bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gossypiboma larynx: a rare cause of post-tracheostomy stridor—case report and review of literature
Authors: Prakash Gagan S. , Satish Vikyath , Raju Bharath , Onkaramurthy Neema Jayachamarajapura , Prakash Sathya 
Published: June 2024

Abstract
Background
Gossypiboma, a retained surgical sponge with a foreign body reaction, is an unusual but serious complication seen in open abdominal surgeries. It is exceptionally rare following head and neck surgeries. Here, we present a case of Gossypiboma of the upper airway following tracheostomy.

Case presentation
A 32-year-old male presented with stridor and difficulty breathing one-month post-tracheostomy after a severe head injury following a road traffic accident. A neck radiograph was unremarkable, and a computed tomography (CT) scan of the neck showed a well-defined homogenous curvilinear membrane extending from the hypopharynx to the upper trachea. Bronchoscopic evaluation of the larynx and upper trachea revealed a retained surgical sponge, which was retrieved. The patient’s breathing improved drastically post intervention.

Conclusion
Gossypiboma may go undetected in radiographs and may also present atypically as a homogenous membrane on a CT scan of the neck. Though rare, retained surgical items can have profound medicolegal and professional consequences on physicians. Hence, a strong clinical suspicion and vigilance for gossypiboma is necessary for patients presenting with respiratory distress post-tracheostomy.
Extracellular matrices of stromal cell subtypes regulate phenotype and contribute to the stromal microenvironment in vivo
Authors: Stone Andrew P. , Rand Emma , Thornes Gabriel , Kay Alasdair G. , Barnes Amanda L. , Hitchcock Ian S. , Genever Paul G. 
Published: June 2024

Abstract
Background
Bone marrow stromal cells (BMSCs) are highly heterogeneous, which may reflect their diverse biological functions, including tissue maintenance, haematopoietic support and immune control. The current understanding of the mechanisms that drive the onset and resolution of heterogeneity, and how BMSCs influence other cells in their environment is limited. Here, we determined how the secretome and importantly the extracellular matrix of BMSCs can influence cellular phenotype.

Methods
We used two immortalised clonal BMSC lines isolated from the same heterogeneous culture as model stromal subtypes with distinct phenotypic traits; a multipotent stem-cell-like stromal line (Y201) and a nullipotent non-stem cell stromal line (Y202), isolated from the same donor BMSC pool. Label-free quantitative phase imaging was used to track cell morphology and migration of the BMSC lines over 96 h in colony-forming assays. We quantified the secreted factors of each cell line by mass spectrometry and confirmed presence of proteins in human bone marrow by immunofluorescence.

Results
Transfer of secreted signals from a stem cell to a non-stem cell resulted in a change in morphology and enhanced migration to more closely match stem cell-like features. Mass spectrometry analysis revealed a significant enrichment of extracellular matrix (ECM) proteins in the Y201 stem cell secretome compared to Y202 stromal cells. We confirmed that Y201 produced a more robust ECM in culture compared to Y202. Growth of Y202 on ECM produced by Y201 or Y202 restored migration and fibroblastic morphology, suggesting that it is the deficiency of ECM production that contributes to its phenotype. The proteins periostin and aggrecan, were detected at 71- and 104-fold higher levels in the Y201 versus Y202 secretome and were subsequently identified by immunofluorescence at rare sites on the endosteal surfaces of mouse and human bone, underlying CD271-positive stromal cells. These proteins may represent key non-cellular components of the microenvironment for bona-fide stem cells important for cell maintenance and phenotype in vivo.

Conclusions
We identified plasticity in BMSC morphology and migratory characteristics that can be modified through secreted proteins, particularly from multipotent stem cells. Overall, we demonstrate the importance of specific ECM proteins in co-ordination of cellular phenotype and highlight how non-cellular components of the BMSC microenvironment may provide insights into cell population heterogeneity and the role of BMSCs in health and disease.
Reprogramming of 3D genome structure underlying HSPC development in zebrafish
Authors: He Min , Li Xiaoli , Xu Bingxiang , Lu Yinbo , Lai Jingyi , Ling Yiming , Liu Huakai , An Ziyang , Zhang Wenqing , Li Feifei 
Published: June 2024

Abstract
Background
Development of hematopoietic stem and progenitor cells (HSPC) is a multi-staged complex process that conserved between zebrafish and mammals. Understanding the mechanism underlying HSPC development is a holy grail of hematopoietic biology, which is helpful for HSPC clinical application. Chromatin conformation plays important roles in transcriptional regulation and cell fate decision; however, its dynamic and role in HSPC development is poorly investigated.

Methods
We performed chromatin structure and multi-omics dissection across different stages of HSPC developmental trajectory in zebrafish for the first time, including Hi-C, RNA-seq, ATAC-seq, H3K4me3 and H3K27ac ChIP-seq.

Results
The chromatin organization of zebrafish HSPC resemble mammalian cells with similar hierarchical structure. We revealed the multi-scale reorganization of chromatin structure and its influence on transcriptional regulation and transition of cell fate during HSPC development. Nascent HSPC is featured by loose conformation with obscure structure at all layers. Notably, PU.1 was identified as a potential factor mediating formation of promoter-involved loops and regulating gene expression of HSPC.

Conclusions
Our results provided a global view of chromatin structure dynamics associated with development of zebrafish HSPC and discovered key transcription factors involved in HSPC chromatin interactions, which will provide new insights into the epigenetic regulatory mechanisms underlying vertebrate HSPC fate decision.
Stereochemically-aware bioactivity descriptors for uncharacterized chemical compounds
Authors: Comajuncosa-Creus Arnau , Lenes Aksel , Sánchez-Palomino Miguel , Dalton Dylan , Aloy Patrick 
Published: June 2024

AbstractStereochemistry plays a fundamental role in pharmacology. Here, we systematically investigate the relationship between stereoisomerism and bioactivity on over 1 M compounds, finding that a very significant fraction (~ 40%) of spatial isomer pairs show, to some extent, distinct bioactivities. We then use the 3D representation of these molecules to train a collection of deep neural networks (Signaturizers3D) to generate bioactivity descriptors associated to small molecules, that capture their effects at increasing levels of biological complexity (i.e. from protein targets to clinical outcomes). Further, we assess the ability of the descriptors to distinguish between stereoisomers and to recapitulate their different target binding profiles. Overall, we show how these new stereochemically-aware descriptors provide an even more faithful description of complex small molecule bioactivity properties, capturing key differences in the activity of stereoisomers.Scientific contributionWe systematically assess the relationship between stereoisomerism and bioactivity on a large scale, focusing on compound-target binding events, and use our findings to train novel deep learning models to generate stereochemically-aware bioactivity signatures for any compound of interest.
MIRACLE—a microphone array impulse response dataset for acoustic learning
Authors: Kujawski Adam , Pelling Art J. R. , Sarradj Ennes 
Published: June 2024

AbstractThis work introduces a large dataset comprising impulse responses of spatially distributed sources within a plane parallel to a planar microphone array. The dataset, named MIRACLE, encompasses 856,128 single-channel impulse responses and includes four different measurement scenarios. Three measurement scenarios were conducted under anechoic conditions. The fourth scenario includes an additional specular reflection from a reflective panel. The source positions were obtained by uniformly discretizing a rectangular source plane parallel to the microphone for each scenario. The dataset contains three scenarios with a spatial resolution of $$23\,\textrm{mm}$$

23

mm

at two different source-plane-to-array distances, as well as a scenario with a resolution of $$5\,\textrm{mm}$$

5

mm

for the shorter distance. In contrast to existing room impulse response datasets, the accuracy of the provided source location labels is assessed and additional metadata, such as the directivity of the loudspeaker used for excitation, is provided. The MIRACLE dataset can be used as a benchmark for data-driven modelling and interpolation methods as well as for various acoustic machine learning tasks, such as source separation, localization, and characterization. Two timely applications of the dataset are presented in this work: the generation of microphone array data for data-driven source localization and characterization tasks and data-driven model order reduction.
A comparative study between aqueous and methanol solutions of barium hydroxide: implications for applying barium protectants in gypsification calcareous relics
Authors: Yan Jingchen , Huang Guang , Li Xiangnan , Liu Qing , Liu Yan , Yang Fuwei , Zhang Kun , Sun Yichen 
Published: June 2024

Abstract
Gypsification is a common problem in weathered calcareous relics. In previous studies, the solutions of barium hydroxide in water and methanol were used as protectants for gypsification calcareous relics and showed significant differences in permeability. In this study, the underlying reasons for permeability differences between these two solutions were investigated using optical microscopy, ultraviolet–visible spectrophotometry, X-ray diffractometry, Fourier transform infrared spectroscopy, the phenolphthalein test and physical property characterizations. The results indicated that the permeability differences were primarily caused by the solutions’ reactivity. Specifically, owing to the high reactivity of barium hydroxide in water, it reacted rapidly with atmospheric CO2 and gypsum (the weathering product) to generate barium carbonate, barium sulfate and calcium hydroxide precipitates. These precipitates hindered the penetration of solution into weathered relics. In contrast, barium hydroxide in methanol did not react with atmospheric CO2 or weathered relics, which also kept the solution in a liquid state during the infiltration process. Therefore, the solution of barium hydroxide in methanol exhibited high permeability. Based on the above findings, this study is meaningful for applying barium protectants in the conservation of gypsification calcareous relics.
STEF: a Swin Transformer-Based Enhanced Feature Pyramid Fusion Model for Dongba character detection
Authors: Ma Yuqi , Chen Shanxiong , Li Yongbo , He Jingliu , Ruan Qiuyue , Xiao Wenjun , Xiong Hailing , Li XiaoLiang 
Published: June 2024

Abstract
The Dongba manuscripts are a unique primitive pictographic writing system that originated among the Naxi people of Lijiang, China, boasting over a thousand years of history. The uniqueness of the Dongba manuscripts stems from their pronounced pictorial and ideographic characteristics. However, the digital preservation and inheritance of Dongba manu manuscripts face multiple challenges, including extracting its rich semantic information, recognizing individual characters, retrieving Dongba manuscripts, and automatically interpreting the meanings of Dongba manuscripts. Developing efficient Dongba character detection technology has become a key research focus, wherein establishing a standardized Dongba detection dataset is crucial for training and evaluating techniques. In this study, we have created a comprehensive Dongba manuscripts detection dataset covering various commonly used Dongba characters and vocabularies. Additionally, we propose a model named STEF. Firstly, the Swin Transformer extracts the complex structures and diverse shapes of Dongba manuscripts’ features. Then, by introducing a Feature Pyramid Enhancement Module, features of different sizes are cascaded to preserve multi-scale information. Subsequently, all features are fused in a FUSION module, resulting in features of various Dongba manuscript styles. Each pixel’s binarisation threshold is dynamically adjusted through a differentiable binarisation operation, accurately distinguishing between foreground Dongba manuscripts and background. Lastly, deformable convolution is introduced, allowing the model to dynamically adjust the convolution kernel’s size and shape based on the Dongba manuscripts’ size, thereby better capturing the detailed information of Dongba characters of different sizes. Experimental results show that STEF achieves a recall rate of 88.88%, a precision rate of 88.65%, and an F-measure of 88.76%, outperforming other text detection algorithms. Visualization experiments demonstrate that STEF performs well in detecting Dongba manuscripts of various sizes, shapes, and styles, especially in blurred handwriting and complex backgrounds.
Effectiveness of exercise modalities on breast cancer patient outcomes: a systematic review and meta-analysis
Authors: Yamani Naser , Ahmed Aymen , Khan Mohammad , Wilson Zachary , Shakoor Muteia , Qadri Syeda Fizza , Unzek Samuel , Silver Marc , Mookadam Farouk 
Published: June 2024

AbstractBackgroundThe effects of exercise in patients with breast cancer (BC), has shown some profit, but consistency and magnitude of benefit remains unclear. We aimed to conduct a meta-analysis to assess the benefits of varying types of exercises in patients with BC.MethodsLiterature search was conducted across five electronic databases (MEDLINE, Web of Science, Scopus, Google Scholar and Cochrane) from 1st January 2000 through 19th January 2024. Randomized controlled trials (RCTs) assessing the impact of different types of exercise on outcomes related to fitness and quality of life (QOL) in patients with BC were considered for inclusion. Outcomes of interest included cardiorespiratory fitness (CRF), health-related quality of life (HRQOL), muscle strength, fatigue and physical function. Evaluations were reported as mean differences (MDs) with 95% confidence intervals (CIs) and pooled using random effects model. A p value < 0.05 was considered significant.ResultsThirty-one relevant articles were included in the final analysis. Exercise intervention did not significantly improved the CRF in patients with BC when compared with control according to treadmill ergometer scale (MD: 4.96; 95%Cl [-2.79, 12.70];P = 0.21), however exercise significantly improved CRF according to cycle ergometer scales (MD 2.07; 95% Cl [1.03, 3.11];P = 0.0001). Physical function was significantly improved as well in exercise group reported by 6-MWT scale (MD 80.72; 95% Cl [55.67, 105.77];P < 0.00001). However, exercise did not significantly improve muscle strength assessed using the hand grip dynamometer (MD 0.55; 95% CI [-1.61, 2.71];P = 0.62), and fatigue assessed using the MFI-20 (MD -0.09; 95% CI [-5.92, 5.74];P = 0.98) and Revised Piper scales (MD -0.26; 95% CI [-1.06, 0.55]P = 0.53). Interestingly, exercise was found to improve HRQOL when assessed using the FACT-B scale (MD 8.57; 95% CI [4.53, 12.61];P < 0.0001) but no significant improvements were noted with the EORTIC QLQ-C30 scale (MD 1.98; 95% CI [-1.43, 5.40];P = 0.25).ConclusionOverall exercise significantly improves the HRQOL, CRF and physical function in patients with BC. HRQOL was improved with all exercise types but the effects on CRF vary with cycle versus treadmill ergometer. Exercise failed to improve fatigue-related symptoms and muscle strength. Large RCTs are required to evaluate the effects of exercise in patients with BC in more detail.
The impact of COVID-19 mRNA vaccines on immune-related adverse events in patients with cancer receiving immune checkpoint inhibitors.
Authors: Guo Mengni , Ahmed Zohaib , Nguyen Phuong , Zaidi Kashaf , Itzkowitz Raphael , Chong Esther G , Castillo Dani Ran , Cao Huynh Le 
Published: June 2024

2648 Background: Cancer patients are a vulnerable population to COVID-19. COVID-19 mRNA vaccines have shown to decrease hospitalization and death risk from COVID-19 in cancer patients. Concurrent COVID-19 vaccination and immune checkpoint inhibitors (ICIs) use may impact immune-related adverse events (irAEs) synergistically. Limited data exist on how COVID-19 mRNA vaccines affect irAEs in ICI-treated cancer patients, especially those with breakthrough infections. Methods: We retrospectively analyzed adult patients with malignant solid tumors receiving ICIs at a single cancer institute (January 2020 to July 2021). Fully vaccinated status is defined as two consecutive doses of mRNA vaccines (BNT162b2 and mRNA-1273). Patients who were partially vaccinated, fully vaccinated post COVID-19 infection, vaccinated with non-mRNA COVID-19 vaccines, or last visit within 30 days post vaccination were excluded. All COVID-19 infections were confirmed by PCR. In the vaccinated group, only post-vaccination irAEs were considered as events. Results: 443 patients were included in our study, with 251 (56.7%) vaccinated and 192 (43.3%) unvaccinated. The baseline characteristics were similar between the two groups, except for age (vaccinated median 68 years, unvaccinated median 62 years, p=0.004). With a median follow-up of 12 months, incidences of all-grade irAEs (19.1% vs. 20.3%, p=0.72) and severe irAEs (5.6% vs. 4.2%, p=0.66) were comparable between vaccinated and unvaccinated groups. 34 breakthrough COVID-19 infections occurred. In the vaccinated group, a non-significant trend of higher all-grade irAEs incidence was noted in the COVID-19 infected subgroup compared to uninfected subgroup (29.4% vs. 17.5%, p = 0.11). Univariate analysis linked COVID-19 vaccination (OR 1.54, 95% CI 1.01-2.35, p=0.04) and ipilimumab + nivolumab use (OR 5.57, 95% CI 1.79-17.35, p=0.003) to a higher risk of all-grade irAEs in the entire cohort. After multivariate adjustment, ipilimumab + nivolumab use remained the only variable associated with all-grade irAEs (OR 4.95, 95% CI 1.57-15.64, p=0.006). Conclusions: Our study suggests that COVID-19 mRNA vaccines do not increase irAE risk in cancer patients on ICIs. Fully vaccinated patients with breakthrough COVID-19 infections may safely continue ICI treatment without an increased irAE risk. [Table: see text]
Message-passing approach for percolation on the networked system: A mini-review
Authors: Qian Cheng , Zhao Dan-Dan , Zhong Ming , Zhang Bo , Peng Hao , Wang Wei 
Published: June 2024

Abstract
Network percolation is one of the core topics in network science, especially in understanding and optimizing the robustness of real-world networks. As a powerful tool, the message-passing approach shows unique advantages in characterizing network percolation compared with the mean-field approach. This approach simulates the behavioural response when the network is damaged by transmitting and updating messages between network nodes, thereby accurately assessing the robustness of the network. This paper reviews the progress of message-passing approaches in network percolation on simple networks, multilayer networks and higher-order networks in recent years and discusses the application of this approach in other research fields. Finally, we discuss future research directions around this approach.
Qian Xuan Pounding the Balustrade
Authors: Augustin Birgitta 
Published: June 2024

Abstract
In the late thirteenth century, the poet-painter Qian Xuan 錢選 (style [zi (字)] Shunju 舜举, sobriquets [hao 號] Zhaxi weng 霅溪翁, Yutan 玉潭; ca. 1235–ca. 1307) created a horizontal, multi-colored landscape painting known today as Wang Xizhi Watching Geese and owned by the Metropolitan Museum of Art in New York; a copy of the painting exists in the collection of the National Palace Museum in Taipei. The work depicts a waterside pavilion in which a figure stands with his right hand seemingly resting on the balustrade. This article offers a new interpretation of the painting's scene, and it will argue that the figure's hand on the balustrade is the key to an additional perspective of the painting's artistic statement. It begins by analyzing the painting composition, which includes the artist's inscription, before proceeding to a discussion of balustrade in Song ci-poetry and its significance in Qian Xuan's painting. A closer look at the architecture of the pavilion further reveals that the subject and theme of this painting is that of a dejected Song scholar-poet who laments his country's fate.
Learning Curve Associated With Thoracoscopic Anterior Vertebral Body Tether and Double Anterior Vertebral Body Tether for Idiopathic Scoliosis: Analysis of Three Independent Surgeons
Authors: Lau Darryl , Kurland David B. , Neifert Sean , Pahys Joshua , Samdani Amer , Hwang Steven 
Published: June 2024

BACKGROUND AND OBJECTIVES:
Anterior vertebral body tether (VBT) is a fusionless approach to treat idiopathic scoliosis, and surgeons are beginning to implement the technique into current practice. This study aims to evaluate the learning curve for single and double VBT.

METHODS:
A retrospective review of 3 surgeons' first 40 single and 20 double VBT was performed. Skeletally immature patients with idiopathic scoliosis who underwent thoracic (single) or thoracolumbar (double) VBT were included. Thoracic VBT was done via video-assisted thoracoscopic surgery and lumbar VBT through a mini-open retroperitoneal approach. Primary outcomes of interest were operative time, radiation exposure, and radiographic correction. Pooled and individual-surgeon analyses were performed.

RESULTS:
A total of 180 patients were included: 120 single and 60 double. Mean age was 12.7 years, and 87.8% were female. Mean segments tethered was 7.8 in single and 11.0 in double. Mean preoperative thoracic scoliosis was 51.5: single 50.5° and double 53.3°. Mean lumbar scoliosis was 36.4°: single 30.0° and double 49.0°. Average operating time was 276.2 minutes; double VBT was significantly longer (217.3 vs 394.0 minutes, P < .001). Mean blood loss was 198.5 mL, and mean fluoroscopy dose was 73.0 mGy. For single VBT, there was a decrease in operative time (283.3-174.8 minutes, P < .001) and fluoroscopy dose (70.1-53.5 mGy, P = .047) over time. Every 10 cases resulted in a 31.4 minute decrease in operative time (P < .001). There were no intraoperative complications. Single VBT resulted in 54.9% thoracic curve correction. Double VBT achieved 53.0% thoracic and 56.7% lumbar correction. There were no differences in curve correction across the learning curve.

CONCLUSION:
VBT is viable fusionless surgical option for scoliosis. As expected, increased experience resulted in shorter operative time; the threshold for such improvement seems to be 10 cases. Importantly, adequate and consistent curve correction can be achieved at the start of the learning curve while mitigating complications.