bluuebunny/crossref_metadata_2025_split huggingface dataset:
Population-level comparisons of gene regulatory networks modeled on high-throughput single-cell transcriptomics data
Authors: Osorio Daniel , Capasso Anna , Eckhardt S. Gail , Giri Uma , Somma Alexander , Pitts Todd M. , Lieu Christopher H. , Messersmith Wells A. , Bagby Stacey M. , Singh Harinder , Das Jishnu , Sahni Nidhi , Yi S. Stephen , Kuijjer Marieke L. 
Published: March 2024

AbstractSingle-cell technologies enable high-resolution studies of phenotype-defining molecular mechanisms. However, data sparsity and cellular heterogeneity make modeling biological variability across single-cell samples difficult. Here we present SCORPION, a tool that uses a message-passing algorithm to reconstruct comparable gene regulatory networks from single-cell/nuclei RNA-sequencing data that are suitable for population-level comparisons by leveraging the same baseline priors. Using synthetic data, we found that SCORPION outperformed 12 existing gene regulatory network reconstruction techniques. Using supervised experiments, we show that SCORPION can accurately identify differences in regulatory networks between wild-type and transcription factor-perturbed cells. We demonstrate SCORPION’s scalability to population-level analyses using a single-cell RNA-sequencing atlas containing 200,436 cells from colorectal cancer and adjacent healthy tissues. The differences between tumor regions detected by SCORPION are consistent across multiple cohorts as well as with our understanding of disease progression, and elucidate phenotypic regulators that may impact patient survival.
Unique transcriptomes of sensory and non-sensory neurons: insights from Splicing Regulatory States
Authors: Ciampi Ludovica , Serrano Luis , Irimia Manuel 
Published: March 2024

AbstractAlternative Splicing (AS) programs serve as instructive signals of cell type specificity, particularly within the brain, which comprises dozens of molecularly and functionally distinct cell types. Among them, retinal photoreceptors stand out due to their unique transcriptome, making them a particularly well-suited system for studying how AS shapes cell type-specific molecular functions. Here, we use the Splicing Regulatory State (SRS) as a novel framework to discuss the splicing factors governing the unique AS pattern of photoreceptors, and how this pattern may aid in the specification of their highly specialized sensory cilia. In addition, we discuss how other sensory cells with ciliated structures, for which data is much scarcer, also rely on specific SRSs to implement a proteome specialized in the detection of sensory stimuli. By reviewing the general rules of cell type- and tissue-specific AS programs, firstly in the brain and subsequently in specialized sensory neurons, we propose a novel paradigm on how SRSs are established and how they can diversify. Finally, we illustrate how SRSs shape the outcome of mutations in splicing factors to produce cell type-specific phenotypes that can lead to various human diseases.
Cell-mediated exon skipping normalizes dystrophin expression and muscle function in a new mouse model of Duchenne Muscular Dystrophy
Authors: Galli Francesco , Bragg Laricia , Rossi Maira , Proietti Daisy , Perani Laura , Bacigaluppi Marco , Tonlorenzi Rossana , Sibanda Tendai , Caffarini Miriam , Talapatra Avraneel , Santoleri Sabrina , Meregalli Mirella , Bano-Otalora Beatriz , Bigot Anne , Bozzoni Irene , Bonini Chiara , Mouly Vincent , Torrente Yvan , Cossu Giulio 
Published: March 2024

AbstractCell therapy for muscular dystrophy has met with limited success, mainly due to the poor engraftment of donor cells, especially in fibrotic muscle at an advanced stage of the disease. We developed a cell-mediated exon skipping that exploits the multinucleated nature of myofibers to achieve cross-correction of resident, dystrophic nuclei by the U7 small nuclear RNA engineered to skip exon 51 of the dystrophin gene. We observed that co-culture of genetically corrected human DMD myogenic cells (but not of WT cells) with their dystrophic counterparts at a ratio of either 1:10 or 1:30 leads to dystrophin production at a level several folds higher than what predicted by simple dilution. This is due to diffusion of U7 snRNA to neighbouring dystrophic resident nuclei. When transplanted into NSG-mdx-Δ51mice carrying a mutation of exon 51, genetically corrected human myogenic cells produce dystrophin at much higher level than WT cells, well in the therapeutic range, and lead to force recovery even with an engraftment of only 3–5%. This level of dystrophin production is an important step towards clinical efficacy for cell therapy.
Photochromism and single-component white light emission from a metalloviologen complex based on 1,5-naphthyridine
Authors: Zhang Ning-Ning , Zhang Ya-Nan , Li Li , Li Zhen-Yu , Liu Ya-Tong , Dong Yunyun , Yan Yong , Wang Ming-Sheng 
Published: March 2024

A novel 1,5-naphthalene based metalloviologen complex with reversible photochromism and intrinsic white light emission was synthesized.
Improved UNet‐based magnetic resonance imaging segmentation of demyelinating diseases with small lesion regions
Authors: Liu Minhui , Wang Tianlei , Liu Dekang , Gao Feng , Cao Jiuwen 
Published: March 2024

AbstractAccurate magnetic resonance imaging (MRI) segmentation plays a critical role in the diagnosis and treatment of demyelinating diseases. But the existing automatic segmentation methods are not suitable for the segmentation of demyelinating lesions with small lesion size, highly diffuse edges and complex boundary shapes. An improved model is proposed for demyelinating diseases MRI segmentation based on the U‐shaped structure convolution neural networks (UNet). A context information weighting fusion (CIWF) module and a modified channel attention (MCA) module are developed and embedded in UNet to address the small lesion region and diffuse edge issues. The CIWF module can dynamically screen and fuse shallow and deep features at different stages, making the model pay more attention to small lesions. The MCA module enables the model to learn diverse features by adding weights to the channel, which helps in diffuse edge segmentation. Comparisons with many existing methods on real‐world demyelinating disease MRI segmentation dataset show that our method achieve the highest Dice metric.
Multi‐agent trajectory prediction with adaptive perception‐guided transformers
Authors: Nguyen Ngan Linh , Yoo Myungsik 
Published: March 2024

AbstractThe ability to predict the trajectory of an autonomous vehicle accurately is crucial for safe and efficient navigation. However, predicting diverse and multimodal futures can be challenging. Recent approaches such as attention and graph neural networks have achieved state‐of‐the‐art performance by considering agent interactions and map contexts. This study focused on multi‐agent prediction using an agent‐centric approach with transformers. This enables parallel computation and a comprehensive understanding of the environment. Two main features are introduced: an adaptive receptive field (ARF) that captures the relevant surroundings for each agent, and perception encoding, which serves as spatial context embeddings. The ARF adapts to the agent's velocity and rotation, focusing attention ahead at high speeds or to the sides when it is slower. Perception encoding divides agents or lanes into levels and encodes the information of each level. This approach enables the efficient encoding of complex spatial relationships. The proposed method combines these advances with transformer modelling for multi‐agent trajectory prediction while ensuring real‐time prediction capabilities. The approach is evaluated on the Argoverse benchmark and better performance than the state‐of‐the‐art baseline is achieved. By addressing challenges such as multimodal outputs and robustness, the study enhances the safety and efficiency of autonomous driving systems by more accurately predicting trajectories.
The Great Dimming of Betelgeuse: The photosphere as revealed by tomography over the past 15 yr
Authors: Jadlovský Daniel , Granzer Thomas , Weber Michael , Kravchenko Kateryna , Krtička Jiří , Dupree Andrea K. , Chiavassa Andrea , Strassmeier Klaus G. , Poppenhäger Katja 
Published: March 2024

Context. Betelgeuse, a red supergiant star of semi-regular variability, reached a historical minimum brightness in February 2020, known as the Great Dimming. Even though the brightness has returned to the values prior to the Great Dimming now, it continues to exhibit highly unusual behavior.
Aims. Understanding the long-term atmospheric motions of Betelgeuse and its variability could be a clue to the nature of the Great Dimming and the mass-loss process in red supergiants. Our goal is to study long-term dynamics of the photosphere, including during the Great Dimming.
Methods. We applied the tomographic method, which allows different layers in the stellar atmosphere to be probed in order to reconstruct depth-dependent velocity fields. The method is based on the construction of spectral masks by grouping spectral lines from specific optical depths. These masks are cross-correlated with the observed spectra to recover the velocity field inside each atmospheric layer.
Results. We obtained about 2800 spectra over the past 15 yr that were observed with the STELLA robotic telescope in Tenerife. We analyzed the variability of five different layers of Betelgeuse’s photosphere. We found phase shift between the layers, as well as between the variability of velocity and photometry. The time variations of the widths of the cross-correlation function reveal propagation of two shockwaves during the Great Dimming. For about 2 yr after the dimming, the timescale of variability was different between the inner and outer photospheric layers. By 2022, all the layers seemingly started to follow a similar behavior as before the dimming, but pulsating with higher frequency corresponding with the first overtone.
Conclusions. The combination of the extensive high-resolution spectroscopic data set with the tomographic method revealed the variable velocity fields in the photosphere of Betelgeuse, for the first time in such detail. We were also able to find new insights related to the Great Dimming event and its aftermath, namely the discovery of another shockwave and the subsequent rearrangement of the photosphere. Our results demonstrate that powerful shocks are the triggering mechanism for episodic mass-loss events, which may be the missing component to explain the mass-loss process in red supergiants.
Prediction of Postoperative Range of Motion after Mobile-Bearing Medial Unicompartmental Knee Arthroplasty from the Preoperative Range of Motion and Other Preoperative Factors
Authors: Anjiki Kensuke , Hiranaka Takafumi , Tanaka Toshikazu , Fujishiro Takaaki , Okamoto Koji , Hayashi Shinya , Kuroda Ryosuke , Matsumoto Tomoyuki 
Published: March 2024

AbstractPostoperative flexion after unicompartmental knee arthroplasty might be predicted from the preoperative range of motion and other preoperative factors, but this has not been sufficiently investigated. Between 2013 and 2017, 198 patients (198 knees) underwent unilateral knee arthroplasty with medial mobile-bearing unicompartmental knee arthroplasty. Range of motion was measured preoperatively and at the time of final follow-up. To investigate the accuracy of the prediction of preoperative to postoperative gain or loss of the flexion angle, we performed receiver operating characteristic analysis. Logistic regression analysis was used to evaluate other predictive factors. Change in flexion angle was significantly strongly and negatively correlated with the preoperative flexion angle (R = − 0.688; 95% confidence interval: −0.755 to −0.607; p < 0.001). Preoperative flexion angle was suggested to be a significant predictor of gain or loss of the flexion angle with the area under the curve of 0.781; the cutoff value calculated using the Youden index was 140 degrees. Logistic regression analysis showed that in addition to the preoperative flexion angle of the operated side, the postoperative flexion range was significantly affected by the patient's height and by the preoperative flexion angle of the contralateral knee. If the preoperative flexion angle in Oxford mobile-bearing medial unicompartmental knee arthroplasty is <140 degrees, the postoperative flexion angle may be improved; if it exceeds 140 degrees, the postoperative flexion angle may worsen. This predictive ability is further improved by consideration of the patient's height and the range of motion on the contralateral side.
Survival and Functional Outcome in Children with Traumatic Brain Injury Requiring Ventilatory Support: A Prospective Observational Pilot Study
Authors: TN Priyanka , Bhatia Nidhi , Jain Kajal , Gupta Sunil K. , Samra Tanvir , Sarna Rashi , Aditya Ashish S. 
Published: March 2024

Abstract
Background In children, incidence of traumatic brain injury is high and identifying predictors of poor outcome can help clinicians make decisions in the acute phase of treatment. We thus planned to analyze the survival and functional outcome of children following traumatic brain injury. Our study included children (1–10 years of age) requiring ventilation and admitted to trauma intensive care unit of our hospital following traumatic brain injury. Our primary aim was to determine patient outcome using the modified Glasgow Outcome Scale at 3 months following hospital discharge. Our secondary objectives included patient outcome at 1 month following discharge and factors which may affect outcome.
Methods Data (epidemiological, clinical, radiological data, and hospital course) of possible factors affecting survival and outcome of pediatric traumatic brain injury patients were collected. Patient outcome was determined using the modified Rankin Scale at the time of hospital discharge and modified Glasgow Outcome Scale at 1and 3 months following discharge.
Results At the time of hospital admission, 60% children had a Glasgow Coma Scale score of 3 to 8, and were admitted with severe head injury. At the time of discharge, 30% children had good functional outcome, with 50 and 58% children being functionally independent at 1 and 3 months following discharge, respectively. Deranged serum sodium level was an independent predictor of poor neurological outcome on multivariate analysis (coefficient: −3.90 [−5.14 to –2.66, p < 0.001]).
Conclusion Fifty-eight percent children, who were admitted to intensive care unit for mechanical ventilatory support, were functionally independent at the end of 3 months following discharge from the hospital, with modified Glasgow Outcome Scale score of 5 or “Normal.” Deranged electrolytes result in secondary brain injury, thus contributing to poor long-term outcome. Effective electrolyte management is essential to improve outcome after traumatic brain injury in children.
Ultrasound Assessment of Diaphragm Function in Traumatic Brain Injury: A Prospective Observational Study
Authors: Das Kalicharan , Kumar Subodh , Bindra Ashish , Kumar Niraj , Pathak Sharmishtha 
Published: March 2024

Abstract
Background Prolonged mechanical ventilation is associated with weaning failure in severe TBI patients. Ultrasound is a noninvasive modality for evaluating diaphragm function. On ultrasonography (USG), diaphragm thickness is observed to decrease over time in mechanically ventilated patients. However, little literature exists on the severity of diaphragmatic dysfunction in traumatic brain injury (TBI) patients. This study aimed to observe the changes occurring in diaphragmatic function in mechanically ventilated TBI patients.
Methods TBI patients aged 18 to 65 years, requiring mechanical ventilation, were included. USG assessment of diaphragm function was done on days 0, 3, 5 and 7 of neurotrauma intensive care unit (NICU) admission in the supine position, during sedation holiday and spontaneous breathing trial. Measurements were done at end expiration (TE) and at maximal inspiration (TI) using 7- to 13-MHz linear array probe for three consecutive times and then averaged. Thickness fraction was calculated as (TI – TE/TE) × 100. Diaphragmatic excursion (DE) was measured in the M mode using 1- to 5-MHz phased array probe, as maximal height of inspiration.
Results Forty patients were evaluated. The mean diaphragmatic thickness fraction (DTF) at days 0, 3, 5, and 7 was 33.58 ± 10.08, 33.4 ± 9.76, 32.32 ± 8.36, and 31.65 ± 8.23, respectively. Change in DTF was statistically significant on day 7 (p = 0.040). The mean DE at days 0, 3, 5, and 7 was 9.61 ± 3.99, 9.02 ± 3.46, 8.87 ± 2.63, 8.56 ± 2.74, respectively. Changes in DE over days 3, 5, and 7 were statistically significant (p < 0.001). The mean DTF was lower on day 3 in patients who were admitted for less than 20 days than those who required hospital admission for more than 20 days (p = 0.044).
Conclusion Decrease in DTF and DE over the period of 7 days was observed with a significant decrease occurring on the 7th day following TBI.
Exploring the factors affecting cruise passengers’ perceptions of value for money expressed in online reviews
Authors: Jiao Yue , Lau Yui-yip , Gao Jing 
Published: March 2024

AbstractThe complexity of cruise tourism is high, and various factors determine the product value. Value for money has an important effect on cruisers’ choices. This paper comprehensively discusses the effect of ship attributes and onboard and onshore experience on cruise passengers’ perception of value for money. This discussion is helpful for cruise companies to identify key attributes and subsequently implement improvement strategies. Taking nearly 100,000 items of tourist review data as samples, this paper primarily discusses the effect of cruisers’ nine-dimensional experience on the perception of value for money and the differences under different market positioning gleaned from content analysis, regression analysis and multi-group comparison. Results show that embarkation, cabin, dining, entertainment, service, fitness, activities, public room and shore excursion experiences have a significant effect on tourists’ perceptions of value for money. From the perspective of brand positioning, the situation of a luxury cruise is quite different from that of a standard and premium cruise, whereas the standard and premium cruise are similar. Furthermore, unlike standard and premium cruises, the physical attributes of luxury cruises such as ship size and launch year have no significant effect on tourists’ perceptions of value for money. Research results will help cruise companies improve tourist satisfaction and value for money based on market positioning and key attributes.
Implementation of field-programmable Gate array-based clock synchronization in the fiber channel communication system
Authors: Xu Huiya , Wang Guangji , Guo Lianping , Zhao Yijiu , Jiang Dongyu , Lian Ke 
Published: March 2024

A sub-nanosecond clock synchronization scheme based on the field programmable gate array (FPGA) is proposed for the Fiber Channel (FC) communication system in this paper. The counter value of the slave node is synchronized to that of the master node through the embedded IEEE 1588 protocol over the communication link. In order to ensure the counter clocks have the same frequency in both nodes, which is recovered from the FC communication link, the clock phase difference is measured by the digital dual mixer time difference technique and the data recovery technique in the Gigabyte Transceiver, and then it is compensated by the mixed-mode clock manager in FPGAs. The proposed clock synchronization approach is evaluated with an FC communication system that has a serial rate of 12.5 Gbps, and the reported experimental results show that the proposed clock synchronization module can achieve a time difference lower than 1 ns.
Matrix-formation dynamics dictate methyl nitrite conformer abundance
Authors: Hockey Emily K. , McLane Nathan , Vlahos Korina , McCaslin Laura M. , Dodson Leah G. 
Published: March 2024

Methyl nitrite has two stable conformational isomers resulting from rotation about the primary C–O–N–O dihedral angle: cis-CH3ONO and trans-CH3ONO, with cis being more stable by ∼5 kJ/mol. The barrier to rotational interconversion (∼45 kJ/mol) is too large for isomerization to occur under ambient conditions. This paper presents evidence of a change in conformer abundance when dilute CH3ONO is deposited onto a cold substrate; the relative population of the freshly deposited cis conformer is seen to increase compared to its gas-phase abundance, measured by in situ infrared spectroscopy. We observe abundance changes depending on the identity of the bath gas (N2, Ar, and Xe) and deposition angle. The observations indicate that the surface properties of the growing matrix influence conformer abundance—contrary to the widely held assumption that conformer abundance in matrices reflects gas-phase abundance. We posit that differences in the angle-dependent host-gas deposition dynamics affect the growing surfaces, causing changes in conformer abundances. Quantum chemistry calculations of the binding energies between CH3ONO and a single bath-gas component reveal that significant energetic stabilization is not observed in 1:1 complexes of N2:CH3ONO, Ar:CH3ONO, or Xe:CH3ONO. From our results, we conclude that the growing surface plays a significant role in trapping cis-CH3ONO more effectively than trans-CH3ONO, likely because cis-CH3ONO is more compact. Taken together, the observations highlight the necessity for careful characterization of conformers in matrix-isolated systems, emphasizing a need for further study into the deposition dynamics and surface structure of chemically inert matrices.
Quantum–classical correspondence and dissipative to dissipationless crossover in magnetotransport phenomena
Authors: Yamada Akiyoshi , Fuseya Yuki 
Published: March 2024

Abstract
The three-dimensional magneto-conductivity tensor was derived in a gauge invariant form based on the Kubo formula considering quantum effects under a magnetic field, such as the Landau quantization and quantum oscillations. We analytically demonstrated that the quantum formula of the magneto-conductivity can be obtained by adding a quantum oscillation factor to the classical formula. This result establishes the quantum–classical correspondence, which has long been missing in magnetotransport phenomena. Moreover, we found dissipative-to-dissipationless crossover in the Hall conductivity by paying special attention to the analytic properties of the thermal Green’s function. Finally, by calculating the magnetoresistance of semimetals, we identified a phase shift in quantum oscillation originating from the dissipationless transport predominant at high fields.
Air-ground multi-agent system cooperative navigation based on factor graph optimization SLAM
Authors: Liu Haiying , Wang Xiaolong , Liu Ruihang , Xie Yangguang , Li Tiexiang 
Published: March 2024

Abstract
In this study, a cooperative navigation algorithm centered on factor graph optimization—simultaneous localization and mapping (FGO-SLAM) is presented for an air-ground multi-agent system. The algorithm prioritizes the control of error statuses during the position and attitude estimation procedure throughout the entire back-end optimization process. In the conventional extended kalman filtering (EKF) algorithm, periodic cumulative errors may arise, introducing uncertainty to the estimation process. The application of the FGO algorithm not only mitigates deviation but also stabilizes errors, thereby eliminating the accumulation of periodic errors. In comparison to the practical EKF-SLAM, FGO-SLAM serves as a semi-offline optimization system that leverages key frames to minimize computational load. During multi-agent simulations, when two or more agents have overlapping field views, landmark data is merged, enhancing the optimization effectiveness. Through simulation experiments, the proposed algorithm demonstrates a 40% reduction in position error and a 41% reduction in attitude error, affirming the efficacy of FGO-SLAM for cooperative navigation.