Wu Zhonglian , Zhang Zhen , Yao Hang , Wang Dong-An 
Published: August 2024

AbstractType II collagen (CII), a key component of cartilaginous tissues, offers an attractive option for fabricating biomimetic scaffolds that provide mechanical support and biochemical signals to facilitate cell adhesion, proliferation, and differentiation. Advances in fabrication technologies have enabled the creation of intricate and multicellular CII-based scaffolds that more accurately replicate the natural structure of tissues. Here, we review the application of CII in tissue engineering and highlight its crucial contributions to the regeneration of hyaline cartilage and intervertebral discs. Additionally, we discuss the versatile roles of CII in other biomedical applications, including disease modeling, bone regeneration, and the development of artificial immune organs.
Ecosystem services “on the move” as a nature-based solution for financing the Global Biodiversity Framework
Authors: Sequeira Ana M. M. , Rashid Sumaila U. , Rogers Abbie A. 
Published: August 2024

AbstractThe Kunming-Montreal Global Biodiversity Framework (GBF) aims to halt global biodiversity loss. However, its implementation process will need strategic financing particularly to address the divide between the Global North and Global South. Highly migratory marine vertebrates (henceforth marine megafauna) connect distant ecosystems providing ecosystem services across jurisdictions with considerably different conservation interests and economic ability to pay for biodiversity protection. Although such migratory behaviour presents a specially challenging case for protection, because it provides a direct link between developed and less-developed countries it can provide a key to unlock the potential for financial support for implementing the GBF and shed light on a nature-based solution for how Official Development Assistance (ODA) could be deployed. Such ODA could ensure the global protection of these charismatic and threatened species, while contributing to the financing of the GBF. Our work emphasises the economic value of marine megafauna ecosystem services provided “on the move” across jurisdictions and highlights the economic value of conserving marine megafauna, our global heritage.