bluuebunny/crossref_metadata_2025_split huggingface dataset:
Feathered Icons: Drivers of Global Attention on Bird Species
Authors: Si Haozhong , Fu Changjian , Yu Fan , Li Zhongqiu 
Published: January 2025

Abstract
Global biodiversity faces profound threats. Efforts to slow biodiversity
loss remain inadequate without greater public engagement. With challenges in the
biases of species knowledge across taxa and regions, many endemic or threatened
species receive insufficient attention. Birds, with their ecological importance
and cultural visibility, present an ideal object for exploring biases in species
knowledge. To understand factors driving scientific and public interest in
birds, we compiled a comprehensive dataset to investigate how phenotypic,
ecological, and cultural factors influence attention toward global bird species.
Our analysis reveals that factors related to public familiarity and species
charisma significantly shape public and scientific priorities. In contrast
species that are threatened or have limited ranges often receive little public
attention. IUCN status alone fails to sustain public interest in these species.
To address this imbalance, we propose comprehensive strategies such as media
campaigns and conservation education to better engage the public and scientific
communities. These efforts are crucial for ensuring conservation efforts could
encompass a sufficient range of species.
A real-time forecasting framework for emerging infectious diseases affecting
animal populations
Authors: Theng Meryl , Baker Christopher M. , Lee Simin , Breed Andrew , Roche Sharon , Sellens Emily , Fraser Catherine , Wood Kelly , Jewell Chris P. , Stevenson Mark A. , Firestone Simon M. 
Published: January 2025

Abstract
Infectious disease forecasting has become increasingly important in public
health, as demonstrated during the COVID-19 pandemic. However, forecasting tools
for emergency animal diseases, particularly those offering real-time decision
support when parameters governing disease dynamics are unknown, remain limited.
We introduce a generalised modelling framework for near-real-time forecasting of
the temporal and spatial spread of infectious livestock diseases using data from
the early stages of an outbreak. We applied the framework to the 2007 equine
influenza outbreak in Australia, generating prediction targets at three
timepoints across four regional clusters. Our targets included future daily case
counts, outbreak size, peak timing and duration, and spatial distributions of
future spread. We evaluated how well the forecasts predicted daily cases and the
spatial distribution of case counts, using skill scores as a benchmark for
future model improvements. Forecast accuracy, certainty, and skill improved
significantly after the outbreak’s peak, while early predictions were more
variable, suggesting that pre-peak forecasts should be interpreted with caution.
Spatial forecasts maintained positive skill throughout the outbreak, supporting
their use in guiding response priorities. This framework provides a tool for
real-time decision-making during livestock disease outbreaks and establishes a
foundation for future refinements and applications to other animal
diseases.
Developmentally regulated actin-microtubule crosstalk in Drosophila
oogenesis
Authors: Chou Wei-Chien , Lakonishok Margot , Lu Wen , Gelfand Vladimir I. , McCartney Brooke M. 
Published: January 2025

Abstract
Actin-microtubules (MT) interactions are essential, but how those mechanisms
are orchestrated in complex developing systems is poorly understood. Here we
show that actin-MT crosstalk regulates actin cable assembly and the assembly and
organization of MTs in Drosophila nurse cells during oogenesis. We found that a
stable MT meshwork develops concurrently with actin cable initiation and
requires acetylation for its maintenance. These γ-tubulin nucleated MTs are
cortically tethered via Patronin and Shortstop, extend into the cytoplasm, and
coalign with the elongating actin cables. The MT network promotes the cortical
enrichment of the actin assembly factors Diaphanous and Enabled and loss of MTs
dramatically reduced actin cable density and growth rate. We further
demonstrated that actin filament assembly promotes cortical tethering of MTs and
that loss of the actin filament bundler Villin/Quail results in fewer, shorter,
and more highly coaligned MTs. Together, our data reveal multiple modes of
coordinated actin-MT crosstalk producing actin cable-MT network synergy that is
instrumental for oogenesis.

Summary
This study demonstrates actin–microtubule crosstalk in Drosophila
oogenesis, revealing coregulation between actin filament assembly/bundling
and microtubule nucleation/organization, highlighting the coordinated
regulation of the cytoskeleton required during development.
A three-dimensionalex vivomodel recapitulatesin vivofeatures
and unravels increased drug resistance in childhood acute lymphoblastic
leukemia
Authors: Kanari Magdalini , Garcia Iria Jimenez , Steffen Fabio D. , Krattiger Lisa A. , Bataclan Charles , Liu Wangjie , Simona Benjamin R. , Deplancke Bart , Naveiras Olaia , Ehrbar Martin , Bornhauser Beat , Bourquin Jean-Pierre 
Published: January 2025

Abstract
Acute lymphoblastic leukemia (ALL) preferentially localizes in the bone
marrow (BM) and displays recurrent patterns of medullary and extra-medullary
involvement. Leukemic cells exploit their niche for propagation and survive
selective pressure by chemotherapy in the BM microenvironment, suggesting the
existence of protective mechanisms. Here, we established a three-dimensional
(3D) BM mimic with human mesenchymal stromal cells and endothelial cells that
resemble vasculature-like structures to explore the interdependence of leukemic
cells with their microenvironment. This model recapitulates recurrent topologic
differences between B-cell and T-cell precursor ALL, whereby B-ALL interacts
more closely with the mesenchymal compartment. Migration versatility was found
to be associated with subtype, consistent with increased motility observed in
T-ALLin vivo. Single-cell RNA signatures revealed
similarities to profiles fromin vivopatient derived
xenografts, suggesting relevant statesex vivo.
Furthermore, enhanced migration, adherence and cell cycle heterogeneity was
visualized in our co-culture model. Finally, drug response profiling experiments
in this 3D system reproduced established response patterns and indicated that
drug resistant leukemic subpopulations may be detected more faithfully compared
to information from two-dimensional models.
Timing and social consequences of divorce in wild great tits: a
phenomenological approach
Authors: Abraham A.D. , Sheldon B.C. , Firth J.A. 
Published: January 2025

Abstract
Social behaviour is a key part of the life of many species. An example of an
important social association is that between breeding partners – a key social
connection in monogamously breeding species. The selection of a breeding partner
begins well before reproduction for many species, and this process can have
consequences for subsequent reproductive success. Thus, the non-breeding season
can shape behaviour during the breeding season. However, it is currently unknown
how outcomes in the breeding season can impact associate choice during the
non-breeding season, as studying this has been limited due to requiring high
volumes of individual social data across both contexts. This study used three
years of wild great tit social data from Wytham Woods, Oxford, UK, to examine
social associations between pairs classified with respect to prior and future
relationship status. We found a distinct behavioural pattern in ’divorced’
pairs, which was present from early in the winter, suggesting that the act of
divorce occurs soon after the completion of the breeding season. Pairs forming
for the first time behaved similarly to divorced pairs earlier in the season,
but became similar to faithful pairs throughout the winter. On a finer
spatiotemporal scale the behaviour of faithful and divorced birds diverged over
the winter. These results provide the first evidence of when divorce occurs in
paired great tits, while suggesting that different behaviours may drive
behavioural divorce at different times.
Putative neofunctionalization of a Poales-specific EXO70 clade
Authors: Bergum Molly , Sklenar Jan , Hernández-Pinzón Inmaculada , Taylor Jodie , Smoker Matthew , Samwald Sebastian , Allen Megan , Thind Anupriya , Green Phon , Moon Hyeran , Menke Frank L. H. , Zipfel Cyril , Rhodes Jack , Faulkner Christine , Moscou Matthew J. 
Published: January 2025

Abstract
EXO70s are uniquely expanded in land plants compared to all other eukaryotic
lineages. The functional implications of this expansion and diversification on
the conserved role of EXO70 as a subunit of the octameric exocyst complex have
remained unresolved. We previously demonstrated barley (Hordeum
vulgare) EXO70FX12, a member of the monocot-specific EXO70FX
clade, is required for resistance to wheat stripe rust in conjunction with the
leucine-rich repeat receptor kinase (LRR-RK) HvPUR1. Through phylogenetic
analysis, we identified unique features of the EXO70FX clade, leading us to
hypothesize that this clade experienced neofunctionalization. Using structural
predictions and protein-protein interaction assays, we demonstrate that
HvEXO70FX12 lost the ability to serve as a subunit within the exocyst complex.
We predict that the EXO70FX clade has largely lost exocyst association and
represents a novel acquisition that emerged during Poales diversification for
immunity.
Highly recurrent multi-nucleotide mutations in SARS-CoV-2
Authors: De Maio Nicola , Smith Kyle , Turakhia Yatish , Goldman Nick 
Published: January 2025

Abstract
Multi-nucleotide mutations (MNMs) simultaneously replace multiple
nu-cleotides. They are a significant contributor to evolution and disease, as
well as to misdiagnosis, misannotation and other biases in genome data
analysis.
MNMs are generally thought to be rare and random events. However, by
processing millions of publicly shared genomes, we show that certain MNMs are
highly recurrent in SARS-CoV-2: they repeatedly and consistently modify the same
multiple nucleotides at the same genome position in the same way. The most
frequent of these MNMs have independently occurred hundreds of times across all
SARS-CoV-2 lineages.
The vast majority of these recurrent MNMs are linked to transcription
regulatory sequences. We propose a mechanism that explains them through template
switching as part of the natural transcription process of the virus.
This previously unknown mutational pattern increases our understanding of
the evolution of SARS-CoV-2 and potentially many other nidoviruses. It also has
important consequences for computational evolutionary biology: we show that for
example recurrent MNMs cause approximately 14% of false positives during
inference of recombination in SARS-CoV-2.
A complete collagen IV fluorophore knock-in toolkit reveals α-chain diversity
in basement membrane
Authors: Srinivasan Sandhya , Ramos-Lewis Willam , Morais Mychel R.P.T. , Chi Qiuyi , Soh Adam W. J. , Williams Emily , Lennon Rachel , Sherwood David R. 
Published: January 2025

Abstract
The type IV collagen triple helix, composed of three ⍺-chains, is a core
basement membrane (BM) component that assembles into a network within BMs.
Endogenous tagging of all ⍺-chains with genetically encoded fluorophores has
remained elusive, limiting our understanding of this crucial BM component.
Through genome editing, we show that the C-termini of theC.
eleganstype IV collagen ⍺-chains EMB-9 and LET-2 can be fused
to a variety of fluorophores to create a strain toolkit with wild-type health.
Using quantitative imaging, our results suggest a preference for
LET-2-LET-2-EMB-9 trimer construction, but also tissue-specific flexibility in
trimers assembled driven by differences in ⍺-chain expression levels. By
taggingemb-9andlet-2mutants
that model human Gould Syndrome, a complex multi-tissue disorder, we further
discover defects in extracellular accumulation and turnover that might help
explain disease pathology. Together, our findings identify a permissive tagging
site that will allow diverse studies on type IV collagen regulation and function
in animals.

Summary
Srinivasan et al., construct a collagen IV fluorophore knock-in toolkit
inC. elegansusing a newly identified
permissive genome editing site and reveal tissue-specific α-chain diversity
and basement membrane turnover defects in collagen IV mutants modeling human
COL4A1/A2 (Gould) syndrome.
Where do I go? Decoding temporal neural dynamics of scene processing and
visuospatial memory interactions using CNNs
Authors: Naveilhan Clément , Zory Raphaël , Ramanoël Stephen 
Published: January 2025

Abstract
Visual scene perception enables rapid interpretation of the surrounding
environment by integrating multiple visual features related to task demands and
context, which is essential for goal-directed behavior. In the present work, we
investigated the temporal neural dynamics underlying the interaction between the
processing of visual features
(i.e., bottom-up
processes) and contextual knowledge
(i.e., top-down
processes) during scene perception. We analyzed EEG data from 30 participants
performing scene memory and visuospatial memory tasks in which we manipulated
the number of navigational affordances available
(i.e., the number of
open doors) while controlling for similar low-level visual features across
tasks. We used convolutional neural networks (CNN) coupled with
gradient-weighted class activation mapping (Grad-CAM) to assess the main
channels and time points underlying neural processing for each task. We found
that early occipitoparietal activity (50-250 ms post-stimulus) contributed most
to the classification of several aspects of visual perception, including scene
color, navigational affordances, and spatial memory content. In addition, we
showed that the CNN successfully trained to detect affordances during scene
perception was unable to detect the same affordances in the spatial memory task
after learning, whereas a similarly trained and tested model for detecting wall
color was able to generalize across tasks. Taken together, these results reveal
an early common window of integration for scene and visuospatial memory
information, with a specific and immediate influence of newly acquired spatial
knowledge on early neural correlates of scene perception.
Neural dynamics hierarchy in motor cortex and striatum across naturalistic
behaviors
Authors: Xing David , Glaser Joshua , Miri Andrew 
Published: January 2025

Abstract
Mammals perform a wide range of movements actuated by diverse patterns of
muscle activity. Primary motor cortex (M1) and striatum are implicated in
controlling these movements, but how their activity dynamics are organized to
accommodate such diversity is poorly understood. We developed a paradigm that
enabled us to investigate neural dynamics across diverse motor behaviors in
mice. In contrast to existing views, we found neither behavior-specific nor
behavior- invariant organization in single-neuron activity, population-level
covariation, and muscle activity correlation. Instead, the similarity of
activity dynamics between behaviors varied differentially across behavior pairs,
forming a hierarchical organization. The same hierarchical organization was
shared between M1 and striatum, despite stronger muscle activity correlation in
M1 and greater behavior specificity in striatum. Network modeling indicated that
striatal activity is sufficient to drive hierarchical dynamics in muscle
pattern-generating circuits. These hierarchical dynamics may reflect a tradeoff
between behavioral specialization and generalization in motor system
function.
Infectivity of a pathogenicity-attenuatedChlamydia muridarummutant in
the genital tract
Authors: Li Caiting , Liu Zhaoyang , Hua Yaoqin , Ma Chunguang , Zhong Guangming 
Published: January 2025

Abstract
AC. muridarummutant designated as intrOv was
evaluated as
anintracellularOral
vaccinevector because it can induce protection in
the genital tract following oral inoculation but does not elicit genital
pathology following intravaginal infection. However, the mechanism of intrOv’s
attenuation is unclear. Here we report that few live organisms were recovered
from vaginal swabs during the early stage of intrOv intravaginal infection in
mice. At a low inoculating dose, an isogenic wild-type control strain
established a productive infection, while intrOv failed to do so. Although a
higher inoculating dose allowed intrOv and its control to productively infect
mice, fewer live intrOv than the control organisms were recovered from the lower
genital tract tissues on day 3 post-infection. By day 7, animals infected with
intrOv or the control shed similar numbers of live organisms, suggesting the
intrOv’s deficiency on day 3 was transient. Consistently, intrOv reduced
invasion of epithelial cells but maintained as robust intracellular replication
as its control. Our results correlate intrOv’s delay in infecting the lower
genital tissues and reduction in invading epithelial cells with its attenuation
in genital pathogenicity, laying the foundation for further revealing the
mechanisms of the intrOv’s attenuation in pathogenicity during genital tract
infection.
Genomics of experimental adaptive radiation in the cryptic coloration of
feather lice
Authors: Baldwin-Brown James , Villa Scott M. , Waight Emiko , Johnson Kevin P. , Bush Sarah E. , Clayton Dale H. , Shapiro Michael D. 
Published: January 2025

1
Abstract
A major challenge faced by living organisms is adaptation to novel
environments. This process is poorly understood because monitoring genetic
changes in natural populations is difficult. One way to simplify the task is to
focus on organisms that can be studied in captivity under conditions that remain
largely natural. Feather lice (Insecta, Phthiraptera, Ischnocera) are
host-specific parasites of birds that live, feed, and breed solely on feathers.
Birds defend themselves against lice, which damage feathers, by killing them
with their beaks during bouts of preening. In response, feather lice have
evolved background-matching cryptic coloration to help them avoid preening. We
experimentally manipulated the color backgrounds of host-specific pigeon lice
(Columbicola columbae) by confining them to
different colored breeds of rock pigeon (Columba
livia) over a period of four years (ca. 60 louse generations).
Over the course of the experiment, we sampled lice from pigeons every six months
for genomic resequencing, and then calculated allele frequency differences and
trajectories to identify putative genomic sites under selection. We documented
many loci that changed in response to selection for color. Most loci putatively
under selection were unshared among replicate populations of lice, indicating
that independent adaptation of distinct lineages to the same novel environment
resulted in similar phenotypes driven by different genotypes.
Expression patterns of blood-based biomarkers of neurodegeneration and
inflammation across adulthood in rhesus macaques
Authors: Metzler Ludwig A.P. , Metzger Jeanette M. , Gerred Keenan J. , Emborg Marina E. , Kapoor Amita 
Published: January 2025

ABSTRACT
As the global human population rapidly ages and diseases of aging become
more prevalent, preclinical models of age-related neurodegenerative disorders
are increasingly important for identifying early diagnostic biomarkers,
monitoring disease progression, and evaluating treatment responsiveness. Rhesus
macaques are an ideal species for studies on neurodegeneration due to their
phylogenetic relatedness to humans and their complex brain anatomy and
physiology. Technological advances in assay sensitivity have facilitated the
identification of blood-based biomarkers of neurodegeneration and inflammation
in human populations. The aim of this study was to translate these methods for
use in male and female rhesus macaques across adulthood. We collected plasma
samples from 47 rhesus macaques representing pre-adult (1-5 years, n=6 female,
n=5 male), young (5-7 years, n=5 female, n=7 male), middle (8-16 years, n=7
female, n=7 male), and older adult (17-22 years, n=6 female, n=4 male) subjects.
Quantified biomarkers included neurofilament light chain (NfL), glial fibrillary
acidic protein (GFAP), amyloid beta (Aβ42, Aβ40, and their ratio), total tau,
phosphorylated tau (pTau181), interleukin (IL) 2, IL-6, IL-8, and IL-10. Plasma
NfL and IL-6 levels were significantly increased with age in both sexes, with a
marked rise during middle adulthood. The ratio of Aβ42/Aβ40 significantly
declined steadily with age, mirroring the aging pattern described in humans.
There was no effect of age or sex on total tau or pTau181 levels. Overall, these
results demonstrate the feasibility of evaluating blood biomarkers of
neurodegeneration and inflammation in rhesus macaques during adulthood.
Finding Salient Multi-Omic Interactomes Relevant to Multiple Biomedical
Outcomes using Graph Ensemble Neural Networks
Authors: Eicher Tara , Chan Jany , Becker Aline P. , Haque S. Jaharul , Fleming Jessica , McElroy Joseph , Meng Wei , Webb Amy , Kelly Rachel S. , Celedón Juan , Clish Clary , Gerszten Robert , McGeachie Michael , Weiss Scott T. , Lasky-Su Jessica , Chakravarti Arnab , Mathé Ewy A. , Machiraju Raghu 
Published: January 2025

Abstract
Although multi-omics integration relevant to patient outcome is typically
characterized by an analyte interactome, current multi-omic integration methods
either (1) model outcome without directly including associations between
analytes, (2) model the interactome without directly evaluating the saliency of
the model in the context of outcome, or (3) model outcome in a high-dimensional
parameter space not suitable for small sample sizes (which are common in
multi-omics studies). We introduce Graph Ensemble Neural Network (GENN), a
methodology that learns the interactome most predictive of outcome in a
low-dimensional parameter space built on complementary attributes for all
possible analyte associations (metafeatures). We show
that GENN is robust to noise in measurements using a theoretical model,
outperforms the predictive performance of existing methods when evaluated on
Tegafur drug response in NCI-60 cancer cell line data, and uncovers potentially
novel multi-omic mechanisms driving total serum IgE levels in pediatric asthma
and patient survival in glioblastomas.