bluuebunny/crossref_metadata_2025_split huggingface dataset:
Characterizing the evolution of defense in a tripartite marine symbiosis using adaptive dynamics
Authors: Singh Prerna , Bruijning Marjolein , Carver Gavriela D , Donia Mohamed S , Metcalf Charlotte Jessica E 
Published: October 2024

Abstract
The evolution and maintenance of symbiotic systems remains a fascinating puzzle. While the coevolutionary dynamics of bipartite (host–symbiont) systems are well-studied, the dynamics of more complex systems have only recently garnered attention with increasing technological advances. We model a tripartite system inspired by the marine symbiotic relationship between the alga Bryopsis sp., its intracellular defensive bacterial symbiont “Candidatus Endobryopsis kahalalidifaciens,” which produces a toxin that protects the alga against fish herbivores, and the sea-slug Elysia rufescens (Zan et al., 2019), which is not deterred by the toxin. We disentangle the role of selection on different actors within this system by investigating evolutionary scenarios where defense evolves as (i) a host-controlled trait that reduces algal reproductive ability; (ii) a symbiont-controlled trait that impacts symbiont transmission; and (iii) a trait jointly controlled by both host and symbiont. Optimal investment in defensive toxins varies based on the characteristics of the host, symbiont, and sea slug; and evolutionary trajectories are modulated by trade-off shape, i.e., a strongly decelerating trade-off between defense and symbiont transmission can drive symbiont diversification via evolutionary branching. Increasing slug herbivory reduces host investment in defense to favor reproduction, while symbiont investment in defense first declines and then increases as host density declines to the degree that horizontal symbiont transmission is no longer beneficial. Increasing vertical transmission selects for reduced defense by the host when it evolves as a jointly controlled trait, as a result of investment by the symbiont. Our theoretical exploration of the evolution of defensive symbiosis in scenarios involving interactions with multiple herbivores provides a first window into the origin and maintenance of the Bryopsis sp. system, and adds another piece to the puzzle of the evolution of symbiotic systems.
From the economic to the pandemic crisis: The impact upon the EU constitutional architecture—Introduction to the Symposium
Authors: Torres Pérez Aida , Solanes Mullor Joan 
Published: October 2024

Abstract
The European Union has evolved significantly, shaped by crises as foreseen by Jean Monnet, who predicted that Europe would be “forged in crises.” Over recent decades, it has faced challenges such as the euro crisis, the COVID-19 pandemic, Brexit, rule-of-law backsliding, and ongoing geopolitical conflicts. These crises have tested and transformed the European Union’s constitutional framework, prompting institutional reforms and innovations in governance without necessarily revising the Treaties. This Symposium explores the European Union’s constitutional evolution through the lens of crises. Key reforms include the reinforcement of budgetary discipline during the euro crisis and the shift toward a stimulus-based approach in response to the pandemic, culminating in the NextGenerationEU framework. Contributors analyze the model of economic governance that has evolved from the convergence of both the economic and pandemic crises, the changing role of regions, the judiciary’s evolving oversight functions and its limits, and rule of law conditionality as a distinctive form of governance. The Symposium will delve into the post-crisis governance landscape of the European Union from a constitutional perspective, focusing on the structural adjustments implemented and their enduring impact. Despite these changes, the European Union has demonstrated resilience and adaptability, forging new governance structures that reflect its deepening constitutional identity. In the end, the Symposium provides a comprehensive examination of these shifts, highlighting how the European Union continues to integrate and innovate in response to ongoing challenges.
Maternal Immunization
Authors: Cho Hye-Kyung , Frivold Collrane , Chu Helen Y 
Published: October 2024

Abstract
Pregnant individuals and infants are at risk from vaccine-preventable diseases like severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and influenza. Maternal vaccination during pregnancy can protect both the mother and child. Recent progress in developing these vaccines is notable, but vaccine hesitancy and the exclusion of pregnant individuals from clinical trials limit their use. Maternal immunization safeguards mothers from severe illness and adverse pregnancy outcomes while providing infants with antibodies through the placenta and breast milk. Inactivated vaccines are generally effective and safe during pregnancy. Limited safety and efficacy data due to exclusion from trials hinder vaccine uptake; however, vaccines like tetanus-diphtheria-acellular pertussis (Tdap), influenza, and SARS-CoV-2 have proven effective, and are recommended vaccines during pregnancy. New vaccines for group B Streptococcus (GBS) and cytomegalovirus are in development, with the GBS vaccine being the most advanced. Combating vaccine hesitancy through strong health care provider recommendations is vital to enhance uptake and protect pregnant individuals and their infants.
Pathological Insights into Lassa Virus-Induced Vestibular Dysfunction in Mice: Histopathological Analysis of the Inner Ear Vestibular Apparatus
Authors: Suzuki Tomoharu , Saito Marina Hosotani , Lin Nantian , Tamura Atsushi , Yun Nadezhda , Koma Takaaki , Maruyama Junki , Paessler Slobodan , Makishima Tomoko 
Published: October 2024

Abstract
Lassa fever (LF), caused by Lassa virus (LASV) infection, typically leads to mild symptoms in humans, but some survivors experience audiovestibular problems. Here we present vestibular histopathological insights in our LF model mice. We observed (1) hemorrhage within the vestibular ganglion and stroma beneath the sensory epithelium, (2) preserved hair cells and supporting cells, (3) LASV antigen presence in the vestibular ganglion cells and the stroma beneath the sensory epithelium, and (4) CD3-positive T-lymphocyte infiltration in the vestibular ganglion and the stroma underlying the sensory epithelium. LASV and/or its immune response likely contributes to the pathogenesis of vestibular dysfunction.
Trace mineral sources influence in vitro fermentation characteristics and trace mineral solubility
Authors: Loh Huey Yi , Spears Jerry W , Guimaraes Octavio , Miller Alexandra C , Thomas Tyler A , Engle Terry E 
Published: October 2024

Abstract
Two experiments were conducted to determine: 1) the impact of strained rumen fluid (SRF) alone or SRF with particle-associated microorganisms (PAO) included and dilution on in vitro dry matter digestibility (DMD) and 2) the impact of trace mineral (TM) source on in vitro fermentation characteristics and TM solubility under simulated abomasal and intestinal conditions. In experiment 1, 3 cannulated steers were adapted to a diet formulated to meet the nutrient requirements for lactating dairy cows. Strained RF was obtained by straining rumen content through 2 layers of cheesecloth. Half of the remaining digesta was washed with McDougall’s buffer and filtered through 2 layers of cheesecloth to obtain PAO. Both SRF and PAO were filtered again through 8 layers of cheesecloth. Strained RF was mixed with either McDougall’s buffer (SRF) or PAO (SRF+ + PAO) at a ratio of 1:2 or 1:4 and incubated at 39 °C for 12 h using the ground basal diet as the substrate. Digestibility of DM was greater in digestion tubes containing SRF and SRF + PAO at a 1:2 ratio. In experiment 2, 8 steers fitted with a ruminal cannula were blocked by body weight and assigned to 1 of the 2 treatment groups. Treatments consisted of 10 mg Cu, 40 mg Mn, and 60 mg Zn/kg DM from either: 1) sulfate (STM) or 2) hydroxychloride (HTM) sources. Steers were housed in individual pens and fed the same diet as described in experiment 1. Dietary TM treatments were mixed with dried distiller grains and mixed in the diet, by hand, immediately after basal diet delivery. Dietary treatments were fed for 14 d. On day 15, SRF + PAO was collected from each steer (STM-RF and HTM-RF) and used in a series of in vitro crossover experiments. In vitro substrates (S) used were the ground diets consumed by the animals on each treatment (STM-S and HTM-S). Incubations containing HTM-S had greater (P &lt; 0.01) total volatile fatty acid (VFA) concentration and propionic acid molar proportions, but lesser (P &lt; 0.01) acetic acid molar proportions than STM-S. Rumen fluid from steers supplemented with HTM had a greater (P &lt; 0.03) total VFA than STM-RF at 24 h post incubation. After 12 h post incubation, the molar proportion of propionic acid in HTM-RF was lesser (P = 0.04) than in STM-RF. After simulated abomasal digestion, soluble Mn concentration in HTM-S was greater (P &lt; 0.01) than in STM-S. These data indicate that the source of TM can influence in vitro rumen fermentation characteristics and Mn solubility under simulated abomasal conditions.
Examining the “unearthly archives”: Spiritualism, Psychical Research, and Psychometric Material Culture in the US and Britain
Authors: Hunnicutt Rachel H R 
Published: October 2024

Abstract
This article examines the intersection of material culture and the occult by exploring the practice of psychometry, drawing parallels between this esoteric mode of object interpretation and more conventional approaches. Coined by physician Joseph Rodes Buchanan in the 1840s, psychometry—meaning “soul or mind measurement”—is the ability of “sensitive” individuals, often women, to read an object’s electrical vibration and glean information about its history, as well as that of its owner, living or deceased. Adopted by spiritualists and psychical researchers in the United States and Britain, psychometry mediated between humans and objects, and humans and their own mortality, in the decades spanning the turn of the twentieth century. Drawing on material culture studies, consumer studies, and histories of spiritualism and psychical research, I contextualize and compare firsthand accounts of psychometric readings with more traditional approaches to object-based inquiry to contend that psychometry is a mode of affective design historical practice, a speculative design history that relies on senses other than vision, and knowledge more intuitive than rational.
Machine learning algorithm approach to complete blood count can be used as early predictor of COVID-19 outcome
Authors: Ramalho-Pinto Cecília Horta , Ventura Lucas Haniel Araújo , Camatta Giovanna Caliman , Silveira-Nunes Gabriela , Gomes Matheus Souza , Sato Hugo Itaru , Costa Murilo Soares , Guimarães Henrique Cerqueira , Barbuto Rafael Calvão , Martins-Filho Olindo Assis , Amaral Laurence Rodrigues , Bertarini Pedro Luiz Lima , Teixeira Santuza Maria Ribeiro , Tupinambás Unaí , Teixeira-Carvalho Andrea , Faria Ana Maria Caetano 
Published: October 2024

Abstract
Although the SARS-CoV-2 infection has established risk groups, identifying biomarkers for disease outcomes is still crucial to stratify patient risk and enhance clinical management. Optimal efficacy of COVID-19 antiviral medications relies on early administration within the initial 5 d of symptoms, assisting high-risk patients in avoiding hospitalization and improving survival chances. The complete blood count (CBC) can be an efficient and affordable option to find biomarkers that predict the COVID-19 prognosis due to infection-induced alterations in various blood parameters. This study aimed to associate hematological parameters with different COVID-19 clinical forms and utilizes them as disease outcome predictors. We performed a CBC in blood samples from 297 individuals with COVID-19 from Belo Horizonte, Brazil. Statistical analysis, as well as ROC Curves and machine learning Decision Tree algorithms were used to identify correlations, and their accuracy, between blood parameters and disease severity. In the initial 4 d of infection, traditional hematological COVID-19 alterations, such as lymphopenia, were not yet apparent. However, the monocyte percentage and granulocyte-to-lymphocyte ratio (GLR) proved to be reliable predictors for hospitalization, even in cases where patients exhibited mild symptoms that later progressed to hospitalization. Thus, our findings demonstrate that COVID-19 patients with monocyte percentages lower than 7.7% and a GLR higher than 8.75 are assigned to the hospitalized group with a precision of 86%. This suggests that these variables can serve as important biomarkers in predicting disease outcomes and could be used to differentiate patients at hospital admission for managing therapeutic interventions, including early antiviral administration. Moreover, they are simple parameters that can be useful in minimally equipped health care units.
The lifespan of corpora lutea in nonpregnant females is positively correlated with gestation length
Authors: Lough-Stevens Michael , Ghione Caleb R , Dean Matthew D 
Published: October 2024

Abstract
In mammals, a temporary endocrine gland called the corpus luteum forms on the ovary shortly after ovulation and is required for the initiation and maintenance of early pregnancy. However, the corpus luteum persists even when fertilization or pregnancy does not occur, and species-specific variation in the length of this persistence remains enigmatic. Here we perform a comparative evolutionary study across 72 species and show that corpus luteum lifespan in nonpregnant females is positively correlated with gestation length. We argue that the most likely explanation for this correlation is physiological inertia. The corpus luteum begins secreting progesterone prior to implantation, and when pregnancy does not occur it takes time for females to degrade it and prepare the next reproductive cycle. Our study suggests that this physiological inertia is stronger in species with long gestation times.
Extreme-value modelling of migratory bird arrival dates: Insights from citizen science data
Authors: Koh Jonathan , Opitz Thomas 
Published: October 2024

Abstract
Citizen science mobilises many observers and gathers huge datasets but often without strict sampling protocols, resulting in observation biases due to heterogeneous sampling effort, which can lead to biased predictions. We develop a spatiotemporal Bayesian hierarchical model for bias-corrected estimation of arrival dates of the first migratory bird individuals at their breeding sites. Higher sampling effort could be correlated with earlier observed dates. We implement data fusion of two citizen-science datasets with fundamentally different protocols (BBS, eBird) and obtain posterior distributions of the latent process, which contains four spatial components endowed with Gaussian process priors: species niche; sampling effort; position and scale parameters of annual first arrival date. The data layer consists of four response variables: counts of observed eBird locations (Poisson); presence-absence at observed eBird locations (Binomial); BBS occurrence counts (Poisson); first arrival dates (Generalised Extreme-Value). We devise a Markov Chain Monte Carlo scheme and check by simulation that the latent process components are identifiable. We apply our model to several migratory bird species in the northeastern United States for 2001−2021 and find that the sampling effort significantly modulates the observed first arrival dates. We exploit this relationship to effectively bias-correct predictions of the true first arrivals.
Broncho biliary fistula, a rare complication after hepatectomy: case report of endoscopic and radiological management
Authors: El Ouali Ibtissam I E , El Graini Soumiya S E , El Aoufir Omar O E , Belaabed Soufya S B , Benkabbou Amine A B , Amrani Laila L A , Bakkar Meriem M B , Omor Youssef Y O , Lahnaoui Oumaima O L , Amalik Sanae S A 
Published: October 2024

Abstract
Bronchobiliary fistula (BBF) is one of the most exceptional complications following hepatic surgery. By integrating evidence-based case studies from existing literature, this review offers critical insights into the efficacy of diverse imaging modalities and therapeutic approaches across a broad spectrum of clinical scenarios. Computed tomography, and magnetic resonance cholangiography or even scintigraphy shows an abnormal tractus between biliary ducts and pulmonary bronchi and minimally invasive techniques using endoscopy are considered the techniques of choice. Surgery should only be considered in complicated cases due to significant morbidity and mortality rate. We report the case of a 46-year-old man with metastatic adenocarcinoma of the rectum involving the liver, treated with metastasectomy, which was complicated by a BBF. The patient underwent radiological external drainage followed by endoscopic placement of biliary endoprosthesis with favorable outcome.
Antiglomerular basement membrane disease
Authors: Segelmark Mårten , Hellmark Thomas 
Published: October 2024

Abstract
Antiglomerular basement membrane (anti-GBM) disease, also known as Goodpasture’s disease, is a rare autoimmune kidney and/or lung disease typically caused by autoantibodies directed against the noncollagenous, C-terminal domain of the α3 chain of type IV collagen (α3(IV)NC1). Epidemiology—bimodal age distribution with peaks in the third and sixth/seventh decades; incidence 0.5 to 2/million population/year. Clinical features—typically presents with isolated, rapidly progressive glomerulonephritis but can also present as a renopulmonary syndrome with the combination of glomerulonephritis and lung haemorrhage, or as isolated lung haemorrhage. Pathology—light microscopy typically reveals crescent formation, often in more than 80% of glomeruli, with linear staining of IgG along the GBM. Management—aside from supportive care, this typically consists of (1) stopping the inflammatory process with high doses of corticosteroid, (2) removal of the pathogenic antibodies by plasma exchange, and (3) stopping production of new antibodies with cyclophosphamide. It is controversial whether patients presenting with dialysis dependency and no pulmonary disease benefit from immunosuppression. Imlifidase, a cysteine protease that cleaves the heavy chains of all human IgG subclasses, has shown promise in an open-label phase 2a clinical study. Prognosis—recent series report mortality at 6 to 12 months of 7 to 36%, with patients’ survival mainly dependent on age and renal function at diagnosis. The most important factor in renal prognosis is the glomerular filtration rate at diagnosis, which is strongly correlated to the proportion of crescents seen in the renal biopsy. Very few patients with dialysis dependency at diagnosis regain enough function to become dialysis independent (0–20% most series). Patients do not need long-term immunosuppression, and the disease rarely recurs. Renal transplantation is safe if performed after autoantibodies have been suppressed or naturally disappeared.
Functional Optimization in Distinct Tissues and Conditions Constrains the Rate of Protein Evolution
Authors: Usmanova Dinara R , Plata Germán , Vitkup Dennis 
Published: October 2024

Abstract
Understanding the main determinants of protein evolution is a fundamental challenge in biology. Despite many decades of active research, the molecular and cellular mechanisms underlying the substantial variability of evolutionary rates across cellular proteins are not currently well understood. It also remains unclear how protein molecular function is optimized in the context of multicellular species and why many proteins, such as enzymes, are only moderately efficient on average. Our analysis of genomics and functional datasets reveals in multiple organisms a strong inverse relationship between the optimality of protein molecular function and the rate of protein evolution. Furthermore, we find that highly expressed proteins tend to be substantially more functionally optimized. These results suggest that cellular expression costs lead to more pronounced functional optimization of abundant proteins and that the purifying selection to maintain high levels of functional optimality significantly slows protein evolution. We observe that in multicellular species both the rate of protein evolution and the degree of protein functional efficiency are primarily affected by expression in several distinct cell types and tissues, specifically, in developed neurons with upregulated synaptic processes in animals and in young and fast-growing tissues in plants. Overall, our analysis reveals how various constraints from the molecular, cellular, and species’ levels of biological organization jointly affect the rate of protein evolution and the level of protein functional adaptation.
Gentrius: Generating Trees Compatible With a Set of Unrooted Subtrees and its Application to Phylogenetic Terraces
Authors: Chernomor Olga , Elgert Christiane , von Haeseler Arndt 
Published: October 2024

Abstract
For a set of binary unrooted subtrees generating all binary unrooted trees compatible with them, i.e. generating their stand, is one of the classical problems in phylogenetics. Here, we introduce Gentrius—an efficient algorithm to tackle this task. The algorithm has a direct application in practice. Namely, Gentrius generates phylogenetic terraces—topologically distinct, equally scoring trees due to missing data. Despite stand generation being computationally intractable, we showed on simulated and biological datasets that Gentrius generates stands with millions of trees in feasible time. We exemplify that depending on the distribution of missing data across species and loci and the inferred phylogeny, the number of equally optimal terrace trees varies tremendously. The strict consensus tree computed from them displays all the branches unaffected by the pattern of missing data. Thus, by solving the problem of stand generation, in practice Gentrius provides an important systematic assessment of phylogenetic trees inferred from incomplete data. Furthermore, Gentrius can aid theoretical research by fostering understanding of tree space structure imposed by missing data.
Evolutionary Dynamics of Proinflammatory Caspases in Primates and Rodents
Authors: Holland Mische , Rutkowski Rachel , C. Levin Tera 
Published: October 2024

Abstract
Caspase-1 and related proteases are key players in inflammation and innate immunity. Here, we characterize the evolutionary history of caspase-1 and its close relatives across 19 primates and 21 rodents, focusing on differences that may cause discrepancies between humans and animal studies. While caspase-1 has been retained in all these taxa, other members of the caspase-1 subfamily (caspase-4, caspase-5, caspase-11, and caspase-12 and CARD16, 17, and 18) each have unique evolutionary trajectories. Caspase-4 is found across simian primates, whereas we identified multiple pseudogenization and gene loss events in caspase-5, caspase-11, and the CARDs. Because caspase-4 and caspase-11 are both key players in the noncanonical inflammasome pathway, we expected that these proteins would be likely to evolve rapidly. Instead, we found that these two proteins are largely conserved, whereas caspase-4's close paralog, caspase-5, showed significant indications of positive selection, as did primate caspase-1. Caspase-12 is a nonfunctional pseudogene in humans. We find this extends across most primates, although many rodents and some primates retain an intact, and likely functional, caspase-12. In mouse laboratory lines, we found that 50% of common strains carry nonsynonymous variants that may impact the functions of caspase-11 and caspase-12 and therefore recommend specific strains to be used (and avoided). Finally, unlike rodents, primate caspases have undergone repeated rounds of gene conversion, duplication, and loss leading to a highly dynamic proinflammatory caspase repertoire. Thus, we uncovered many differences in the evolution of primate and rodent proinflammatory caspases and discuss the potential implications of this history for caspase gene functions.