bluuebunny/crossref_metadata_2025_split huggingface dataset:
Correlated evolution of multiple traits gives butterflies a false head
Authors: Yumnam Tarunkishwor , Kodandaramaiah Ullasa 
Published: November 2024

AbstractMany butterflies possess a combination of characters at the posterior hindwing end, superficially resembling their head. This‘false head’has been hypothesised to deflect predator attacks towards the false head area. A clear understanding of the diversity and evolution of false head traits across butterflies is lacking. Here, we tested whether false head traits evolved from simple to complex in order to achieve a greater resemblance to a head. We also tested if false head traits formed an adaptive constellation and, thus, evolved correlatedly. Using a phylogenetic framework with 944 lycaenid species, our results illustrate evolutionary patterns of five false traits - (i) false antennae, (ii) spot, (iii) conspicuous colouration in the false head area, (iv) false head contour in the false head area, and (v) convergent lines. We found that false traits (i)–(iv) evolved in a correlated fashion across the phylogeny, likely driven by a common selective pressure. Our findings support the idea that false head functions as an adaptive constellation for predator attack deflection.
Age-dependent effects of intranasal oxytocin administration were revealed by resting brain entropy (BEN)
Authors: Song Donghui , Wang Ze 
Published: November 2024

AbstractBrain entropy (BEN) reflects the irregularity, disorderliness, and complexity of brain activity and has gained increased interest in recent years. The demonstrated sensitivity of BEN to caffeine and medicine suggests the existence of neurochemical effects of BEN. Oxytocin (OT), a neuropeptide associated with childbirth and lactation, affects both social behavior and brain activity. The purpose of this study was to examine whether OT affects BEN in young and old adults.A randomized, double-blind, placebo-controlled, two-factor (Age × OT) between-subjects design was used, and a total of seventy-five eligible healthy participants were included in the experiment. In the young adult group (YA), 23 participants received intranasal OT administration, while 18 received a placebo (PL) administration. In the older adult group (OA), 16 participants received intranasal OT administration, and 18 received PL administration.Using fMRI-based BEN mapping, we found the age-dependent effect of intranasal OT in the left temporal parietal junction (TPJ), where BEN increased in YA and BEN decreased in OA. A whole-brain functional connectivity (FC) analysis with the left TPJ as the seed and we found that FC between the left TPJ and right TPJ increased in both YA and OA. FC of left and right TPJ and plasma OT contribute to left TPJ BEN just found in YA with intranasal OT administration. These results indicate that BEN is sensitive to age-related effects of neurochemical signals and highlight plasma OT on the effects of intranasal OT in young adults.
Social and spatial drivers of the multitiered structure of zebra finch social networks
Authors: Zhang Yixuan , Jiang Xinyi , Aplin Lucy M. , Wang Daiping , Farine Damien R. 
Published: November 2024

AbstractSocial network structure plays a key role in shaping processes in animal populations. These networks often show distinct patterns in humans and other large mammals, with relationship strengths organized into different tiers. Here, we used continuous, fine-scale tracking of four large captive colonies of zebra finches (Taeniopygia guttata), revealing that zebra finches consistently have 1-2 closest contacts, 6-7 close contacts, and 22-24 strong contacts. The identities of these contacts remain stable across days, with strong contacts maintained by spatial affinity while closest and close contacts are maintained by social choice. These results suggest that zebra finches egocentric networks and social structure are made up of consistent, differentiated relationships forming a multitiered social structure.The similarities in patterns to other species suggest that fundamental principles, such as limitations in time and the ability to move through social space, could drive common structural properties in animal social networks.
An operational framework to map Essential Life Support Areas (ELSAs) for biodiversity, climate, and sustainable development
Authors: Venter Oscar , Ervin Jamison , Stilger Virnig Anne Lucy , Atkinson Scott , Marigo Marion , Zhang Di , Supples Christina , Paniagua Enrique , Phillips Lea , Schuster Richard , Llano Xavier , Pence Genevieve , Arcese Peter , de Assis Barros Luizmar , Belgubaeva Aray , Borja Daniel , Brumby Steve , Burgess Neil D. , Cardozo Leticia , Cordero Vega Carlos , Cordova Maria Veronica , Corzo Liliana , Delgado-Altamirano Esteban , Fonseca Claudia , Game Edward , Georges Yvio , Grantham Hedley , Guerra Daniel , Hansen Andrew , Hawley Greer , Hout Naborey , Jallah Berexford , Deepak KC , Llactayo Leon William , Leslie James , Lihong Dy , Llosa Casandra , Mahmood Abu Rushed Jamil , Makholela Tsepang , Mathis Mark , Miller Granados Cornelia , McGowan Jennifer , Monge Rafael , Mhene Nokutula , Muñoz-Fuentes Violeta , Neubert Sandra , Panta Neupane Menaka , Nuñez Neyra Fabiola , Olarte Diego , Olatunji Emmanuel T. , Jn Paul Dorine , Recondo Veronica , Pierre Gerty , Possingham Hugh , Rodríguez Buriticá Susana , Samarkhanov Kanat , Singh Vijaya , van Soesbergen Arnout , Taukenov Talgat , Telcy David , Telhado Cristina , Tumbey E. Abraham T. , Visconti Piero , Zambrano Holger , Watson James 
Published: November 2024

AbstractAlmost all countries are making increasingly bold commitments to halt and reverse biodiversity loss, minimise the impacts of climate change, and transition to more sustainable development. The effective achievement of many of these commitments relies on integrated spatial planning frameworks that are adaptable to national circumstances, priorities and capabilities. This need is formally recognized by Target 1 of the Kunming-Montreal Global Biodiversity Framework (GBF), which specifies that all areas should be under such planning. Here, we describe the development and application of an operational framework for national-level integrated spatial planning: Essential Life Support Areas (ELSAs). This framework facilitates the identification of areas that - if protected, restored, or sustainably managed - can support the achievement of national commitments to biodiversity, climate, and sustainable development. The process of mapping ELSAs relies heavily on leadership by national experts and stakeholders and the integration of spatial data using systematic conservation planning tools. We showcase the ELSA process carried out for Ecuador, where the use of real-time scenario analyses enabled diverse stakeholder groups to collaborate to assess national priorities for nature, climate, and sustainable development, view trade-offs and synergies, and arrive at a spatial plan to guide national action. ELSA presented an actionable approach for Ecuador, and 12 other pilot countries, to create a spatial plan aimed at fulfilling their national and international commitments to nature, including to the GBF.
The accelerating exposure of European protected areas to climate change
Authors: Cimatti Marta , Mezzanotte Valerio , Heikkinen Risto K. , Hällfors Maria H. , Karger Dirk Nikolaus , Di Marco Moreno 
Published: November 2024

1.AbstractAll ecosystems are affected by climate change, but differences in the pace of change will render some areas more exposed than others. Such spatial patterns of risk are important when assessing the continued functionality of protected area (PA) networks or planning for their expansion. Europe is undertaking an expansion of the PA network to cover 30% of its land and sea surface, but this must account for climate risk. Here, we estimate four metrics of future climate risk across Europe – local velocity, distance velocity, magnitude, and residence time – and assess the level of climate exposure of European PAsvsnon-protected control sites. We also evaluate the intensity of climate risks on >1,000 European species of conservation concern, associated with Natura2000 sites. Our results show large spatial differences in climate change exposure across Europe, with faster pace and farther shifts in climate in the Boreal, Steppic, and Pannonian regions but slower changes in the Mediterranean, Alpine, Artic, and Macronesian regions. Climate change magnitude was higher for the Alpine, Mediterranean, and Steppic regions, implying large local differences between present and future climate. These spatial risk patterns were largely consistent across scenarios, but with up to three times higher risk under the most pessimisticvsthe most optimistic scenario. Large variation in climate exposure for species of conservation concern was revealed, including 11 species which are highly dependent on Natura2000 sites and predicted to experience rapid climate change. Our results provide guidance for managing European PAs, and expanding their coverage, by pinpointing areas offering more stable climates. We emphasize the need for connectivity across the network, to support species adaption via range shifting. This is especially the case in areas facing high climate change magnitude but low climate velocity, implying that climate conditions similar to current ones will be found nearby.
Chromosome-scale genome assembly and linkage map forSilene uniflorareveal the recombination landscape in a rapidly evolving plant species
Authors: Osborne Owen G , Wood Daniel P , Dobreva Mariya P , Dunning Luke T. , Tucker Rachel , Coates Sarah ER , Pellicer Jaume , Holmberg Jon , Algar Adam C , Bocedi Greta , Gubry-Rangin Cecile , Herrera-Alsina Leonel , Juliandi Berry , Lancaster Lesley T , Touzet Pascal , Travis Justin MJ , Papadopulos Alexander ST 
Published: November 2024

AbstractThe genusSileneis an important model system for fields as diverse as sex chromosome evolution, speciation and disease ecology. However, genomic resources remain scarce in the genus. Here, we present a chromosome-scale genome assembly forS. uniflora, a hermaphroditic/gynodioecious species which is an important model for rapid adaptation to anthropogenic disturbance and the role of phenotypic plasticity in adaptive evolution. Using a combination of long-read and Hi-C sequencing technologies, we generated a 1,268 Mb genome assembly with a scaffold N50 of 40.72 Mb and 682 Mb assembled into 12 chromosomes. We annotated the genome using evidence from transcriptome and protein mapping in combination withab initiogene prediction, resulting in 41,603 protein-coding genes and a BUSCO completeness score of 91%. We also present a linkage map which we used to validate the genome assembly and estimate local recombination rate across the genome. Comparison to the only two otherSilenespecies with chromosome-scale genome assemblies reveals widespread genome rearrangements in the genus, suggestingSilenemay be a promising study system for the role of genome rearrangement in evolution, particularly in the evolution of sex chromosomes and adaptation.Significance statementPlant species in the genusSilene(campions) are important study organisms in multiple areas of ecology and evolution. Sea campion (Silene uniflora) is an important model for investigations into rapid adaptation, phenotypic plasticity and parallel evolution. However, only two species have high-quality genome assemblies available, hampering studies of their genetics and evolution. We present a high-quality genome assembly, genetic map and gene annotation for sea campion. These will be important genomic resources for future studies of sea campion, other species in the genusSileneand the family Caryophyllaceae more generally.
AI-driven Classification of Heart Failure Preserved and Reduced Ejection Fraction Patients Using the Total Protein Approach
Authors: Lenzi Alessio , Carvalho Luis B. , Teigas-Campos Pedro A.D. , Biagini Denise , Ghimenti Silvia , Armenia Silvia , Pugliese Nicola R. , Masi Stefano , Di Francesco Fabio , Lomonaco Tommaso , Lodeiro Carlos , Capelo-Martinez Jose-Luis , Santos Hugo M. 
Published: November 2024

AbstractHeart failure (HF) presents two major subtypes: HF with preserved ejection fraction (HFpEF) and HF with reduced ejection fraction (HFrEF), each one with distinct metabolic characteristics. This study utilized artificial intelligence, high-resolution mass spectrometry and the Total Protein Approach (TPA) to identify key features differentiating these subtypes. Aldolase A (ALDOA), a glycolytic enzyme, was found upregulated in HFrEF patients, reflecting an increased glycolysis pathway, while Arginase 1 (ARG1), a key enzyme in the urea cycle, was also elevated, indicating an increased urea pathway. In contrast, HFpEF patients showed TPA ALDOA and ARG1 levels similar to healthy controls. The combined use of ALDOA and ARG1 TPA values successfully classified 82% of patients (14 out of 17). Additionally, most HFpEF patients were over 80 years old, suggesting an age-related metabolic shift. The combination of ALDOA and ARG1 are promising biomarkers for distinguishing HFpEF and HFrEF using the TPA approach, with potential implications for targeted therapies.
A Double-Blind Replication Attempt of Offline 5Hz-rTUS-Induced Corticospinal Excitability
Authors: Fong Po-Yu , Kop Benjamin R. , Evans Carys , Wijaya Vidya Gani , Lin Yongling , Cappotto Drew , Lee Jenny S. A. , Latorre Anna , Song Joy , Treeby Bradley , Martin Eleanor , Rothwell John , Verhagen Lennart , Bestmann Sven 
Published: November 2024

AbstractIntroductionTranscranial ultrasound stimulation (TUS) is a promising new form of non-invasive neuromodulation. As a nascent technique, replication of its effects on brain function is important. Of particular interest is offline 5Hz repetitive TUS (5Hz-rTUS), originally reported by Zeng and colleagues [1] to elicit lasting corticospinal excitability increases, with large effect sizes.Material and methodHere, we conducted a pre-registered (https://osf.io/p5n4q) replication of this protocol that benefitted from three additional features: double-blind application of TUS, neuronavigation for consistent TMS positioning, and acoustic simulations to assess M1 target exposure to TUS. Changes in resting motor thresholds (rMT), motor-evoked potential (MEP) amplitude, short-interval intracortical inhibition (SICI) and intracortical facilitation (ICF) in response to TUS (5Hz-rTUS vs. sham) were measured in the right first dorsal interosseous (FDI), abductor digiti minimi (ADM) and abductor pollicis brevis (APB) muscles, with unbiased selection of participants. Transducer location was determined by the TMS-hotspot for motor representations of the right FDI, as in the original work.ResultsNo significant effects of 5Hz-TUS (vs sham) were observed. Post-hoc simulations showed considerable variability of the acoustic focus, which was outside the anatomical M1-hand area in 67% of participants – in line with the known poor correspondence of TMS-hotspot location and M1-hand area.ConclusionOur results indicate that the effect sizes of the neuromodulatory effects of 5Hz-rTUS on M1 may be more variable than previously appreciated. We suggest that double-blinding, neuronavigated TMS, individualised acoustic simulations for TUS targeting and pre-registration will aid reproducibility across studies.
CRISPRa-mediated disentanglement of the Dux-MERVL axis in the 2C-like state, totipotency and cell death
Authors: Chammas Paul , Xie Sheila Q , Sepulveda-Rincon Lessly P , Leeke Bryony J , Dore Marian H , Dormann Dirk , Wagner Ryan T , McManus Michael T , Karimi Mohammad M , Young George , Percharde Michelle 
Published: November 2024

AbstractTransposable elements (TEs) provide sequences that are powerful cis-regulatory drivers of gene expression programmes. This is particularly apparent during early development when many TEs become de-repressed. MERVL elements are highly yet transiently upregulated in mouse totipotent 2-cell (2C) embryos during major zygotic genome activation (ZGA), and in 2C-like cells in vitro. One of the most powerful activators of MERVL is the pioneer transcription factor, Dux. However, apparent differences lie in the requirement for Dux versus MERVL activation in embryos, for unclear reasons. Moreover, sustained Dux activation causes cell toxicity in multiple cell types, which may or may not be linked to MERVL activation. Using a CRISPR-activation, 2C-GFP reporter system, we have unpicked the relative role of Dux and MERVL in ZGA, totipotent-like characteristics and cell toxicity. We find that direct MERVL activation comprises only a portion of the Dux-dependent transcriptome, and which is sufficient for expanded fate potential, but not other totipotency features. Conversely, Dux-induced pathology is independent of MERVL activation and involves induction of the pro-apoptotic factor, Noxa. Our study highlights the complexity of the Dux-MERVL transcriptional network and uncovers a new player in Dux-driven pathology.
H- and m-channel overexpression promotes seizure-like events by impairing the ability of inhibitory neurons to process correlated inputs
Authors: Rich Scott , Valiante Taufik A. , Lefebvre Jeremie 
Published: November 2024

AbstractChannelopathies affecting h- and m-channels present a paradox in epilepsy research: while both over- and underexpression of these channels can be epileptogenic, channel overexpression does not appear to increase the excitatory-inhibitory (E-I) balance as caused by channel underexpression. We here derive a viable mechanism for ictogenesis driven by h- and m-channel overexpression from analysis of anin silicospiking neuronal microcircuit exhibiting spontaneous seizure-like events (SLEs). Such SLEs are dependent upon sufficiently strong gain in two adaptation terms phenomenologically modeling these channels’ effects: voltage homeostasis (h-current) and spike-frequency adaptation (m-current). Excessive gain of these adaptation terms interferes with the circuit’s processing of highly correlated input, promoting a sequence of network-level events that collectively provoke an SLE. Importantly, these changes do not cause increased excitability in isolated neurons, nor does this cascade require a change in the amplitude of external input to the circuit, suggesting an ictogenic pathway independent of classical changes to the E-I balance. The viability of this mechanism for SLE onset is strengthened by the host of experimentally-characterized features of seizure produced in this model reliant upon the presence of these adaptation terms, including the irregular initiation and termination of seizure-like events and time-varying peak frequency of oscillations during such events (i.e., chirps). Moreover, the cell-type dependent effects of changes in these adaptation terms, as delineated in our analyses, represent experimentally-testable predictions for future study of h- and m-channelopathies. These computational results provide vital new insights into the epileptogenic nature of h- and m-channel overexpression currently absent in the experimental literature.
Effective metabarcoding of endophytic fungi through host-exclusive primer design for nanopore long-read sequencing
Authors: He Ting , Jansonius Koert , Li Xiao , Reilly Alison M. , Sevgin Bahar , Setroikromo Rita , Hackl Thomas , Haslinger Kristina 
Published: November 2024

SummaryMetabarcoding is a powerful tool to simultaneously identify multiple taxa within a DNA sample. However, despite its power, metabarcoding poses challenges when applied to host-associated microbiomes, primarily due to the substantial co-amplification of host DNA.Here we developed a host-exclusive primer design workflow, to selectively generate amplicons from target taxa while excluding the host. This workflow is centered around a new computational tool, mbc-prime, that can generate a list of discriminative candidate primers and score them. We showcase the use of this tool in the process of designing primers for the long-read metabarcoding of endophytic fungi inVinca minor.Four new forward and two new reverse primers reliably amplify large regions of the fungal rDNA of a fungal mock community and the extracted holobiont genomic DNA. Primers exhibit high specificity for fungal rDNA and robust amplification across a diverse range of fungal taxa: with the best primer pairs, we produced fungal amplicons free of plant DNA.Our workflow can be used to study the composition of complex host-associated microbiomes. This workflow should furthermore be universally applicable for the design of discriminative primers in a user-friendly and practical manner and thus be of use for various researchers in?microbiome research.
Ultra-high-throughput screening of antimicrobial combination therapies using a two-stage transparent machine learning model
Authors: Reuter Margaret M. , Lev Katherine L. , Albo Jon , Arora Harkirat Singh , Liu Nemo , Tan Shenghao , Shay Madeline R. , Sarkar Debmalya , Robida Aaron , Sherman David H. , Richardson Rudy J. , Cira Nate J. , Chandrasekaran Sriram 
Published: November 2024

ABSTRACTHere, we present M2D2, a two-stage machine learning (ML) pipeline that identifies promising antimicrobial drug combinations, which are crucial for combating drug resistance. M2D2 addresses key challenges in drug combination discovery by predicting drug synergies using computationally generated drug-protein interaction data, thereby circumventing the need for expensive omics data. The model improves the accuracy of drug target identification using high-throughput experimental and computational methods via feedback between ML stages. M2D2’s transparent framework provides mechanistic insights into drug interactions and was benchmarked against chemogenomics, transcriptomics, and metabolomics datasets. We experimentally validated M2D2 using high-throughput screening of 946 combinations of Food and Drug Administration (FDA)- approved drugs and antibiotics againstEscherichia coli. We discovered synergy between a cerebrovascular drug and a widely used penicillin antibiotic and validated predicted mechanisms of action using genome-wide CRISPR inhibition screens. M2D2 offers a transparent ML tool for rapidly designing combination therapies and guides repurposing efforts while providing mechanistic insights.
Engaging cancer patients on their attitudes towards microbiome engineering technologies
Authors: Owen Kimberley A. , Rutter Jack W. , Holland Claire , Le HB Trung , Shapira Philip , Lewis Clare , Kinross James M. , Barnes Chris P. 
Published: November 2024

AbstractMicrobiome engineering aims to develop engineered live biotherapeutic products to diagnose and treat human disease. One of the most active areas is in the engineering of modified bacteria that act as cancer therapeutics, with many products currently in clinical trials. With the emergence of any novel technologies, it is important to consult the public and end users throughout their development to address any concerns that may arise from their use. This is particularly true for therapeutics, for which it is vital that both clinicians and patients have confidence in the treatments that are available to them. Here, we surveyed a cohort of cancer patients and their relatives to gauge their knowledge of modern microbiome engineering techniques. We focus predominately on the use of bacterial eLBPs to treat cancer. Overall, most participants indicated that they would be comfortable taking cancer treatment options based on microbiome engineering technologies.