bluuebunny/crossref_metadata_2025_split huggingface dataset:
Material surface conjugated with fibroblast growth factor-2 for pluripotent stem cell culture and differentiation
Authors: Sung Tzu-Cheng , Pan Zhi-Xian , Wang Ting , Lin Hui-Yu , Chang Chia-Lun , Hung Ling-Chun , Subbiah Suresh Kumar , Renuka Remya Rajan , Chou Shih-Jie , Chiou Shih-Hwa , Joanna Idaszek , Lee Henry Hsin-Chung , Wu Gwo-Jang , Higuchi Akon 
Published: January 2025

Abstract
Fibroblast growth factor-2 (FGF-2) is a critical molecule for sustaining the pluripotency of human pluripotent stem (PS) cells. However, FGF-2 is extremely unstable and cannot be stored long periods at room temperature. Therefore, the following FGF-2-conjugated cell culture materials were developed to stabilize FGF-2: FGF-2-conjugated polyvinyl alcohol (PVAI-C-FGF) hydrogels and FGF-2-conjugated carboxymethyl cellulose-coated (CMC-C-FGF) dishes. Human induced pluripotent stem (iPS) cells were proliferated on recombinant vitronectin (rVN)-coated PVAI-C-FGF hydrogels and CMC-C-FGF dishes in medium without FGF-2. Human iPS cells could not be cultivated on rVN-coated PVAI-C-FGF hydrogels for more than two passages but could proliferate on rVN-coated CMC-C-FGF dishes. These results indicated that the amount of immobilized FGF-2 and the base cell materials are important, including the amount of immobilized rVN and the conformation of FGF-2 on the surfaces. When human iPS cells were proliferated on rVN-coated CMC-C-FGF surfaces in medium containing no FGF-2 for 10 passages, their pluripotency and potential to differentiate into cells originating from three germ layers were maintained in vivo and in vitro. Furthermore, the cells could extensively differentiate into cardiomyocytes, which can be used for cardiac infarction treatment in future and retinal pigment epithelium for retinal pigmentosa treatment in future. The FGF-2-immobilized surface could enable human PS cell culture in medium that does not need to contain unstable FGF-2. The amount of FGF-2 immobilization on the rVN-coated CMC-C-5FGF and CMC-C-20FGF dishes was reduced to 93.6 and 52.2 times, respectively, which is less than the conventional amount of FGF-2 used in culture medium for one passage (6 days) of human iPS cell culture. This reduction resulted from the stabilization of unstable FGF-2 by the immobilization of FGF-2, which was achieved by utilizing optimal base materials (CMC), coating materials (rVN) and long-joint segment (PEG4-SPDP) design.
Tocilizumab and rituximab for systemic sclerosis interstitial lung disease: a real-world cohort analysis
Authors: Goldman Nina R , Nihtyanova Svetlana I , Beesley Claire F , Wells Athol U , Denton Christopher P , Renzoni Elisabetta A , Mageed Rizgar , Ong Voon H 
Published: January 2025

Abstract

Objectives
SSc-interstitial lung disease (ILD) is one of the leading causes of mortality in SSc. Data from randomized controlled trials (RCTs) support rituximab and tocilizumab monotherapy but there are limited data regarding their use for those who fail standard immunomodulatory therapies.

Methods
SSc patients treated with rituximab or tocilizumab were retrospectively identified in a single centre cohort. Linear mixed effect models were used to analyse before and after treatment lung function trajectory, and identify patient characteristics associated with treatment response.

Results
A total of 127 patients were included for analysis. Fifty-one of 94 (54.2%) and 13 of 33 (39.4%) of the rituximab and tocilizumab cohorts, respectively, were receiving concurrent MMF. Pre-treatment decline in absolute change % forced vital capacity (%FVC)/year and % diffusion capacity for carbon monoxide (%DLCO)/year, respectively, was similar in both cohorts (−3.2% and −4.0% rituximab, and −3.2% and −3.6% tocilizumab). Both treatments resulted in lung function stabilization (%FVC/year and %DLCO/year: 1.2% and +0.2% rituximab cohort, 1.0% and 1.0% tocilizumab cohort). Anti-topoisomerase antibody (ATA)-positive patients had a significant response on %FVC/year to tocilizumab compared with ATA-negative patients. Gender had a significant impact on %FVC/year response to rituximab, with males responding to a greater degree than females. Age, ILD extent and skin subset had no impact on treatment response.

Conclusion
Combination rituximab or tocilizumab with background immunosuppressive therapy is associated with stabilization in lung function trajectory among those who remain refractory to standard immunosuppressives. Specific patient characteristics have an impact on lung function response. Improved FVC response among ATA patients receiving tocilizumab validate data from RCTs.
Augmentation of Interstitial Cystitis–Bladder Pain Syndrome Treatment With Meditation and Yoga
Authors: Dao Angela N. , Komesu Yuko M. , Jansen Sierra M. , Petersen Timothy R. , Meriwether Kate V. 
Published: January 2025

OBJECTIVE:
To investigate whether yoga and meditation added to usual care improves treatment response in women with interstitial cystitis–bladder pain syndrome.

METHODS:
This randomized trial compared women with interstitial cystitis–bladder pain syndrome receiving standard care alone (control group) with those receiving standard care plus meditation and yoga (mind–body group). Standard care was defined as behavioral changes or medications recommended by the American Urological Association. Individuals in the control group received standard care, and those in the mind–body group received standard care augmented with a commercially available meditation application and standardized yoga tutorial video. Both groups continued their current interstitial cystitis–bladder pain syndrome standard care treatments. The primary outcome was the modified GRA (Global Response Assessment), comparing responders (moderately, markedly improved) with nonresponders at 12 weeks. On power analysis assuming α=5% and β=80%, a sample size of 82 participants was required to find 30% difference on the GRA between groups. Weekly GRA scores over 12 weeks were also compared. Secondary outcomes included ICPI (Interstitial Cystitis Problem Index)/ICSI (Interstitial Cystitis Symptom Index), pain, pain interference, anxiety/depression, and self-efficacy scores and treatment escalation over 12 weeks.

RESULTS:
Among 97 randomized participants (49 mind–body group, 48 control group), groups did not differ in characteristics or symptoms at baseline. The mind–body group had more GRA responders compared with the control group at 12 weeks (31/43 [72.1%] vs 10/39 [25.6%], relative risk [RR] 2.8, 95% CI, 1.6–4.6), corroborated by superior weekly GRA results over 12 weeks. The mind–body group had superior beneficial change on the ICPI (RR 1.8, 95% CI, 0.5–3.1), ICSI (RR 1.9, 95% CI, 0.2–3.6), and pain (RR 1.4, 95% CI, 0.4–2.5) scores than the control group at 12 weeks. The mind–body group required less treatment escalation than the control group (2/45 [4.4%] vs 14/42 [33.3%], RR 0.13, 95% CI, 0.03–0.55).

CONCLUSION:
The addition of meditation and yoga to standard interstitial cystitis–bladder pain syndrome care was associated with improved treatment response and required fewer additional interventions compared with standard care alone.

CLINICAL TRIAL REGISTRATION:
ClinicalTrials.gov, NCT04820855.
Silver-Coated Foley Catheters to Reduce UTIs: A Randomized Clinical Trial
Authors: Lewis Kelsey , Crisp Catrina , Ray Marlana , Bonglack Mildrede , Carrel-Lammert Meredith , Aldrich Emily , Pauls Rachel , Hoehn Jonathan , Yeung Jennifer 
Published: January 2025

Importance
This study is important as it challenges the effectiveness of silver-coated catheters in reducing urinary tract infections (UTIs) after pelvic floor surgery (PFS).

Objective
The aim of this study was to investigate the incidence of UTIs in patients using silver-coated silicone transurethral indwelling catheters (TICs) compared with standard silicone TICs among women with postoperative urinary retention following PFS.

Study Design
This was a double-blind, randomized controlled trial of women undergoing PFS between June 2022 and February 2024 with postoperative urinary retention. Participants were randomized to a silver-coated silicone TIC or a standard silicone TIC. The primary outcome was the incidence of symptomatic, culture-proven UTI within 30 days of surgery. Secondary outcomes included the categorization of uropathogens as well as adverse symptoms potentially related to the catheter. A sample size of 155 participants per arm was calculated to find a relative decrease of 47%, from 30% to 16%.

Results
Of 310 participants randomized, 303 were included in the analysis: 154 controls and 149 silver catheter. Demographics were similar for both groups. For our primary outcome, 56 patients in the control group and 52 patients in the silver catheter group were diagnosed with a UTI (36.4% vs 34.9%; P = 0.81). No adverse reactions to the silver catheter were noted. Analysis of the urinary microbiomes demonstrated Escherichia coli was the most represented uropathogen, found in 43% of the urine cultures overall.

Conclusion
There was no difference in incidence of symptomatic, culture-confirmed UTIs in patients who received silver-coated silicone TICs compared with standard silicone TICs in women undergoing PFS.
Control of odor sensation by light and cryptochrome in
theDrosophilaantenna
Authors: Thakur Dhananjay , Hunt Sydney , Tsou Tiffany , Petty Miles , Rodriguez Jason M. , Montell Craig 
Published: January 2025

Abstract
Olfaction is a sense employed by insects to differentiate safe from harmful
food options, evaluate potential mates, and identify oviposition sites. Here, we
found that the fruit fly,Drosophila melanogaster,
responds differently to a set of repulsive odors depending on ambient light
conditions. Ultraviolet (UV) or blue light reduces the behavioral aversion and
electrophysiological responses of olfactory receptor neurons (ORNs) to certain
repellent odors, such as benzaldehyde. We found
thatcryptochrome(cry)
is strongly expressed in the antennal support cells that lie adjacent to ORNs,
and mutation ofcryeliminates the light-dependent
reduction in aversion. Thus, these data demonstrate that support cells in an
olfactory organ serve a sensory function as light receptor cells. It has been
shown that light activation of Cry creates reactive oxygen species (ROS), and
ROS activates the TRPA1 channel. We demonstrate that the TRPA1-C isoform is
expressed and required in ORNs for benzaldehyde repulsion, and that TRPA1-C is
activatedin vitroby benzaldehyde. Overexpression
of dual oxygenase, which generates hydrogen peroxide, reduced the aversion under
dark conditions. Our data support the model that light-dependent creation of
hydrogen peroxide persistently activates TRPA1-C. Consequently, the channel is
no longer effectively activated by benzaldehyde. Since flies sleep much more at
night, and begin feeding at dawn, we propose that the light-induced reduction in
aversion to certain odors provides a mechanism to lower the barrier to feeding
following the transition from night to day.
Functional fingerprinting for the developing brain using deep metric
learning: an ABCD study
Authors: Xu Rui , Zhao Shuwan , Jin Qianhui , Wang Zeyao , Zhao Kun , Zhong Suyu , Zhang Jiaying , Liu Yong , Qi Ting , Wei Yongbin 
Published: January 2025

ABSTRACT
Brain fingerprinting is a promising approach for characterizing the
uniqueness of individual brain functioning using functional magnetic resonance
imaging (fMRI) data. Here, we propose a novel deep learning framework, the
metric-BoIT, for brain fingerprinting and demonstrate its effectiveness in
capturing individual variability among early adolescents undergoing dramatic
brain changes. Utilizing resting-state fMRI data from the Adolescent Brain
Cognitive Development (ABCD) dataset, we identified brain functional
fingerprints that achieved remarkable individual identification accuracy,
reaching 97.6% within a single session and maintaining 86.6% accuracy over a
four-year developmental period. Annotation analysis revealed that higher-order
association regions, particularly those within the default-mode network,
contributed most significantly to these distinctive brain fingerprints
(t= 5.618,p<
0.001). Moreover, these brain fingerprints were relevant to cognitive functions,
as evidenced by significant correlations with fluid intelligence
(F= 1.282,p= 0.027)
and crystallized intelligence (F=
1.405,p< 0.001). The extracted brain
fingerprints were additionally associated with genetics, showing that
individuals with strong genomic relationships exhibited more similar brain
fingerprint patterns (t=
−12.330,p< 0.001). Together, our study not
only presents an innovative approach to brain functional fingerprinting but also
provides valuable insights into the individual variability underlying adolescent
neurodevelopment.
Spatial drug asymmetry modulates phenotypic diversity-migration relationships
under resistance evolution
Authors: Hu Zhijian , Wu Yuzhen , Wood Kevin 
Published: January 2025

Abstract
At long timescales, resistant phenotypes will emerge and be selected within
the bacterial population as an evolutionary response to drug exposure. This
phenomenon reduces the efficacy of drug therapies and thus compromises patient
health. In spatially heterogeneous drug environments, recent evidence shows that
migration can either promote or decelerate the evolution of antibiotic
resistance, thereby affecting the rate of resistant phenotype emergence.
However, another important quantitative aspect of resistance evolution—bacterial
phenotypic diversity—has often been overlooked and remains challenging to
investigate in spatially extended systems, both experimentally and clinically.
In order to study how diversity is reshaped by migration across space, here we
designed a minimal 2-well experimental system with spatial drug asymmetry. One
well contained a bacteriostatic drug (Linezolid) at the minimum inhibitory
concentration, while the other well served as a sanctuary with just media. We
found that the relationship between diversity and migration follows the
“Intermediate Disturbance Hypothesis” (IDH), with migration as the disturbance
to each well. By varying the selective drug concentrations, we observed that the
diversity-migration relationship changes, and IDH can disappear. This behavior
was explained by an asymmetry parameter derived from a two-phenotype
growth-migration dynamic model.
To further validate how different spatial drug asymmetries modulate the
diversity-migration relationship through this asymmetry parameter, we applied
another bactericidal drug, Ampicillin, and observed similar results. In a more
complex scenario involving both Linezolid and Ampicillin, four distinct
phenotypes, including cross-resistant variants, emerged. Our asymmetry parameter
successfully explained the diversity-migration relationship, with unique
diversity dynamics such as multiple peaks appearing from the model. The minimal
generalist-specialist framework predicted these unique behaviors through global
fitness advantages. Our findings provide experimental support and theoretical
explanations for the emergence of phenotypic diversity in clinical settings,
such as gut-lung translocation. These insights may pave the way for improved
clinical strategies to manage antibiotic resistance evolution.
ConvMut: A Web tool to analyze viral convergent mutations along
phylogenies
Authors: Bernasconi Anna , Fanfoni Emma , Alfonsi Tommaso , Focosi Daniele 
Published: January 2025

Abstract
Convergent evolution in protein antigens is common across pathogens and has
also been documented in SARS-CoV-2; the most likely reason is the need to evade
the selective pressure exerted by previous infection- or vaccine-elicited
immunity. There is a pressing need for tools that allow automated analysis of
convergent mutations.
In response to this need, we developed ConvMut, a tool for identifying
patterns of recurrent mutations in SARS-CoV-2 evolution. To this end, we
exploited the granular phylogenetic tree representation developed by PANGO,
allowing us to observe what we call deltas, i.e., groups of mutations that are
acquired on top of the immediately upstream tree nodes. Deltas comprise both
amino acid substitutions and deletions. ConvMut can perform individual protein
analysis to identify the most common single mutations acquired independently in
a given subtree (starting from a user-selected root). Such mutations are
represented in a barplot that can be sorted by frequency or position and
filtered by region of interest. Lineages are then gathered into clusters
according to their sets of shared mutations. Finally, an interactive graph
orders the clusters, details the acquired amino acid changes for each
sublineage, and allows us to the evolutive path until a selected
lineage.
Other unique tools are paired with the main functionality of ConvMut to
support a complete analysis, such as a frequency analysis for a given nucleotide
or amino acid changes at a given residue across a selected phylogenetic
subtree.
We expect that ConvMut will facilitate the design of antiviral anti-Spike
monoclonal antibodies and Spike-based vaccines with longer-lasting efficacy,
minimizing development and marketing failures.
An Emirati pangenome incorporating a diploid telomere-to-telomere
reference
Authors: Olbrich Michael , Mousa Mira , Wohlers Inken , Aamri Amira Al , Alnaqbi Halima , Alsuwaidi Aisha Hanaya , Manoharan Hima Vadakkeveettil , Marzouka Nour al-dain , Ramachandran Sanjay Erathodi , Thomas Anju Annie , Alameri Mohammed , Tay Guan K , Hamoudi Rifat , Ibrahim Saleh , Ghaithi Noura Al , Alsafar Habiba 
Published: January 2025

Abstract
Reference data on genomic variation forms the basis of genetics research.
Limitations in identifying genetic variation from single reference sequences
have recently been addressed through improvements in sequencing technologies,
allowing the generation of pangenomic references from multiple accurate
chromosome-levelde novoassemblies. Nevertheless,
global pangenomes to date have yet to include genomes from the populations of
the Middle Eastern Region. To address this shortcoming, this study provides an
Emirati genome reference. Its core is a diploid assembly with a Quality Value
(QV) of 60 that includes ten telomere-to-telomere chromosomes. This assembly is
incorporated into a pangenome graph constructed of 52 additional high-quality
assemblies, half of which are trio-based. This Emirati pangenome reveals a
similar level of genomic variation as the one compiled by the Human Pangenome
Reference Consortium, underscoring its utility for the identification of both
global and population-centered genomic variation, even in genome regions that
have been traditionally challenging to assemble but are covered by the Emirati
telomere-to-telomere assembly. As such, the Emirati genome reference
significantly contributes to genomic research globally and is an essential
resource for genomics-based personalized medicine in the United Arab Emirates
and other parts of the Middle East.
From spiking neuronal networks to interpretable dynamics: a
diffusion-approximation framework
Authors: Mohammadi Nosrat , Truccolo Wilson , Cash Sydney S , Giraud Anne-Lise , Proix Timothée 
Published: January 2025

Abstract
Modeling and interpreting the complex recurrent dynamics of neuronal spiking
activity is essential to understanding how networks implement behavior and
cognition. Nonlinear Hawkes process models can capture a large range of spiking
dynamics, but remain difficult to interpret, due to their discontinuous and
stochastic nature. To address this challenge, we introduce a novel framework
based on a piecewise deterministic Markov process representation of the
nonlinear Hawkes process (NH-PDMP) followed by a diffusion approximation. We
analytically derive stability conditions and dynamical properties of the
obtained diffusion processes for single-neuron and network models. We
established the accuracy of the diffusion approximation framework by comparing
it with exact continuous-time simulations of the original neuronal NH-PDMP
models. Our framework offers an analytical and geometric account of the neuronal
dynamics repertoire captured by nonlinear Hawkes process models, both for the
canonical responses of single-neurons and neuronal-network dynamics, such as
winner-take-all and traveling wave phenomena. Applied to human and nonhuman
primate recordings of neuronal spiking activity during speech processing and
motor tasks, respectively, our approach revealed that task features can be
retrieved from the dynamical landscape of the fitted models. The combination of
NH-PDMP representations and diffusion approximations thus provides a novel
dynamical analysis framework to reveal single-neuron and neuronal-population
dynamics directly from models fitted to spiking data.
Premotor cortex hemodynamics reflect internal auditory category, not reported
category
Authors: Boucher Jeff , Shamma Shihab , Boubenec Yves 
Published: January 2025

1
Abstract
In sensory decision-making tasks, animals’ decisions are driven by
perception, but also by non-perceptual factors. Because of external and internal
noise, stimuli may be internally misclassified, leading to perceptual errors.
But other, non-sensory factors such as impulsivity or exploratory behavior can
lead to non-perceptual errors. Here we exploited the neural traces of these
errors in frontal cortex to provide insights into their role in sensory decision
making. Using functional ultrasound imaging (fUS), we investigated how the
premotor cortex (PMC) in ferrets represents stimuli in a categorization task,
varying the difficulty in order to manipulate the rates of perceptual errors. We
found that PMC activity reflects the objective (and not the chosen) stimulus
category on incorrect Easy trials, when non-perceptual errors are more likely.
In contrast, PMC responses correlate with the chosen category (and not objective
category) on incorrect Difficult trials, when perceptual errors are more likely.
These results suggest that PMC encodes the ferret’s perceptual decision but not
necessarily the final motor decision. Perceptual errors could be refined further
by assessing licking patterns, but licking patterns alone did not explain the
effect. This study advances our understanding of the functional role of the
frontal cortex in decision making, suggesting that the PMC integrates sensory
inputs to guide behavior based on perceptual, rather than motivational,
information.