bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structure, relationships and diversity in the community of aphids and aphidophagous species in alfalfa
Authors: Nikolova Ivelina 
Published: November 2024

AbstractThere is a need for comprehensive research on the species structure and the population dynamics of the most common aphidophagous species. A critical factor of the effectiveness of aphid biocontrol is the ratio of beneficial polyphagous (generalist) to oligo- or monophagous (specialist) species within the various trophic groups. Aphids' population density and environmental conditions influence the development and potential feeding of useful insects. The present study aimed to determine the community structure, relationships and diversity between aphids and their aphidophagous species in alfalfa fields using the following methods: sweeping with an entomological net, the quadratic method, coloured sticky board method, route survey method and visual observations. Research on the structure of the aphid–aphidophagous community revealed that aphidophagous species belong to three groups: (1) polyphagous predatory bugs from the families Anthocoridae and Nabidae, (2) oligophagous and polyphagous predators from the families Coccinellidae, Syrphidae and Chrysopidae; and (3) monophagous and oligophagous parasitoids, primarily from the families Aphidiidae and Ichneumonidae. From mid-May to June, there was a sufficiently large potential for aphidophagous species (Coccinellidae, Syrphidae, Chrysopidae, Anthocoridae and Nabidae) to control aphids, while in September, predatory ladybirds from the Coccinellidae family were the main biological control agents. Coccinellidae (Coleoptera) exhibited the highest values of diversity, dominance and richness indices among insect groups in the aphid–aphidophagous community. The existence of diverse aphidophagous species in alfalfa fields suggests that these predators can complement each other, leading to effective biological control of aphids. The synergy among different predator species holds promise for enhancing the overall efficacy of integrated pest management strategies.
Long-term fertilization strategies for improving productivity, profitability and water-use efficiency of soybean–wheat cropping systems
Authors: Panday Suresh Chandra , Parihar Manoj , Meena Rajendra Prasad , Choudhary Mahipal , Meena Vijay Singh , Mondal Tilak , Khati Priyanka , Singh Ashish Kumar , Bisht Jaideep Kumar , Kant Lakshmi , Pattanayak Arunava , Singh R. D. 
Published: November 2024

Abstract
In order to recognize the best nutrient supply options for profitable and sustainable production systems, observations were recorded from 2001 to 2020 (20 years) in a long-term fertilizer experiment initiated in 1995–96 with soybean–wheat cropping systems (SWCSs) under irrigated conditions. The experiment comprised of seven treatments including control, organic, inorganic and their combinations. A combined use of 10 Mg farmyard manure (FYM)/ha (M) along with 120 kg N/ha provided statistically (P < 0.05) similar yield and economic benefits to the M + NPK and also provided a positive yield trend (30.0 and 16.2 kg/ha/year) and net return (14.7 and 5.81 US$/ha/year) over the year in both wheat and soybean, respectively. The combined use of organic and chemical fertilizers, provided 32–41% higher production efficiency than their individual use. In contrast, long-term chemical fertilization provided a negative yield trend in both the crops with the highest reduction in sole N-fertilized plots ranged from −39 to −42 kg/ha/year. Water-use efficiency ranged from 3.20 to 12.3 kg/ha/mm in soybean–wheat rotation and increased almost 1.74–3.15 times in wheat and 1.30–1.80 times in soybean due to fertilizer application. A similar trend was observed for water-expense efficiency and remain closely associated with fertilization practice. Long-term chemical fertilizers declined the yield potential of the studied crops while their conjoint application with FYM in the winter season considered as an input efficient approach to sustain the overall productivity and profitability of SWCSs.
Modulation in Teleconnections of the El Nino Southern Oscillation by Atlantic Multidecadal Sea Surface Temperature Variability
Authors: Wreford D. , McGregor S. , Naha R. 
Published: November 2024

AbstractThis manuscript uses idealized AGCM experiments to explore impacts of observed decadal Atlantic sea surface temperature (SST) changes on El Nino Southern Oscillation teleconnections. Significant regional changes are observed in numerous locations (e.g., Indo‐Pacific and Central Africa) due to the addition of the AMV anomalies. In some regions the teleconnection impacts of AMV forcing appeared to scale with the magnitude of the AMV forcing. However, the AMV induced modulation of temperature and precipitation teleconnections is regionally specific with changes in magnitude, statistical strength, and spatial connection dependent on region. These ENSO teleconnection changes were found to be asymmetric between AMV phases, with negative anomalies appearing to have a larger effect. We hypothesize these changes may be underpinned by a AMV induced modulation and migration of ENSO's equatorial precipitation response.
Coastal Supra‐Permafrost Aquifers of the Arctic and Their Significant Groundwater, Carbon, and Nitrogen Fluxes
Authors: Demir Cansu , McClelland James W. , Bristol Emily , Charette Matthew A. , Cardenas M. Bayani 
Published: November 2024

AbstractFresh submarine groundwater discharge (FSGD) can deliver significant fluxes of water and solutes from land to sea. In the Arctic, which accounts for ∼34% of coastlines globally, direct observations and knowledge of FSGD are scarce. Through integration of observations and process‐based models, we found that regardless of ice‐bonded permafrost depth at the shore, summer SGD flow dynamics along portions of the Beaufort Sea coast of Alaska are similar to those in lower latitudes. Calculated summer FSGD fluxes in the Arctic are generally higher relative to low latitudes. The FSGD organic carbon and nitrogen fluxes are likely larger than summer riverine input. The FSGD also has very high CO2 making it a potentially significant source of inorganic carbon. Thus, the biogeochemistry of Arctic coastal waters is potentially influenced by groundwater inputs during summer. These water and solute fluxes will likely increase as coastal permafrost across the Arctic thaws.
Light Limitation of Poleward Coral Reef Expansion During Past Warm Climates
Authors: Kruijt A. L. , Brachert T. , Sluijs A. , Middelburg J. J. 
Published: November 2024

AbstractThe latitudinal range of modern shallow‐water tropical corals is controlled by temperature, and presently limited to waters warmer than 16–18°C year‐round. However, even during Cenozoic climates with such temperatures in polar regions, coral reefs are not found beyond >50° latitude. Here, we test the hypothesis that daily available solar radiation limited poleward expansion of coral reefs during warm climates, using a new box model of shallow marine coral calcification. Our results show that calcification rates start to decline beyond 40° latitude and drop severely beyond 50° latitude, due to decreasing winter light intensity and day length, irrespective of aragonite saturation. This suggests that light ultimately prohibits further poleward expansion in warm climates. In addition, fossil coral reef distribution is not a robust proxy for water temperatures and poleward expansion of reefs beyond 50° latitude is not an expected carbon cycle feedback of climate warming.
Deep generative AI models analyzing circulating orphan non-coding RNAs enable detection of early-stage lung cancer
Authors: Karimzadeh Mehran , Momen-Roknabadi Amir , Cavazos Taylor B. , Fang Yuqi , Chen Nae-Chyun , Multhaup Michael , Yen Jennifer , Ku Jeremy , Wang Jieyang , Zhao Xuan , Murzynowski Philip , Wang Kathleen , Hanna Rose , Huang Alice , Corti Diana , Nguyen Dang , Lam Ti , Kilinc Seda , Arensdorf Patrick , Chau Kimberly H. , Hartwig Anna , Fish Lisa , Li Helen , Behsaz Babak , Elemento Olivier , Zou James , Hormozdiari Fereydoun , Alipanahi Babak , Goodarzi Hani 
Published: November 2024

AbstractLiquid biopsies have the potential to revolutionize cancer care through non-invasive early detection of tumors. Developing a robust liquid biopsy test requires collecting high-dimensional data from a large number of blood samples across heterogeneous groups of patients. We propose that the generative capability of variational auto-encoders enables learning a robust and generalizable signature of blood-based biomarkers. In this study, we analyze orphan non-coding RNAs (oncRNAs) from serum samples of 1050 individuals diagnosed with non-small cell lung cancer (NSCLC) at various stages, as well as sex-, age-, and BMI-matched controls. We demonstrate that our multi-task generative AI model, Orion, surpasses commonly used methods in both overall performance and generalizability to held-out datasets. Orion achieves an overall sensitivity of 94% (95% CI: 87%–98%) at 87% (95% CI: 81%–93%) specificity for cancer detection across all stages, outperforming the sensitivity of other methods on held-out validation datasets by more than ~ 30%.
Integrated molecular and functional characterization of the intrinsic apoptotic machinery identifies therapeutic vulnerabilities in glioma
Authors: Fernandez Elizabeth G. , Mai Wilson X. , Song Kai , Bayley Nicholas A. , Kim Jiyoon , Zhu Henan , Pioso Marissa , Young Pauline , Andrasz Cassidy L. , Cadet Dimitri , Liau Linda M. , Li Gang , Yong William H. , Rodriguez Fausto J. , Dixon Scott J. , Souers Andrew J. , Li Jingyi Jessica , Graeber Thomas G. , Cloughesy Timothy F. , Nathanson David A. 
Published: November 2024

AbstractGenomic profiling often fails to predict therapeutic outcomes in cancer. This failure is, in part, due to a myriad of genetic alterations and the plasticity of cancer signaling networks. Functional profiling, which ascertains signaling dynamics, is an alternative method to anticipate drug responses. It is unclear whether integrating genomic and functional features of solid tumours can provide unique insight into therapeutic vulnerabilities. We perform combined molecular and functional characterization, via BH3 profiling of the intrinsic apoptotic machinery, in glioma patient samples and derivative models. We identify that standard-of-care therapy rapidly rewires apoptotic signaling in a genotype-specific manner, revealing targetable apoptotic vulnerabilities in gliomas containing specific molecular features (e.g., TP53 WT). However, integration of BH3 profiling reveals high mitochondrial priming is also required to induce glioma apoptosis. Accordingly, a machine-learning approach identifies a composite molecular and functional signature that best predicts responses of diverse intracranial glioma models to standard-of-care therapies combined with ABBV-155, a clinical drug targeting intrinsic apoptosis. This work demonstrates how complementary functional and molecular data can robustly predict therapy-induced cell death.
Glycan-induced structural activation softens the human papillomavirus capsid for entry through reduction of intercapsomere flexibility
Authors: Feng Yuzhen , van Bodegraven Dominik , Kádek Alan , L. B. Munguira Ignacio , Soria-Martinez Laura , Nentwich Sarah , Saha Sreedeepa , Chardon Florian , Kavan Daniel , Uetrecht Charlotte , Schelhaas Mario , Roos Wouter H. 
Published: November 2024

AbstractHigh-risk human papillomaviruses (HPVs) cause various cancers. While type-specific prophylactic vaccines are available, additional anti-viral strategies are highly desirable. Initial HPV cell entry involves receptor-switching induced by structural capsid modifications. These modifications are initiated by interactions with cellular heparan sulphates (HS), however, their molecular nature and functional consequences remain elusive. Combining virological assays with hydrogen/deuterium exchange mass spectrometry, and atomic force microscopy, we investigate the effect of capsid-HS binding and structural activation. We show how HS-induced structural activation requires a minimal HS-chain length and simultaneous engagement of several binding sites by a single HS molecule. This engagement introduces a pincer-like force that stabilizes the capsid in a conformation with extended capsomer linkers. It results in capsid enlargement and softening, thereby likely facilitating L1 proteolytic cleavage and subsequent L2-externalization, as needed for cell entry. Our data supports the further devising of prophylactic strategies against HPV infections.
Cryo-EM structures of apo-APC/C and APC/CCDH1:EMI1 complexes provide insights into APC/C regulation
Authors: Höfler Anna , Yu Jun , Yang Jing , Zhang Ziguo , Chang Leifu , McLaughlin Stephen H. , Grime Geoffrey W. , Garman Elspeth F. , Boland Andreas , Barford David 
Published: November 2024

AbstractAPC/C is a multi-subunit complex that functions as a master regulator of cell division. It controls progression through the cell cycle by timely marking mitotic cyclins and other cell cycle regulatory proteins for degradation. The APC/C itself is regulated by the sequential action of its coactivator subunits CDC20 and CDH1, post-translational modifications, and its inhibitory binding partners EMI1 and the mitotic checkpoint complex. In this study, we took advantage of developments in cryo-electron microscopy to determine the structures of human APC/CCDH1:EMI1 and apo-APC/C at 2.9 Å and 3.2 Å resolution, respectively, providing insights into the regulation of APC/C activity. The high-resolution maps allow the unambiguous assignment of an α-helix to the N-terminus of CDH1 (CDH1α1) in the APC/CCDH1:EMI1 ternary complex. We also identify a zinc-binding module in APC2 that confers structural stability to the complex, and we confirm the presence of zinc ions experimentally. Finally, due to the higher resolution and well defined density of these maps, we are able to build, aided by AlphaFold predictions, several intrinsically disordered regions in different APC/C subunits that likely play a role in proper APC/C assembly and regulation of its activity.
An evolutionarily conserved metabolite inhibits biofilm formation in Escherichia coli K-12
Authors: Guo Jingzhe , Van De Ven Wilhelmina T , Skirycz Aleksandra , Thirumalaikumar Venkatesh P. , Zeng Liping , Zhang Quanqing , Balcke Gerd Ulrich , Tissier Alain , Dehesh Katayoon 
Published: November 2024

AbstractMethylerythritol cyclodiphosphate (MEcPP) is an intermediate in the biosynthesis of isoprenoids in plant plastids and in bacteria, and acts as a stress signal in plants. Here, we show that MEcPP regulates biofilm formation in Escherichia coli K-12 MG1655. Increased MEcPP levels, triggered by genetic manipulation or oxidative stress, inhibit biofilm development and production of fimbriae. Deletion of fimE, encoding a protein known to downregulate production of adhesive fimbriae, restores biofilm formation in cells with elevated MEcPP levels. Limited proteolysis-coupled mass spectrometry (LiP-MS) reveals that MEcPP interacts with the global regulatory protein H-NS, which is known to repress transcription of fimE. MEcPP prevents the binding of H-NS to the fimE promoter. Therefore, our results indicate that MEcPP can regulate biofilm formation by modulating H-NS activity and thus reducing fimbriae production. Further research is needed to test whether MEcPP plays similar regulatory roles in other bacteria.
Effect of XBB.1.5-adapted booster vaccination on the imprinting of SARS-CoV-2 immunity
Authors: Pušnik Jernej , Monzon-Posadas Werner O. , Osypchuk Emmanuil , Dubiel Aleksandra Elzbieta , Baum Maximilian , Fehring Paulina , Büning Antonia , Klant Tobias , Streeck Hendrik 
Published: November 2024

AbstractIn the present study, Pušnik et al. investigated whether the XBB.1.5-adapted booster can overcome the persistent imprinting of SARS-CoV-2 immunity by wild-type based vaccines. The findings demonstrate increased plasma neutralization against the homologous variant following the booster vaccination. Formation of de novo humoral response against the mutated epitopes of XBB.1.5 variant’s surface proteins was observed in 3/20 individuals. The booster vaccination had no significant effect on T-cell response.
The Parkinson’s disease drug entacapone disrupts gut microbiome homeostasis via iron sequestration
Authors: Pereira Fátima C. , Ge Xiaowei , Kristensen Jannie M. , Kirkegaard Rasmus H. , Maritsch Klara , Szamosvári Dávid , Imminger Stefanie , Seki David , Shazzad Juwairiyah B. , Zhu Yifan , Decorte Marie , Hausmann Bela , Berry David , Wasmund Kenneth , Schintlmeister Arno , Böttcher Thomas , Cheng Ji-Xin , Wagner Michael 
Published: November 2024

AbstractMany human-targeted drugs alter the gut microbiome, leading to implications for host health. However, the mechanisms underlying these effects are not well known. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single-cell chemical imaging to investigate the impact of two widely prescribed drugs on the gut microbiome. Physiologically relevant concentrations of entacapone, a treatment for Parkinson’s disease, or loxapine succinate, used to treat schizophrenia, were incubated ex vivo with human faecal samples. Both drugs significantly impact microbial activity, more so than microbial abundance. Mechanistically, entacapone can complex and deplete available iron resulting in gut microbiome composition and function changes. Microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Further, entacapone-induced iron starvation selected for iron-scavenging gut microbiome members encoding antimicrobial resistance and virulence genes. These findings reveal the impact of two under-investigated drugs on whole microbiomes and identify metal sequestration as a mechanism of drug-induced microbiome disturbance.
CFTR expression decreases with age in several airway cell types
Authors: Corcoran Timothy E. , Broerman Matthew J. , Kliment Corrine R. , Lo Cecilia 
Published: November 2024

AbstractThe mucociliary clearance (MC) system is a vital host defense against infection in the lung. MC system function is dependent on ciliary density, structure, and function and airway surface liquid (ASL) composition and hydration. Animal and human studies indicate that MC rate decreases with age which may contribute to the increased rates of pulmonary infection experienced by older people. The Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene encodes an anion channel on epithelial surfaces that plays a key role in maintaining ASL hydration. Failure or dysfunction of CFTR could result in the dehydration of airway mucus, depressing MC. Here we use two available databases including bulk (GTEx) and single-cell (CELLxGENE) sequencing data from the lung to determine if CFTR expression decreases with age. Bulk expression data and single-cell expression data from goblet, club, and respiratory basal cells all demonstrated patterns of decreasing CFTR expression with age. Ciliated airway cells did not. Secretory cells (including club and goblet cells) and basal cells are the largest source of CFTR expression in the airway. This indicates that changes in CFTR expression and ASL dehydration may contribute to the decreasing MC associated with aging.
Deep learning based emulator for predicting voltage behaviour in lithium ion batteries
Authors: Oka Kanato , Tanibata Naoto , Takeda Hayami , Nakayama Masanobu , Noguchi Syuto , Karasuyama Masayuki , Fujiwara Yoshiya , Miyuki Takuhiro 
Published: November 2024

AbstractThis study presents a data-driven battery emulator using long short-term memory deep learning models to predict the charge–discharge behaviour of lithium-ion batteries (LIBs). This study aimed to reduce the economic costs and time associated with the fabrication of large-scale automotive prototype batteries by emulating their performance using smaller laboratory-produced batteries. Two types of datasets were targeted: simulation data from the Dualfoil model and experimental data from liquid-based LIBs. These datasets were used to accurately predict the voltage profiles from the arbitrary inputs of various galvanostatic charge–discharge schedules. The results demonstrated high prediction accuracy, with the coefficient of determination scores reaching 0.98 and 0.97 for test datasets obtained from the simulation and experiments, respectively. The study also confirmed the significance of state-of-charge descriptors and inferred that a robust model performance could be achieved with as few as five charge–discharge training datasets. This study concludes that data-driven emulation using machine learning can significantly accelerate the battery development process, providing a powerful tool for reducing the time and economic costs associated with the production of large-scale prototype batteries.
Soluble endoglin as a biomarker of successful rheopheresis treatment in patients with age-related macular degeneration
Authors: Blaha Vladimir , Rathouska Jana Urbankova , Langrova Hana , Blaha Milan , Studnicka Jan , Andrys Ctirad , Loefflerova Veronika , Lanska Miriam , Vejrazkova Eva , Nachtigal Petr , Stepanov Alexandr 
Published: November 2024

AbstractAge-related macular degeneration (AMD) is a progressive chronic disease causing visual impairment or central vision loss in the elderly. We hypothesized that successful rheopheresis would be associated with positive changes in soluble endoglin (sENG), PSCK9, alpha-2-macroglobulin (A2M), and hs-CRP levels. 31 elderly patients with the dry form of AMD, treated with rheopheresis with a follow-up period of at least 5 years and an average age of 68 ± 4 years, were evaluated. Each treated patient received a series of 8 procedures in 10 weeks and, after the 2-year period, another 2 procedures within 1 week. Then, the patients were followed up every 6 months and divided into the successfully treated and therapeutic failure group according to best-corrected visual acuity (BCVA), size of the drusen area, and the drusenoid pigment epithelium detachment (DPED). Based on the ophthalmological assessment, rheopheresis treatment was successful in 73% of AMD patients. The therapy was associated with a significant decrease in total cholesterol, LDL-C, HDL-C, apoprotein B, lipoprotein (a) levels, and rheologically important parameters, irrespective of the therapy’s success or failure. The success of rheopheresis therapy was exclusively related to a significant decrease in sENG and A2M levels. Over the long term, rheopheresis prevented the decline of BCVA, reduced the DPED and area of macular drusen, and improved the preservation of an intact photoreceptor ellipsoid zone in most patients. Moreover, we showed for the first time that sENG and A2M could be potentially sensitive biomarkers of successful rheopheresis procedure, irrespective of lipid parameters changes.