bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural Analysis of Cerebral Organoids Using Confocal Microscopy and Transmission/Scanning Electron Microscopy
Authors: Noh Seulgi , Park Yurim , Kim Beomsue , Mun Ji Young 
Published: February 2025

Abstract
Cerebral organoid cultures from human-induced pluripotent stem cells are widely used to study complex human brain development; however, there is still limited ultrastructural information regarding the development. In this study, we examined the structural details of cerebral organoids using various microscopy techniques. Two protocols were chosen as representative methods for the development of brain organoids: the classic whole-cerebral organoid (Whole-CO) culture technique, and the air–liquid interface-cerebral organoid (ALI-CO) culture technique. Immunostained confocal laser scanning microscopy (CLSM) revealed the formation of the CTIP2- and TBR1-positive cortical deep layer on days 90 and 150, depending on the developmental progress of both methods. Furthermore, the presence of astrocytes and oligodendrocytes was verified through immunostained CLSM utilizing two-dimensional and three-dimensional reconstruction images after a 150-day period. Transmission electron microscopy analysis revealed nanometer-resolution details of the cellular organelles and neuron-specific structures including synapses and myelin. Large-area scanning electron microscopy confirmed the well-developed neuronal connectivity from each culture method on day 150. Using those microscopy techniques, we clearly showed significant details within two representative culture protocols, the Whole-CO and ALI-CO culture methods. These multi-level images provide ultrastructural insight into the features of cerebral organoids depending on the developmental stage.
Characterization of interstellar carbon dust analogues synthesized by dielectric barrier discharge and evolution after irradiation with 3 MeV H+
Authors: Gerber Ioana Cristina , Mihaila Ilarion , Pohoata Valentin , Sandu Andrei , Agheorghiesei Catalin , Soroaga Laurentiu Valentin , Iancu Decebal , Andrei Radu Florin , Burducea Ion , Straticiuc Mihai , Duca Dumitru , Egorov Dmitrii , Carpentier Yvain , Chazallon Bertrand , Faccinetto Alessandro , Nuns Nicolas , Focsa Cristian , Pirim Claire , Topala Ionut 
Published: February 2025

Abstract
‘Fluffy’ hydrogenated amorphous carbon (a-C:H) was synthesized using a dielectric barrier discharge plasma, driven by nanosecond high voltage pulses at 1 kHz frequency in a helium-butane mixture. The a-C:H samples were characterized by scanning and transmission electron microscopy, laser-assisted and secondary ion mass spectrometry, and Raman and Fourier-transform infrared spectroscopy. We find that a-C:H samples exhibit infrared absorption features in good agreement with those observed for carbonaceous dust in IRAS 08572+3915 galaxy. We discuss their nano to microscale structure and derive their hydrogen to carbon (H/C) ratios from the results obtained by three distinct experimental characterization techniques. Relying on the average H/C value determined by mass spectrometry and Raman spectroscopy, we can then constrain the absorption strengths values to those best corresponding to our dust analogue, and calculate the H/C ratio from the infrared spectra. Altogether, we find that our dust analogue consists of a dominant hydrogen-rich aliphatic network, with small, isolated, aromatic regions. The a-C:H dust analogue was then irradiated with 3 MeV H+ and subsequently analyzed ex situ. Morphological and chemical changes, including the evolution of H/C, CH2/CH3, and sp2/sp3 ratios, were observed with increasing proton fluence, indicating dehydrogenation and graphitization. Proton bombardment shifted the initial location of a-C:H in the hydrocarbon ternary phase diagram toward the central region defined by IRAS 08572+3915 observations. The decay of the 3.4 μm band with proton fluence was used to calculate CH destruction cross-sections, results consistent with a direct effect of cosmic rays on the disappearance of the 3.4 μm band.
Long-Time 2D Simulations of Fallback Supernovae: A Systematic Investigation of Explosions Dynamics and Mass Ejection
Authors: Sykes Bailey , Müller Bernhard 
Published: February 2025

Abstract
We present a set of eight fallback simulations of zero-metallicity progenitors with masses between 60 M⊙ and 95 M⊙. The simulations are computed in 2D with the general relativistic CoCoNuT-FMT code for the first few seconds after black hole formation, and then mapped to the Newtonian code Prometheus for long-duration simulations to shock breakout. All simulations produce successful explosions with final energies ranging from 0.41 × 1051 erg to 2.5 × 1051 erg and black hole masses from 20.7 M⊙ to 34.4 M⊙. Explosion energies and remnant masses do not vary monotonically with progenitor mass, but the mass cuts cluster near the outer edge of the helium core. A supplementary model with decreased neutrino heating provides a tentative indication that successful explosions require the shock to reach the sonic point in the infall profile by the time of black hole formation. The propagation of the shock to the surface is only approximately captured by proposed shock invariants, but these may still be sufficient to extrapolate the final black hole mass from the first seconds of evolution. We also discuss potential multi-messenger signatures of the predicted fallback explosions. The enrichment of the ejecta in intermediate mass and iron-group elements varies considerably and is non-negligible for the more powerful explosions. Low-level neutrino emission after black hole formation from these very massive progenitors may be detectable in the case of a Galactic event.
On the progenitor of the Crab pulsar
Authors: Cruz-Cruz Elvira , Kochanek C S 
Published: February 2025

Abstract
We investigate the progenitor of the Crab supernova by examining the remnant’s surrounding stellar population. The Crab is interesting because of the apparently low energy and mass of the supernova remnant. We also know it was not a binary at death and that the explosion formed a neutron star. Using Gaia EDR3 parallaxes and photometry, we analyze stars inside a cylinder with a projected radius of 100 pc and spanning distances from ∼1600 to 2300 pc set by the 2σ uncertainties in the Crab’s parallax. We also individually model the most luminous stars local to the Crab. The two most luminous stars are blue, roughly main sequence stars with masses of ∼11M⊙. We estimate the stellar population’s age distribution using Solar metallicity PARSEC isochrones. The estimated age distribution of the 205 MG &lt; 0 stars modestly favor lower mass stars, consistent with an AGB star or a lower mass binary merger as the progenitor, but statistically we cannot rule out higher masses. This may be driven by contamination due to the ∼700 pc span of the cylinder in distance.
Structures of the cyanobacterial nitrogen regulators NtcA and PipX complexed to DNA shed light on DNA binding by NtcA and implicate PipX in the recruitment of RNA polymerase
Authors: Forcada-Nadal Alicia , Bibak Sirine , Salinas Paloma , Contreras Asunción , Rubio Vicente , Llácer José L 
Published: February 2025

Abstract
The CRP-FNR (cAMP receptor protein-fumarate/nitrate reductase regulator) superfamily of transcriptional regulators includes the cyanobacterial master regulator NtcA, which orchestrates large responses of cyanobacteria to nitrogen scarcity. NtcA uses as allosteric activator 2-oxoglutarate (2OG), a signal of nitrogen poorness and carbon richness, and binds a co-activating protein (PipX) that shuttles between the signaling protein PII and NtcA depending on nitrogen richness, thus connecting PII signaling and gene expression regulation. Here, combining structural (X-ray crystallography of six types of crystals including NtcA complexes with DNA, 2OG, and PipX), modeling, and functional [electrophoretic mobility shift assays and bacterial two-hybrid (BACTH)] studies, we clarify the reasons for the exquisite specificity for the binding of NtcA to its target DNA, its mechanisms of activation by 2OG, and its co-activation by PipX. Our crystal structures of PipX–NtcA–DNA complexes prove that PipX does not interact with DNA, although it increases NtcA–DNA contacts, and that it stabilizes the active, DNA-binding-competent conformation of NtcA. Superimposition of this complex on a very recently reported cryo-electron microscopy structure of NtcA in a transcription activity complex with RNA polymerase (RNAP), shows that PipX binding helps recruit RNAP by PipX interaction with RNAP, particularly with its gamma and sigma (region 4) subunits, a structural prediction supported here by BACTH experiments.
Synapsin III promotes neuronal-like transdifferentiation of glioblastoma stem cells by disrupting JAG1-Notch1 interaction
Authors: Deng Yilin , Yuan Zheng , Jin Xiong , Wang Zekun , Gong Rui , Ren Shuai , Park Jong Bae , Shi Bingyang , Yin Jinlong 
Published: February 2025

Abstract

Background
Glioblastoma (GBM), a formidable and highly aggressive form of brain cancer, is predominantly driven by GBM stem cells (GSCs), which are characterized by their ability for self-renewal and aberrant differentiation. Targeting the terminal differentiation of GSCs represents a promising therapeutic strategy. This study aimed to elucidate the role of synapsin III (SYN3) in driving the differentiation of GSCs into neuron-like cells and its effect on the tumor-suppressive pathways in GBM.

Method
Proliferation assays, limited dilution assays, immunocytochemistry, western blot, RT-qPCR, and GSC tumor models were used to determine gene function and assess the role of γ-secretase inhibitors. Co-immunoprecipitation and microscale thermophoresis were conducted to explore the underlying regulatory mechanisms. Intracranial orthotopic injection of adeno-associated virus (AAV) was performed to evaluate therapeutic potential.

Results
We demonstrate that SYN3, uniquely within the synapsin family, acts as a tumor suppressor by steering GSCs toward neuronal-like transdifferentiation. Mechanistically, SYN3 enhances the expression of Neuregulin 3 (NRG3), which serves as a non-canonical antagonist of Notch signaling by competitively binding to specific epitopes within the EGF-like domain of JAG1, a critical site for the canonical engagement of Notch receptors. This critical interaction disrupts the JAG1-Notch1 signaling pathway, a key mechanism driving GSCs toward neuronal-like transdifferentiation, thereby reducing their stemness. Furthermore, SYN3 demonstrated significant antineoplastic activity in a mouse model harboring GSCs. AAV-mediated overexpression of SYN3 markedly impeded GBM progression.

Conclusion
Our research reveals the therapeutic potential of SYN3 in regulating GSC fate and offers a novel differentiation-based approach for GBM therapy.
Under cover of darkness: Refuge from artificial light at night may mitigate risks to stranded seabirds
Authors: Brown Taylor M , Baker Kaitlyn , Wilhelm Sabina I , Burness Gary 
Published: February 2025

Abstract
Artificial light at night is an anthropogenic pollutant that has wide-ranging effects on wildlife. Fledgling seabirds of order Procellariiformes exhibit phototaxis toward artificial lights on their first flights from the nest, causing them to become grounded in human settlements, where they are subject to increased predation risk. Limited evidence suggests certain light types may be less attractive than others, yet there is also evidence for an aversion to light under certain circumstances. We investigated differences in phototactic behavior, activity level, and shelter-seeking behavior of grounded Hydrobates leucorhous (Leach’s Storm-Petrel) fledglings exposed to artificial light in 3 experiments: a Y-maze choice experiment, an open field test, and a modified open field test with a hide box provided (“safe haven test”). When provided with combinations of different light types in the Y-maze, storm-petrels typically remained stationary in the darkest parts of the apparatus (farthest from light stimuli) and exhibited no preferred response toward one light type over another. This was consistent with results from the open field test: individuals were less active in darkness than when exposed to 2 of 3 light conditions (warm white light-emitting diode and high-pressure sodium). More than half of individuals entered the hide box in light conditions, compared to none in darkness. Considered together, our results indicate that most (but not all) H. leucorhous fledglings exhibit photophobic behavior after stranding, which may be part of a behavioral strategy to avoid predation. Further, we demonstrate the utility of providing hide boxes to protect stranded seabird fledglings in locations where lighting cannot be eliminated or where rescue efforts are limited in spatial or temporal coverage. However, hide boxes would have limited utility in dark locations. Hide boxes constitute a novel mitigation measure that merits future testing for its ability to reduce stranding-induced mortality, especially in imperiled procellariiform species.
The Big Green Button: Stratospheric Aerosol Injection as a Geopolitical Dilemma During Strategic Competition Between the United States and China, and Implications for Expanding Aerosol Injection Near-term Research
Authors: Nielsen Jeffrey 
Published: February 2025

Abstract
This research examines stratospheric aerosol injection (SAI) policy options through a dyadic international relations framework between the United States and People’s Republic of China (China). Deploying large-scale SAI to manage solar radiation presents states with a novel source of geopolitical influence through influencing global climate systems. While multiple political bodies like the United Nations, European Union, United States, China, and India could feasibly deploy SAI without full global consent, the United States and China are powerful enough to deploy large-scale SAI unilaterally. The United States and China currently perceive themselves as locked in “great power competition” with each other which exposes a mutual SAI national security gap and accompanying policy dilemma. Given their divergent global power strategies but mutual global climate interests, this research assesses how the United States and China could compete or cooperate on SAI strategies. This research’s dyadic analysis of four policy scenarios provides three conclusions. First, the United States and China could each benefit from SAI cooperation whether they are cooperating to deter or deploy SAI. Second, SAI cooperation presents a potential political off-ramp from great power competition that aligns with each state’s mutual climate security interests. Third, expanding SAI research and conventional mitigation could support near-term United States and China policymaking regardless of whether they ultimately pursue SAI deployment or deterrence strategies. SAI advocates and critics alike can use these scenarios and conclusions to better discuss SAI as a geopolitical security dilemma.
Echoes of authenticity: Reclaiming human sentiment in the large language model era
Authors: Wang Yifei , Eshghi Ashkan , Ding Yi , Gopal Ram 
Published: February 2025

Abstract
This paper scrutinizes the unintended consequences of employing large language models (LLMs) like ChatGPT for editing user-generated content (UGC), particularly focusing on alterations in sentiment. Through a detailed analysis of a climate change tweet dataset, we uncover that LLM-rephrased tweets tend to display a more neutral sentiment than their original counterparts. By replicating an established study on public opinions regarding climate change, we illustrate how such sentiment alterations can potentially skew the results of research relying on UGC. To counteract the biases introduced by LLMs, our research outlines two effective strategies. First, we employ predictive models capable of retroactively identifying the true human sentiment underlying the original communications, utilizing the altered sentiment expressed in LLM-rephrased tweets as a basis. While useful, this approach faces limitations when the origin of the text—whether directly crafted by a human or modified by an LLM—remains uncertain. To address such scenarios where the text's provenance is ambiguous, we develop a second approach based on the fine-tuning of LLMs. This fine-tuning process not only helps in aligning the sentiment of LLM-generated texts more closely with human sentiment but also offers a robust solution to the challenges posed by the indeterminate origins of digital content. This research highlights the impact of LLMs on the linguistic characteristics and sentiment of UGC, and more importantly, offers practical solutions to mitigate these biases, thereby ensuring the continued reliability of sentiment analysis in research and policy.
Solvation, geometry, and assembly of the Tobacco Mosaic Virus
Authors: Spirandelli Ivan , Evans Myfanwy E 
Published: February 2025

Abstract
Biological self-assembly is a fundamental aspect in the development of complex structures in nature. A paradigm for such a process is the assembly of Tobacco Mosaic Virus capsid proteins into helical rods around the viral genome. The self-assembly process of the virus is typically modelled through attractive interactions between protein subunits, however capsid proteins also interact with their aqueous environment through solvation free energy. An open question is what role solvation plays in virus self-assembly. Here we show that a purely geometric model of non-polar solvation free energy, the morphometric approach, is sufficient to simulate the assembly of up to three protein subunits of Tobacco Mosaic Virus. The lowest solvation free energy states we find in a geometric simulation setting are remarkably close to the correctly assembled states of various experimentally determined structures. This demonstrates that van der Waals forces and entropic considerations are sufficient to guide assembly in the absence of attractive interactions between protein subunits. It further illustrates the impact of the morphometric approach as a computationally efficient model for non-polar solvation free energy of solutes, in particular those with complicated geometry. This demonstration of the role of solvation raises important questions about the driving forces behind biological self-assembly and the paramount role of geometry.
Minimal structure for neutrino mass matrix
Authors: Kumar Manoj , Awasthi Nikhila , Randhawa Monika , Gupta Manmohan 
Published: February 2025

Abstract
Taking clue from the minimal structure of texture 4-zero hermitian mass matrices, which are very successful in accommodating quark mixing data, we propose a form of texture 2-zero complex symmetric neutrino mass matrix with only one phase parameter. This minimal mass matrix not only accommodates the available neutrino oscillation data, but also makes interesting predictions for the unknown parameters like the lightest neutrino mass $m_{\nu _1}$ (for normal ordering(NO)), Jarlskog’s rephasing invariant JCP, Dirac type CP violating phase δCP and effective neutrino mass &lt;mee &gt;. We also explore the correlations between the parameters of the model, that lead us to minimizing the parameters further.
Representation in clinical trials sponsored by the United States Department of Veterans Affairs
Authors: Gomez Gabriela T , Turner Brandon E , Steinberg Jecca R , Lam Miranda B , Wren Sherry M 
Published: February 2025

Abstract

Background
This study was conducted to determine whether demographic representation among U.S. Department of Veterans Affairs (VA)-sponsored trials differs from trials without VA sponsorship, with reference to VA patient demographics.

Methods
U.S. clinical trials registered between 1 March 2000 and 1 February 2022 were stratified into VA and non-VA groups. Outcomes included the combined percentage of non-White participants in each trial and enrollment of each demographic subgroup. Trial strata were summarized using medians; Wilcoxon rank sum and one-sample signed rank tests were used to compare demographic representation between (i) VA and non-VA trials and (ii) VA trials and Veterans Health Administration (VHA) patient demographics, respectively.

Results
We identified 13,826 trials with available data, including 521 VA and 13,305 non-VA-sponsored trials. Median non-White enrollment was 68% greater in VA trials (P &lt; .001) than in non-VA trials, driven by greater enrollment of Black participants (23.5% vs. 10.4%; P &lt; .001). Black participant enrollment in VA trials exceeded representation among VHA beneficiaries (23.5% vs. 15.8%, P &lt; .001).

Conclusions
This study highlights the increased Black representation in VA-sponsored clinical trials, which is greater than expected after accounting for VHA clinical population demographics. Partnership with the VA may represent a meaningful avenue for increasing Black representation in clinical trials.
Medical treatment of type 2 diabetes in children and adolescents
Authors: Doyle Elizabeth A. 
Published: February 2025

ABSTRACT
Over the last 20 years, the incidence of type 2 diabetes (T2D) has increased among the pediatric population. This increase is of great concern, as T2D tends to be far more aggressive when diagnosed at an earlier age. This article reviews the incidence, prevalence, diagnosis, and management of T2D in children and adolescents. Implications for NP practice are also discussed.
Associations between ambient pollen exposure and measures of cognitive performance
Authors: Corpening Baylee , Bürgler Alexandra , Tamási Bálint , Gehrig Regula , Gan Kexin , Alonso Hellweg Ana , Luyten Axel , Glick Sarah , Beigi Minaya , Hartmann Karin , Eeftens Marloes 
Published: February 2025

Background:
Prior research suggests pollen allergies may be associated with cognitive function, although the effect sizes and specific cognitive outcomes varied across studies. With pollen seasons starting earlier and intensifying due to climate change, understanding the effects of pollen exposure on cognition is increasingly relevant. This study investigated the relationship between ambient pollen exposure and cognitive performance in Swiss adults.

Methods:
Four cognitive assessments were used to measure the daily performance of 392 participants (299 with pollen allergies) over a 10-day period during pollen season. We used generalized additive mixed models to assess the exposure-response relationship between individualized pollen exposure and cognitive performance, as well as allergic symptom severity and cognitive performance, adjusting for individual characteristics and time-varying environmental and individual confounders (e.g., air pollution, weather, and coffee intake).

Results:
We did not find any statistically significant relationships between pollen exposure or severity of allergic symptoms and overall score or reaction time on tests of response inhibition, attention, and visual-spatial memory. We observed a 1% increase [95% confidence interval (CI) = 0.13%, 2.0%] in average reaction time on a test of grammatical reasoning for allergic participants at an exposure of 300 pollen/m3 (12-hour average).

Conclusion:
Overall, our study population did not exhibit changes in cognitive performance related to pollen exposure or perceived allergic symptoms. A marginal, but statistically significant effect on the response time of pollen-allergic individuals was observed for a test of verbal reasoning, however, this is likely to be a chance finding considering the number of exposures and outcomes evaluated.