bluuebunny/crossref_metadata_2025_split huggingface dataset:
Potent AMA1-specific human monoclonal antibody against Plasmodium vivax Pre-erythrocytic and Blood Stages
Authors: Winnicki Anna C. , Dietrich Melanie H. , Yeoh Lee M. , Carias Lenore L. , Roobsoong Wanlapa , Drago Chiara L. , Malachin Alyssa N. , Redinger Karli R. , Feufack-Donfack Lionel Brice , Baldor Lea , Jung Nicolai C. , McLaine Olivia S. , Skomorovska-Prokvolit Yelenna , Orban Agnes , Opi D. Herbert , Kirtley Payton , Nielson Kiersey , Aleshnick Maya , Zanghi Gigliola , Rezakhani Nastaran , Vaughan Ashley M. , Wilder Brandon K. , Sattabongkot Jetsumon , Tham Wai-Hong , Popovici Jean , Beeson James G. , Bosch Jürgen , King Christopher L. 
Published: December 2024

AbstractNew therapeutics are necessary for preventing Plasmodium vivax malaria due to easy transmissibility and dormancy in the liver that increases the clinical burden due to recurrent relapse. In this manuscript we characterize 12 Pv Apical Membrane Antigen 1 (PvAMA1) specific human monoclonal antibodies from Peripheral Blood Mononuclear Cells of a Pv-exposed individual. PvAMA1 is essential for sporozoite and merozoite invasion, making it a unique therapeutic target. We show that humAb 826827 blocks the invasion of human reticulocytes using Pv clinical isolates and inhibits sporozoite invasion of human hepatocytes in vitro (IC50 of 0.3 – 3.7 µg/mL). Inoculation of human liver transgenic (FRG-humHep) female mice with humAb 826827 significantly reduces liver infection in vivo. The crystal structure of rPvAMA1 bound to 826827 shows that 826827 partially occupies the highly conserved hydrophobic groove in PvAMA1 that binds its known receptor, RON2. We have isolated a potent humAb that is isolate-transcendent, blocks both pre-erythrocytic and blood stage infection, and could be a potential therapy for Pv.
Two-stage binding of mitochondrial ferredoxin-2 to the core iron-sulfur cluster assembly complex
Authors: Steinhilper Ralf , Boß Linda , Freibert Sven-A. , Schulz Vinzent , Krapoth Nils , Kaltwasser Susann , Lill Roland , Murphy Bonnie J. 
Published: December 2024

AbstractIron-sulfur (FeS) protein biogenesis in eukaryotes begins with the de novo assembly of [2Fe-2S] clusters by the mitochondrial core iron-sulfur cluster assembly (ISC) complex. This complex comprises the scaffold protein ISCU2, the cysteine desulfurase subcomplex NFS1-ISD11-ACP1, the allosteric activator frataxin (FXN) and the electron donor ferredoxin-2 (FDX2). The structural interaction of FDX2 with the complex remains unclear. Here, we present cryo-EM structures of the human FDX2-bound core ISC complex showing that FDX2 and FXN compete for overlapping binding sites. FDX2 binds in either a ‘distal’ conformation, where its helix F interacts electrostatically with an arginine patch of NFS1, or a ‘proximal’ conformation, where this interaction tightens and the FDX2-specific C terminus binds to NFS1, facilitating the movement of the [2Fe-2S] cluster of FDX2 closer to the ISCU2 FeS cluster assembly site for rapid electron transfer. Structure-based mutational studies verify the contact areas of FDX2 within the core ISC complex.
Models optimized for real-world tasks reveal the task-dependent necessity of precise temporal coding in hearing
Authors: Saddler Mark R. , McDermott Josh H. 
Published: December 2024

AbstractNeurons encode information in the timing of their spikes in addition to their firing rates. Spike timing is particularly precise in the auditory nerve, where action potentials phase lock to sound with sub-millisecond precision, but its behavioral relevance remains uncertain. We optimized machine learning models to perform real-world hearing tasks with simulated cochlear input, assessing the precision of auditory nerve spike timing needed to reproduce human behavior. Models with high-fidelity phase locking exhibited more human-like sound localization and speech perception than models without, consistent with an essential role in human hearing. However, the temporal precision needed to reproduce human-like behavior varied across tasks, as did the precision that benefited real-world task performance. These effects suggest that perceptual domains incorporate phase locking to different extents depending on the demands of real-world hearing. The results illustrate how optimizing models for realistic tasks can clarify the role of candidate neural codes in perception.
Group 2 innate lymphoid cells are a non-redundant source of interleukin-5 required for development and function of murine B1 cells
Authors: Troch Karoline F. , Jakob Manuel O. , Forster Patrycja M. , Jarick Katja J. , Schreiber Jonathan , Preusser Alexandra , Guerra Gabriela M. , Durek Pawel , Tizian Caroline , Sterczyk Nele , Helfrich Sofia , Duerr Claudia U. , Voehringer David , Witkowski Mario , Artis David , Rollenske Tim , Kruglov Andrey A. , Mashreghi Mir-Farzin , Klose Christoph S. N. 
Published: December 2024

AbstractTissue-resident immune cells, such as innate lymphoid cells, mediate protective or detrimental immune responses at barrier surfaces. Upon activation by stromal or epithelial cell-derived alarmins, group 2 innate lymphoid cells (ILC2s) are a rapid source of type 2 cytokines, such as IL-5. However, due to the overlap in effector functions, it remains unresolved whether ILC2s are an essential component of the type 2 response or whether their function can be compensated by other cells, such as T cells. Here we show a non-redundant role of ILC2s in supporting the development and function of B1 cells. We demonstrate that B1 cells fail to develop properly in the absence of ILC2s and identify the IL-33 receptor on ILC2s as an essential cell-intrinsic regulator of IL-5 production. Further, conditional deletion of Il5 in ILC2s results in defective B1 cell development and immunoglobulin production. Consequently, B1 cells with phosphatidylcholine specific B cell receptor rearrangements are diminished in ILC2-deficient mice. Thus, our data establish an essential function of ILC2s in supporting B1 cells and antibody production at barrier surfaces.
SHIV remission in macaques with early treatment initiation and ultra long-lasting antiviral activity
Authors: Daly Michele B. , Dinh Chuong , Holder Angela , Rudolph Donna , Ruone Susan , Swaims-Kohlmeier Alison , Khalil George , Sharma Sunita , Mitchell James , Condrey Jillian , Kim Daniel , Pan Yi , Curtis Kelly , Williams Peter , Spreen William , Heneine Walid , García-Lerma J. Gerardo 
Published: December 2024

AbstractStudies in SIV-infected macaques show that the virus reservoir is particularly refractory to conventional suppressive antiretroviral therapy (ART). We posit that optimized ART regimens designed to have robust penetration in tissue reservoirs and long-lasting antiviral activity may be advantageous for HIV or SIV remission. Here we treat macaques infected with RT-SHIV with oral emtricitabine/tenofovir alafenamide and long-acting cabotegravir/rilpivirine without (n = 4) or with (n = 4) the immune activator vesatolimod after the initial onset of viremia. We document full suppression in all animals during treatment (4-12 months) and no virus rebound after treatment discontinuation (1.5-2 years of follow up) despite CD8 + T cell depletion. We show efficient multidrug penetration in virus reservoirs and persisting rilpivirine in plasma for 2 years after the last dose. Our results document a type of virus remission that is achieved through early treatment initiation and provision of ultra long-lasting antiviral activity that persists after treatment cessation.
Dynamics of the blood plasma proteome during hyperacute HIV-1 infection
Authors: Nazziwa Jamirah , Freyhult Eva , Hong Mun-Gwan , Johansson Emil , Årman Filip , Hare Jonathan , Gounder Kamini , Rezeli Melinda , Mohanty Tirthankar , Kjellström Sven , Kamali Anatoli , Karita Etienne , Kilembe William , Price Matt A. , Kaleebu Pontiano , Allen Susan , Hunter Eric , Ndung’u Thumbi , Gilmour Jill , Rowland-Jones Sarah L. , Sanders Eduard , Hassan Amin S. , Esbjörnsson Joakim 
Published: December 2024

AbstractThe complex dynamics of protein expression in plasma during hyperacute HIV-1 infection and its relation to acute retroviral syndrome, viral control, and disease progression are largely unknown. Here, we quantify 1293 blood plasma proteins from 157 longitudinally linked plasma samples collected before, during, and after hyperacute HIV-1 infection of 54 participants from four sub-Saharan African countries. Six distinct longitudinal expression profiles are identified, of which four demonstrate a consistent decrease in protein levels following HIV-1 infection. Proteins involved in inflammatory responses, immune regulation, and cell motility are significantly altered during the transition from pre-infection to one month post-infection. Specifically, decreased ZYX and SCGB1A1 levels, and increased LILRA3 levels are associated with increased risk of acute retroviral syndrome; increased NAPA and RAN levels, and decreased ITIH4 levels with viral control; and increased HPN, PRKCB, and ITGB3 levels with increased risk of disease progression. Overall, this study provides insight into early host responses in hyperacute HIV-1 infection, and present potential biomarkers and mechanisms linked to HIV-1 disease progression and viral load.
Fully printed zero-static power MoS2 switch coded reconfigurable graphene metasurface for RF/microwave electromagnetic wave manipulation and control
Authors: Xiao Xiaoyu , Peng Zixing , Zhang Zirui , Zhou Xinyao , Liu Xuzhao , Liu Yang , Wang Jingjing , Li Haiyu , Novoselov Kostya S. , Casiraghi Cinzia , Hu Zhirun 
Published: December 2024

AbstractReduction of power consumption is the key target for modern electronic devices. To this end, a lot of attention is paid to zero-static power switches, being able to change their state between highly resistive and highly conductive and remain in this state even in the absence of external voltage. Still, the implementation of such switches is slow because of compatibility issues of new materials with CMOS technology. At the same time, printable technology enables low-cost processes at ambient temperature and integration of devices onto flexible substrates. Here we demonstrate that printed Ag/MoS2/Ag heterostructures can be used as zero-static power switches in radiofrequency/microwave spectrum and fully-integrated reconfigurable metasurfaces. Combined with graphene, our printed platform enables reconfigurable metasurface for electromagnetic wave manipulation and control for wireless communications, sensing, and holography. In addition, it is also demonstrated that the localised MoS2 phase change may have promoted Ag diffusion in forming conductive filaments.
Self-assembly of 1T/1H superlattices in transition metal dichalcogenides
Authors: Luo Chaojie , Cao Guohua , Wang Beilin , Jiang Lili , Zhao Hengyi , Li Tongrui , Tai Xiaolin , Lin Zhiyong , Lin Yue , Sun Zhe , Cui Ping , Zhang Hui , Zhang Zhenyu , Zeng Changgan 
Published: December 2024

AbstractHeterostructures and superlattices composed of layered transition metal dichalcogenides (TMDs), celebrated for their superior emergent properties over individual components, offer significant promise for the development of multifunctional electronic devices. However, conventional fabrication techniques for these structures depend on layer-by-layer artificial construction and are hindered by their complexity and inefficiency. Herein, we introduce a universal strategy for the automated synthesis of TMD superlattice single crystals through self-assembly, exemplified by the NbSe2-xTex 1T/1H superlattice. The core principle of this strategy is to balance the formation energies of T (octahedral) and H (trigonal prismatic) phases. By adjusting the Te to Se stoichiometric ratio in NbSe2-xTex, we reduce the formation energy disparity between the T and H phases, enabling the self-assembly of 1T and 1H layers into a 1T/1H superlattice. The resulting 1T/1H superlattices retain electronic characteristics of both 1T and 1H layers. We further validate the universality of this strategy by achieving 1T/1H superlattices through substituting Nb atoms in NbSe2 with V or Ti atoms. This self-assembly for superlattice crystal synthesis approach could extend to other layered materials, opening new avenues for efficient fabrication and broad applications of superlattices.
Coxsackievirus and adenovirus receptor expression facilitates enteroviral infections to drive the development of pancreatic cancer
Authors: Bastea Ligia I. , Liu Xiang , Fleming Alicia K. , Pandey Veethika , Döppler Heike , Edenfield Brandy H. , Krishna Murli , Zhang Lizhi , Thompson E. Aubrey , Grandgenett Paul M. , Hollingsworth Michael A. , Fairweather DeLisa , Clemens Dahn , Storz Peter 
Published: December 2024

AbstractThe development of pancreatic cancer requires both, acquisition of an oncogenic mutation in KRAS as well as an inflammatory insult. However, the physiological causes for pancreatic inflammation are less defined. We show here that oncogenic KRas-expressing pre-neoplastic lesion cells upregulate coxsackievirus (CVB) and adenovirus receptor (CAR). This facilitates infections from enteroviruses such as CVB3, which can be detected in approximately 50% of pancreatic cancer patients. Moreover, using an animal model we show that a one-time pancreatic infection with CVB3 in control mice is transient, but in the presence of oncogenic KRas drives chronic inflammation and rapid development of pancreatic cancer. We further demonstrate that a knockout of CAR in pancreatic lesion cells blocks these CVB3-induced effects. Our data demonstrate that KRas-caused lesions promote the development of pancreatic cancer by enabling certain viral infections.
Arrayed CRISPR libraries for the genome-wide activation, deletion and silencing of human protein-coding genes
Authors: Yin Jiang-An , Frick Lukas , Scheidmann Manuel C. , Liu Tingting , Trevisan Chiara , Dhingra Ashutosh , Spinelli Anna , Wu Yancheng , Yao Longping , Vena Dalila Laura , Knapp Britta , Guo Jingjing , De Cecco Elena , Ging Kathi , Armani Andrea , Oakeley Edward J. , Nigsch Florian , Jenzer Joel , Haegele Jasmin , Pikusa Michal , Täger Joachim , Rodriguez-Nieto Salvador , Bouris Vangelis , Ribeiro Rafaela , Baroni Federico , Bedi Manmeet Sakshi , Berry Scott , Losa Marco , Hornemann Simone , Kampmann Martin , Pelkmans Lucas , Hoepfner Dominic , Heutink Peter , Aguzzi Adriano 
Published: December 2024

Abstract
Arrayed CRISPR libraries extend the scope of gene-perturbation screens to non-selectable cell phenotypes. However, library generation requires assembling thousands of vectors expressing single-guide RNAs (sgRNAs). Here, by leveraging massively parallel plasmid-cloning methodology, we show that arrayed libraries can be constructed for the genome-wide ablation (19,936 plasmids) of human protein-coding genes and for their activation and epigenetic silencing (22,442 plasmids), with each plasmid encoding an array of four non-overlapping sgRNAs designed to tolerate most human DNA polymorphisms. The quadruple-sgRNA libraries yielded high perturbation efficacies in deletion (75–99%) and silencing (76–92%) experiments and substantial fold changes in activation experiments. Moreover, an arrayed activation screen of 1,634 human transcription factors uncovered 11 novel regulators of the cellular prion protein PrPC, screening with a pooled version of the ablation library led to the identification of 5 novel modifiers of autophagy that otherwise went undetected, and ‘post-pooling’ individually produced lentiviruses eliminated template-switching artefacts and enhanced the performance of pooled screens for epigenetic silencing. Quadruple-sgRNA arrayed libraries are a powerful and versatile resource for targeted genome-wide perturbations.
Communicative health literacy and associated variables in nine European countries: results from the HLS19 survey
Authors: Metanmo Salvatore , Finbråten Hanne Søberg , Bøggild Henrik , Nowak Peter , Griebler Robert , Guttersrud Øystein , Bíró Éva , Unim Brigid , Charafeddine Rana , Griese Lennert , Kucera Zdenek , Le Christopher , Schaeffer Doris , Vrdelja Mitja , Mancini Julien ,   The HLS19 Consortium, Pelikan Jürgen , Straßmayr Christa , Griebler Robert , Dietscher Christina , van den Broucke Stephan , Charafeddine Rana , Yanakieva Antoniya , Dzhafer Nigyar , Kucera Zdeněk , Steflova Alena , Bøggild Henrik , Sørensen Andreas Jull , Mancini Julien , Allaire Cécile , Schaeffer Doris , Schmidt-Gernig Alexander , Bíró Éva , Bruton Lucy , Gibney Sarah , Levin-Zamir Diane , Palmieri Luigi , Galeone Daniela , Pettersen Kjell Sverre , Le Christopher , da Costa Andreia Jorge Silva , de Arriaga Miguel Telo , Lopatina Maria , Drapkina Oxana , Klocháňová Zuzana , Vrdelja Mitja , Kolnik Tamara Štemberger , De Gani Saskia Maria , Gasser Karin 
Published: December 2024

Abstract
Our study aimed to report on variables associated with communicative health literacy (COM-HL) in European adults. The HLS19 survey was conducted in 2019–2021 including nine countries which measured COM-HL by using a validated questionnaire (HLS19-COM-P-Q6 with a score ranging from 0 to 100). Linear regression models were used to study variables associated with COM-HL globally (multilevel model with random intercepts and slopes and at country level) and in each country. Additional models studied each of the HLS19-COM-P-Q6 items separately. The mean COM-HL score ranged between 62.5 and 76.6 across countries. Among the 18,137 pooled participants, COM-HL was positively associated with age, a higher self-perceived social status, previous training in healthcare, an increasing number of general practitioner visits; and negatively associated with female sex, reported financial difficulties, having a chronic condition and an increasing number of specialist visits. These effects were heterogeneous from one country to another, and from one item to another when analysing the different COM-HL items separately. However, there was a consistent statistically significant association between COM-HL (score and each item) and financial difficulties as well as self-perceived social status in all countries. Interventions to improve communication between patients and physicians should be a high priority to limit communication disparities.
Dual gene set enrichment analysis (dualGSEA); an R function that enables more robust biological discovery and pre-clinical model alignment from transcriptomics data
Authors: Bull Courtney , Byrne Ryan M. , Fisher Natalie C. , Corry Shania M. , Amirkhah Raheleh , Edwards Jessica , Hillson Lily V. S. , Lawler Mark , Ryan Aideen E. , Lamrock Felicity , Dunne Philip D. , Malla Sudhir B. 
Published: December 2024

AbstractGene set enrichment analysis (GSEA) tools can identify biological insights within gene expression-based studies. Although their statistical performance has been compared, the downstream biological implications that arise when choosing between the range of pairwise or single sample forms of GSEA methods remain understudied. We compare the statistical and biological results obtained from various pre-ranking methods/options for pairwise GSEA, followed by a stand-alone comparison of GSEA, single sample GSEA (ssGSEA) and gene set variation analysis (GSVA). Pairwise GSEA and fGSEA provide similar results when deployed using a range of gene pre-ranking methods. However, pairwise GSEA can overgeneralise biological enrichment, as when the most statistically significant signatures were assessed using single sample approaches, there was a complete absence of biological distinction between these groups. To avoid these issues, we developed a new dualGSEA tool, which provides users with multiple statistics and visuals to aid interpretation of results. This new tool removes the possibility of users inadvertently interpreting statistical findings as equating to biological distinction between samples within groups-of-interest. dualGSEA provides a more robust basis for discovery research, one which allows user to compare both statistical significance alongside biological distinctions in their data.
Mediterranean seagrasses provide essential coastal protection under climate change
Authors: Agulles M. , Marbà N. , Duarte C. M. , Jordà G. 
Published: December 2024

AbstractSeagrasses are vital in coastal areas, offering crucial ecosystem services and playing a relevant role in coastal protection. The decrease in the density of Mediterranean seagrasses over recent decades, due to warming and anthropogenic stressors, may imply a serious environmental threat. Here we quantify the role of coastal impact reduction induced by seagrass presence under present and future climate. We focus in the Balearic Islands, a representative and well monitored region in the Mediterranean. Our results quantify how important the presence of seagrasses is for coastal protection. The complete loss of seagrasses would lead to an extreme water level (eTWL) increase comparable to the projected sea level rise (SLR) at the end of the century under the high end scenario of greenhouse gases emissions. Under that scenario, the eTWL could increase up to ~ 1.4 m, with 54% of that increase attributed to seagrass loss. These findings underscore the importance of seagrass conservation for coastal protection.
The impact of multiple agricultural land uses in sustaining earthworm communities in agroecosystems - A global meta-analysis
Authors: Betancur-Corredor Bibiana , Zaitsev Andrey , Russell David J. 
Published: December 2024

AbstractThe impact of agricultural land use on biodiversity has been extensively examined through efforts to synthesize available data. Nevertheless, there is still a lack of a thorough synthesis describing the earthworm response to agricultural land-use Our meta-analysis compared undisturbed ecosystems (i.e., undisturbed grassland, primary forest) as controls against agricultural land-use treatments, with data extracted from 113 publications across 44 countries, yielding 1040 pairwise comparisons of earthworm density and biomass, and 536 pairwise comparisons of earthworm diversity. We also evaluated how agricultural land use effects on earthworms depend on soil, climate, and management practices reported in the studies. Arable cropland had significantly lower earthworm density (-18%), biomass (-15%), and species richness (-27%) compared to undisturbed sites. Conversely, higher earthworm density, biomass and species richness were observed in pastures, sites under agroforestry, crop management with fallow periods and crop-livestock integration. In regions with continental climates characterized by cool summers, agricultural land use exhibited positive effects on earthworm density and biomass. In sites with higher soil bulk density and lower organic matter content the adverse effects of agricultural land use are exacerbated. However, highly heterogeneous earthworm responses cannot be explained by the individual evaluation of climatic, soil-related, or management factors. Our results guide future efforts to address the data limitations that enable us to enhance our understanding of the interactive effects of various factors on earthworm responses to agricultural land use, as well as evidence-based and management strategies targeted at promoting sustainable agricultural systems while preserving soil biodiversity.