bluuebunny/crossref_metadata_2025_split huggingface dataset:
Childhood traumatic experiences and sleepwalking events in the lower GDP counties in Hungary
Authors: Correa Vivian M. 
Published: March 2024

AbstractPurposeThe aim of the study was to identify injurious behavior during sleepwalking events and childhood traumatic experiences.Study designEight questions from a sleepwalking study (02/2023) in different counties in Hungary were analyzed to find a relationship between traumatic experiences in the life of the participants, such as physical, emotional, or sexual abuse in childhood, and injurious behaviors during sleepwalking.MethodsWe estimated an association between the Hungarian counties by GDP per capita and individuals that reported injurious sleepwalking events and childhood trauma by logistic regression.ResultsA total of 749 participants agreed to answer all questions, of which 357 were over 50 years old and 363 males. The results have shown that sleepwalking events were reported in patients with childhood trauma significantly more frequently in the lower GDP counties in Hungary (OR:5.8, 1.21-27.99, P:0.02) even without family predisposition.ConclusionThe results suggest that a childhood traumatic experience could be a ssociated with sleepwalking activities. Thus, family history and traumatic experiences can increase the probability of injurious behavior during sleepwalking in Hungary.
A distinctive tumor compartment in pancreatic lobules defined by nascent stroma and classical tumor cell phenotype
Authors: Söderqvist Sara , Viljamaa Annika , Geyer Natalie , Strell Carina , Hekmati Neda , Engstrand Jennie , Sparrelid Ernesto , Salmén Caroline , Heuchel Rainer L. , Zacharouli Argyro , Ghorbani Poya , Harrizi Sara , Hamidi Yousra , Khorosjutina Olga , Milanova Stefina , Schmierer Bernhard , Bozóky Béla , Moro Carlos Fernández , Gerling Marco 
Published: March 2024

AbstractPancreatic ductal adenocarcinoma (PDAC) is a highly aggressive tumor type characterized by a particularly extensive stroma. While different types of cancer-associated fibroblasts (CAFs) in this desmoplastic stroma have been described, areas of early invasion and nascent stroma are understudied. Here, we identify a distinctive PDAC niche within the pancreatic lobules, a compartment dominated by pancreatic exocrine cells and slender stroma. Cellular interaction profiling using machine learning on whole slide images of human PDAC reveals that the tumor invasion front in the lobules is dominated by specific interactions of tumor cells and exocrine cells that have undergone acinar-to-ductal metaplasia (ADM). Multiplex protein and mRNA stains confirm that tumor growth in the lobules is closely linked to ADM in the lobules, and reveal stromal protein gradients from the gracile lobular stroma to the characteristic desmoplastic stroma. We identify nascent CAFs (nCAFs), co-expressing expressing nerve growth factor receptor (NGFR) and platelet-derived growth factor receptor alpha (PDGFRa) that are absent in the mature, desmoplastic stroma. Lobular invasion and nCAFs are intertwined with phenotypic changes of the cancer cells, such that tumor cells in lobules express classical subtype markers, while those embedded in the desmoplastic are on the basal end of the phenotypic continuum. In mice, the PDAC subtype – basal or classical – similarly depends on tissue location, suggesting microenvironmental factors rather than clonal selection as important drivers of tumor phenotype identity. Clinically, our results mandate factoring in tumor tissue location when calling PDAC subtypes. Biologically, they identify pancreatic lobules as a distinctive tissue niche associated with nascent stroma, and they suggest that lobular colonization by tumor cells is a significant route of PDAC progression.
A hemagglutinin and neuraminidase biased immunological memory shapes the dynamics of antibody responses to Influenza A virus
Authors: Lin Xia , Wang Jiaqi , Ling Shiman , Xiao Cheng , Liang Zaolan , Chow Cheuk Long , Yang Bingyi , Xiao Biying , Cowling Benjamin , Webby Richard , Zanin Mark , Wong Sook-San 
Published: March 2024

AbstractInfluenza A virus (IAV) infection establishes a more diverse immunological memory to different viral proteins compared to vaccination. We hypothesized that the relative abundance of pre-existing immune memory to different viral antigens could skew post-infection antibody responses. To explore this, we generated mouse models with either an IAV hemagglutinin (HA)- or neuraminidase (NA)-biased immunological memory. We inoculated groups of mice with cocktails of isogenic viruses bearing antigenically-distinct HA (H3v) or NA (N2v) chosen to span the IAV H3N2 human circulation history. We challenged the mice with two H3N2 strains of opposing virulence and antigenic distance (AD) and examined the post-infection antibody landscapes. In both challenges, immune-naïve mice seroconverted to both HA and NA whereas in primed mice, antibody response was detected to the antigen for which there is no pre-existing memory. In cases where the homologous antibody response was blunted, there was diversification on the breadth of response to antigenically-related strains with low baseline titers. Our findings clarifies the concept of “original antigenic sin” and demonstrate a mechanism by which the dynamics of antibody responses to HA and NA after infection can be altered by pre-existing immunity.
Olfaction in Tephritidae: a balance between detection and discrimination
Authors: Ramiaranjatovo Gaëlle , Charlery de la Masselière Maud , Dekker Teun , Duyck Pierre-François , Larsson Herrera Sebastian , Reynaud Bernard , Jacob Vincent 
Published: March 2024

AbstractPhytophagous insects are capable of detecting and locating suitable hosts, which emit volatile compounds. Polyphagous species appear to have a complex olfactory strategy given that their numerous hosts have diverse emission profiles. In particular, their hosts’ volatile emissions share some of the same compounds, providing chemical bridges between them. However, the behavioural plasticity observed in insect host selection suggests that other volatiles have a complementary role. Here we explore how the specialization of polyphagous Tephritidae fruit fly in detecting and discriminating between host fruits has driven their chemical selectivity. The volatile emissions from intact or mechanically damaged fruit of 28 different species were analysed using gas chromatography-mass spectrometry and fed into a neuronal model of an olfactory system. We predictedin silicoa functional trade-off between the two tasks, with optimal performance depending on detecting a higher proportion of shared fruit compounds, but with lower sensitivity compared to unshared compounds, or vice-versa. Using triple point electroantennography and a behavioural assay, we studied the olfactory response of Tephritidae fruit fly species that oviposit on fruit. Amplitude of the olfactory responses of eight species were negatively correlated with the compound’s degree of sharedness among fruit emissions, while response probability was previously shown to correlate positively with a similar metric. A dose-dependent switch in the fly’s preference confirmed the ecological importance of both shared and unshared fruit compounds. Thus, we propose that insect olfactory systems are chemically tuned to detect suitable hosts and accurately discriminate between them.
ProAffinity-GNN: A Novel Approach to Structure-based Protein-Protein Binding Affinity Prediction via a Curated Dataset and Graph Neural Networks
Authors: Zhou Zhiyuan , Yin Yueming , Han Hao , Jia Yiping , Koh Jun Hong , Kong Adams Wai-Kin , Mu Yuguang 
Published: March 2024

AbstractProtein-protein interactions (PPIs) are crucial for understanding biological processes and disease mechanisms, contributing significantly to advances in protein engineering and drug discovery. The accurate determination of binding affinities, essential for decoding PPIs, faces challenges due to the substantial time and financial costs involved in experimental and theoretical methods. This situation underscores the urgent need for more effective and precise methodologies for predicting binding affinity. Despite the abundance of research on PPI modeling, the field of quantitative binding affinity prediction remains underexplored, mainly due to a lack of comprehensive data.This study seeks to address these needs by manually curating pairwise interaction labels on all available 3D structures of proteins complexes, with experimentally determined binding affinities, creating the largest dataset for structure-based pairwise protein interaction with binding affinity to date. Subsequently, we introduce “ProAffinity-GNN”, a novel deep learning framework using protein language model and graph neural network (GNN) to improve the accuracy of prediction of structure-based protein-protein binding affinities. The evaluation results across several benchmark test sets demonstrate that ProAffinity-GNN not only outperforms existing models in terms of accuracy but also shows strong generalization capabilities.
Effects of Feed Processing Type, Protein Source, and Environmental Salinity onLitopenaeus vannameiFeeding Behaviour
Authors: Moss Amina S. , Brooker Adam J. , Ozioko Stella N. , Nederlof Marit A. J. , Debnath Sudip , Schrama Johan 
Published: March 2024

AbstractIn an 8-week trial, the effects of feed processing types (extruded vs. steamed pellets) and protein source (soya/pea vs. fish meal) onLitopenaeus vannameiwere studied under 30 ppt (first 30 days) and 5 ppt (last 15 days) salinity conditions. Diets included D1-SE soya/pea extruded, D2-SS soya/pea steamed, D3-FE fishmeal extruded, and D4 (FS) fishmeal steamed pellets. No significant weight differences were observed. Survival rates (80-97% at 30 ppt) decreased at reduced salinity and were significantly higher for shrimp fed steamed pellets (D2:80.00%, D4:76.67%) compared to extruded (D1: 50.00%, p<0.05). Shrimp fed D2-SS and D4-FS diets had increased lipid content (6.79%, 6.36%, p<0.05). Significantly lower lysine and isoleucine were noted in D2-SS. Behaviourally, at 30 ppt, D3-FE attracted significantly more shrimp (84.72%) than D1-SE (74.49%) and D2-SS (75.70%, p<0.05). Click analysis showed D1-SE and D2-SS with the shortest durations (17.97, 17.24ms, respectively), and D3-FE and D4-FS the longest (20.10, 23.89ms, respectively, p<0.05). Click frequency was also significantly higher in fishmeal–based diets, whereas the number of clicks was higher in shrimp fed extruded feed. Overall, extruded pellets and fishmeal diets were more favourable. These findings emphasize the importance of tailored feed strategies that consider nutritional content, feed physical properties and environmental factors for optimal shrimp feeding.
Construction of an Immunoinformatics-Based Multi-Epitope Vaccine Candidate targeting Kyasanur Forest Disease Virus
Authors: Kasibhatla Sunitha M. , Rajan Lekshmi S. , Shete Anita M. , Jani Vinod , Patil Savita , Joshi Yash , Sahay Rima R. , Patil Deepak Y. , Mohandas Sreelekshmy , Majumdar Triparna , Sonavane Uddhavesh , Joshi Rajendra , Yadav Pragya D. 
Published: March 2024

AbstractKyasanur Forest Disease (KFD) is one of the neglected tick-borne viral zoonoses. KFD virus was initially considered endemic to the Western Ghats region of Karnataka. Still, over the years, there have been reports of its spread to newer areas within and outside Karnataka. The absence of an effective treatment for KFD expedites the need for further research and development of novel vaccines. The present study was designed to develop a multi-epitope vaccine candidate against KFDV using immunoinformatic tools. After analyzing 74 complete KFDV genome sequences for genetic recombination and phylogeny, different prioritized B and T cell epitopes were combined using various linkers to construct the vaccine candidate. Docking analysis of the designed vaccine construct revealed a stable interaction with the TLR2-TLR6 receptor complex. After confirming the stability of the vaccine receptor complex, codon optimization was done to ensure the efficient translation of the designed multi-epitope vaccine in the prokaryotic host system, and the subsequentin-silicocloning into the pET30b(+) expression vector was carried out. Immunoinformatics analysis of the multi-epitope vaccine in the current study is satisfactory as it can significantly accelerate the initial stages of vaccine development by narrowing down potential vaccine candidates and providing insights into their design. Experimental validation of the potential multi-epitope vaccine candidate remains crucial to confirm effectiveness and safety in real-world conditions.
Antagonistic behavior of brain networks mediated by low-frequency oscillations: electrophysiological dynamics during internal–external attention switching
Authors: Hammer Jiri , Kajsova Michaela , Kalina Adam , Krysl David , Fabera Petr , Kudr Martin , Jezdik Petr , Janca Radek , Krsek Pavel , Marusic Petr 
Published: March 2024

AbstractAntagonistic activity of brain networks likely plays a fundamental role in how the brain optimizes its performance by efficient allocation of computational resources. A prominent example involves externally/internally oriented attention tasks, implicating two anticorrelated, intrinsic brain networks: the default mode network (DMN) and the dorsal attention network (DAN). To elucidate electrophysiological underpinnings and causal interplay during attention switching, we recorded intracranial EEG (iEEG) from 25 epilepsy patients with electrode contacts localized in the DMN and DAN. We show antagonistic network dynamics of activation-related changes in high-frequency (> 50 Hz) and low-frequency (< 30 Hz) power. The temporal profile of information flow between the networks estimated by effective connectivity suggests that the activated network inhibits the other one, gating its activity by increasing the amplitude of the low-frequency oscillations. Insights about inter-network communication may have profound implications for various brain disorders in which these dynamics are compromised.
Differential Patterns of Cross-Protection against Antigenically Distinct Variants in Small Animal Models of SARS-CoV-2 Infection
Authors: Selvaraj Prabhuanand , Stauft Charles B. , Liu Shufeng , Sangare Kotou , Wang Tony T. 
Published: March 2024

AbstractContinuous evolution of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) will likely force more future updates of vaccine composition. Based on a series of studies carried out in human ACE2 transgenic mice (K18-hACE2) and Syrian hamsters, we show that immunity at the respiratory tract, acquired through either previous infection or vaccination with an in-house live attenuate virus, offers protection against antigenically distinct variants in the absence of variant spike-specific neutralizing antibodies. Interestingly, immunity acquired through infection of a modern variant (XBB.1.5) was insufficient in preventing brain infection by the ancestral virus (WA1/2020) in K18-hACE2 mice. Similarly, previous infection with WA1/2020 did not protect against brain infection by XBB.1.5. Our results highlight the importance of immune components other than neutralizing antibodies in maintaining protection against new variants in the respiratory tract, but also paint scenarios where a monovalent vaccine based on a contemporary variant may be less effective against the ancestral strain.ImportanceMany studies have assessed the cross neutralization of various SARS-CoV-2 variants induced by breakthrough infections or vaccine boosters. Few studies, however, have modeled a more severe type of breakthrough infection. Here, we show that immunity acquired through a previous infection by either a historical virus (WA1/2020) or a contemporary variant (XBB.1.5) failed to protect against brain infection of K18-hACE2 mice by an antigenically distinct virus, although it largely protected the respiratory tract. Our results provided a potential model to investigate the role of different immune components in curbing SARS-CoV-2 infection.
Global climate change effect on AsianMus musculus; Implication from last glacial maximum to the end of the 21stcentury
Authors: Afzali Yaser Amir 
Published: March 2024

ABSTRACTGlobal climate change poses unprecedented challenges to biodiversity, prompting urgent investigations into its effects on various species. This study focuses onMus musculus, a small rodent species and a crucial indicator of ecosystem health. Spanning from the last glacial maximum to the end of the 21stcentury, employed Species Distribution Models (SDMs) to assess the impacts of climate change onMus musculusand its four subspecies across Asia (M. m musculus,M. m domesticus,M. m castaneus, andM. m bactrianus). The SDMs reveal nuanced responses among subspecies, withM. m. domesticus,M. m. musculus, andM. m. castaneusfacing potential habitat contractions, whileM. m. bactrianusshows habitat expansion. Variable importance analysis highlights the significance of temperature-related variables, indicating the growing impact of rising temperatures on distribution patterns. Findings underscore the ecological implications of these shifts, emphasizing the need for tailored conservation strategies. The robustness of models, as indicated by high Area Under the Curve (AUC) values, enhances confidence in the reliability of predictions. Despite data limitations, this study contributes valuable insights into the complex dynamics between climate change andMus musculuspopulations, guiding future conservation efforts in the face of ongoing global environmental transformations.
Female-dominated disciplines have lower evaluated research quality and funding success rates, for men and women
Authors: James Alex , Buelow Franca , Gibson Liam , Brower Ann 
Published: March 2024

AbstractWe use data from 30 countries and find that the more women in a discipline, the lower quality the research in that discipline is evaluated to be and the lower the funding success rate is. This affects men and women, and is robust to age, number of research outputs, and bibliometric measures where such data are available. Our work builds on others’ findings that women’s work is valued less, regardless of who performs that work.
Late Miocene transformation of Mediterranean Sea biodiversity
Authors: Agiadi Konstantina , Hohmann Niklas , Gliozzi Elsa , Thivaiou Danae , Bosellini Francesca R. , Taviani Marco , Bianucci Giovanni , Collareta Alberto , Londeix Laurent , Faranda Costanza , Bulian Francesca , Koskeridou Efterpi , Lozar Francesca , Mancini Alan Maria , Dominici Stefano , Moissette Pierre , Campos Ildefonso Bajo , Borghi Enrico , Iliopoulos George , Antonarakou Assimina , Kontakiotis George , Besiou Evangelia , Zarkogiannis Stergios D. , Harzhauser Mathias , Sierro Francisco Javier , Coll Marta , Vasiliev Iuliana , Camerlenghi Angelo , García-Castellanos Daniel 
Published: March 2024

AbstractUnderstanding deep-time marine biodiversity change under the combined effects of climate and connectivity changes is fundamental for predicting the impacts of modern climate change in semi-enclosed seas. We quantify the Late Miocene–Early Pliocene (11.63–3.6 Ma) taxonomic diversity of the Mediterranean Sea for calcareous nannoplankton, dinocysts, foraminifera, ostracods, corals, molluscs, bryozoans, echinoids, fishes, and marine mammals. During this time, marine biota was affected by global climate cooling and the restriction of the Mediterranean’s connection to the Atlantic Ocean that peaked with the Messinian Salinity Crisis. Although the net change in species richness from the Tortonian to the Zanclean varies by group, species turnover is greater than 30% in all cases. The results show clear perturbation already in the pre-evaporitic Messinian (7.25–5.97 Ma), with patterns differing among groups and sub-basins.
A Preliminary list of Birds from Laguna de Matusagarati: A Wildlife Refuge in Darien Province, Panama
Authors: Garzón Jorge L. , Pimentel-Peralta Gumercindo , Castillo-Caballero Pedro L. , Medina Jorge L. , Alfaro Yennifer , Carrera Jean Paul , Valderrama Anayansi 
Published: March 2024

SUMMARYThe wetland Laguna de Matusagarati, in the province of Darien, eastern Panama region, possesses an approximate extension of 56, 000 hectares, the largest wetland in Panama and one of the biggest of Central America. Despite 70% of this wetland is on protected areas by Ministerio de Ambiente Panama, there are areas where the anthropogenic impact is notable, livestock, rice and oil palm crops, logging and deforestation are the most intense activities that have led to habitat loss. As part of a comprehensive One Health initiative focused on the surveillance of emerging diseases in the Darien region, we have undertaken simultaneous investigation on the biodiversity (mosquitos, birds, mammals, reptiles and amphibians) of Matusagarati. Here we report the results of the avifauna diversity undertaken in October 2018 and June 2019. We used mist nests, direct observation with binoculars and photographic cameras to report the species. A total of 169 species were reported, 49 families and 19 orders that represent 17% of the birds from Panama. Here we present the first checklist of birds from the Humedal Laguna de Matusagarati, with this we expect to improve the knowledge of the biodiversity of this wetland and provide data to authorities to improve the policies of conservation in this unique ecosystem.
Single cell view of tumor microenvironment gradients in pleural mesothelioma
Authors: Giotti Bruno , Dolasia Komal , Zhao William , Cai Peiwen , Sweeney Robert , Merritt Elliot , Kiner Evgeny , Kim Grace , Bhagwat Atharva , Hegde Samarth , Fitzgerald Bailey , Shroff Sanjana , Dawson Travis , Garcia-barros Monica , Abdul-ghafar Jamshid , Chen Rachel , Gnjatic Sacha , Soto Alan , Brody Rachel , Kim-Schulze Seunghee , Chen Zhihong , Beaumont Kristin G. , Merad Miriam , Flores Raja , Sebra Robert , Horowitz Amir , Marron Thomas U , Tocheva Anna , Wolf Andrea , Tsankov Alexander M. 
Published: March 2024

ABSTRACTImmunotherapies have shown great promise in pleural mesothelioma (PM), yet most patients still do not achieve significant clinical response, highlighting the importance of improving understanding of the tumor microenvironment (TME). Here, we utilized high-throughput, single-cell RNA-sequencing tode novoidentify 54 expression programs and construct a comprehensive cellular catalogue of the PM TME. We found four cancer-intrinsic programs associated with poor disease outcome and a novel fetal-like, endothelial cell population that likely responds to VEGF signaling and promotes angiogenesis. Throughout cellular compartments, we observe substantial difference in the TME associated with a cancer-intrinsic sarcomatoid signature, including enrichment in fetal-like endothelial cells, CXCL9+ macrophages, cytotoxic, exhausted, and regulatory T cells, which we validated using imaging and bulk deconvolution analyses on two independent cohorts. Finally, we show, both computationally and experimentally, that NKG2A-HLA-E interaction between NK and tumor cells represents an important new therapeutic axis in PM, especially for epithelioid cases.Statement of SignificanceThis manuscript presents the first single-cell RNA-sequencing atlas of pleural mesothelioma (PM) tumor microenvironment. Findings of translational relevance, validated experimentally and using independent bulk cohorts, include identification of gene programs predictive of survival, a fetal-like endothelial cell population, and NKG2A blockade as a promising new immunotherapeutic intervention in PM.