bluuebunny/crossref_metadata_2025_split huggingface dataset:
Review of airborne oceanic lidar remote sensing
Authors: Chen Weibiao , Chen Peng , Zhang Hongwei , He Yan , Tang Junwu , Wu Songhua 
Published: October 2023

AbstractAirborne oceanic lidars act as an active remote sensing technique have been proved to be one of the most effective and reliable means of oceanic profile remote sensing. This review aims to provide a comprehensive overview of the principles, methodologies, applications, and prospects of oceanic lidar remote sensing. A survey of the previous studies and works related to these techniques is presented in this paper, emphasizing the different mechanism in system design as well as data processing algorithms and their applications in the remote sensing of oceanic environmental parameters. The airborne lidar systems with multi-channels are designed to significantly improve the data quality and resolution of oceanic biological and geographic profiles. Algorithms for biological product retrieval and simulation based on typical radiation transfer models are described here to stimulate future research into ocean biogeochemistry. The advancement of airborne lidar applications in the near future is also presented.
Long-term health impacts of COVID-19 among 242,712 adults in England
Authors: Atchison Christina J. , Davies Bethan , Cooper Emily , Lound Adam , Whitaker Matthew , Hampshire Adam , Azor Adriana , Donnelly Christl A. , Chadeau-Hyam Marc , Cooke Graham S. , Ward Helen , Elliott Paul 
Published: October 2023

AbstractThe COVID-19 pandemic is having a lasting impact on health and well-being. We compare current self-reported health, quality of life and symptom profiles for people with ongoing symptoms following COVID-19 to those who have never tested positive for SARS-CoV-2 infection and those who have recovered from COVID-19. Overall, 276,840/800,000 (34·6%) of invited participants took part. Mental health and health-related quality of life were worse among participants with ongoing persistent symptoms post-COVID compared with those who had never had COVID-19 or had recovered. In this study, median duration of COVID-related symptoms (N = 130,251) was 1·3 weeks (inter-quartile range 6 days to 2 weeks), with 7·5% and 5·2% reporting ongoing symptoms ≥12 weeks and ≥52 weeks respectively. Female sex, ≥1 comorbidity and being infected when Wild-type variant was dominant were associated with higher probability of symptoms lasting ≥12 weeks and longer recovery time in those with persistent symptoms. Although COVID-19 is usually of short duration, some adults experience persistent and burdensome illness.
An interferon-integrated mucosal vaccine provides pan-sarbecovirus protection in small animal models
Authors: Yuen Chun-Kit , Wong Wan-Man , Mak Long-Fung , Lam Joy-Yan , Cheung Lok-Yi , Cheung Derek Tsz-Yin , Ng Yau-Yee , Lee Andrew Chak-Yiu , Zhong Nanshan , Yuen Kwok-Yung , Kok Kin-Hang 
Published: October 2023

AbstractA pan-sarbecovirus or pan-betacoronavirus vaccine that can prevent current and potential future beta-coronavirus infections is important for fighting possible future pandemics. Here, we report a mucosal vaccine that cross-protects small animal models from sarbecoviruses including SARS-CoV-1, SARS-CoV-2 and its variants. The vaccine comprises a live-but-defective SARS-CoV-2 virus that is envelope deficient and has the orf8 segment replaced by interferon-beta, hence named Interferon Beta Integrated SARS-CoV-2 (IBIS) vaccine. Nasal vaccination with IBIS protected mice from lethal homotypic SARS-CoV-2 infection and hamsters from co-housing-mediated transmission of homotypic virus. Moreover, IBIS provided complete protection against heterotypic sarbecoviruses, including SARS-CoV-2 Delta and Omicron variants, and SARS-CoV-1 in both mice and hamsters. Besides inducing a strong lung CD8 + T cell response, IBIS specifically heightened the activation of mucosal virus-specific CD4 + T cells compared to the interferon-null vaccine. The direct production of interferon by IBIS also suppressed virus co-infection of SARS-CoV-2 in human cells, reducing the risk of genetic recombination when using as live vaccines. Altogether, IBIS is a next-generation pan-sarbecovirus vaccine and warrants further clinical investigations.
Construction of a novel prognostic model in skin cutaneous melanoma based on chemokines-related gene signature
Authors: Ding Xiaoxia , Wang Wenwen , Tao Xiaohua , Li Zhiming , Huang Youming 
Published: October 2023

AbstractSkin cutaneous melanoma, SKCM, is one of the most aggressive treatment-resistant tumours. Despite the fact that the BRAF oncogene and immunological checkpoints such as PD-1/PD-L1 and CTLA-4 have enhanced the therapeutic efficacy of SKCM, the subsequent resistance mechanisms and remedies have raised concerns. Chemokines have a significant role in the immunological milieu of tumor, which may increase the efficacy of checkpoint blockade and serve as a possible therapeutic intervention route. However, there is still no chemokine-based typing and risk model to provide a prognosis and therapeutic efficacy assessment for SKCM patients. In this study, we verified the distinct differences of prognostic stratification as well as immune characteristics between two chemokine-related clusters in SKCM patients. Two clusters of DEGs were discovered to be primarily enriched in B and T cell receptor signaling pathways as well as TNF signaling via NF-kappa-B. Based on 14 prognosis-related DEGs from aforementioned two clusters (CCL8, GBP2, GBP4, SRNG, HLA-DMB, RARRES3, HLA-DQA1, PARP12, APOL3, IRF1, HLA-DRA, UBE2L6, IL2RA and CD38), a chemokine-related 14-gene prognostic model was established. At the same time, researchers explored differences between the low-risk and high-risk groups in clinical traits, the proportion of infiltration of 22 different types of immune cells, and how well medications worked. The risk score model’s immunotherapy and prognostic predictions were also confirmed in testing groups. Based on the finding, we can claim that there is a clear link between chemokines and TME in SKCM. The risk score may perform as a trustworthy prediction model, giving therapeutic benefits for both chemotherapy and immunotherapy, as well as being beneficial for clinical decision making in SKCM patients.
Performance of baseline FDG-PET/CT radiomics for prediction of bone marrow minimal residual disease status in the LyMa-101 trial
Authors: Bodet-Milin Caroline , Morvant Cyrille , Carlier Thomas , Frecon Gauthier , Tournilhac Olivier , Safar Violaine , Kraeber-Bodere Françoise , Le Gouill Steven , Macintyre Elizabeth , Bailly Clément 
Published: October 2023

AbstractThe prognostic value of 18F-Fluorodeoxyglucose positron emission tomography/computed tomography (FDG-PET/CT) at baseline or the predictive value of minimal residual disease (MRD) detection appear as potential tools to improve mantle cell lymphoma (MCL) patients’ management. The LyMa-101, a phase 2 trial of the LYSA group (ClinicalTrials.gov:NCT02896582) reported induction therapy with obinutuzumab, a CD20 monoclonal antibody. Herein, we investigated the added prognostic value of radiomic features (RF) derived from FDG-PET/CT at diagnosis for MRD value prediction. FDG-PET/CT of 59 MCL patients included in the LyMa-101 trial have been independently, blindly and centrally reviewed. RF were extracted from the disease area with the highest uptake and from the total metabolic tumor volume (TMTV). Two models of machine learning were used to compare several combinations for prediction of MRD before autologous stem cell transplant consolidation (ASCT). Each algorithm was generated with or without constrained feature selections for clinical and laboratory parameters. Both algorithms showed better discrimination performances for negative vs positive MRD in the lesion with the highest uptake than in the TMTV. The constrained use of clinical and biological features showed a clear loss in sensitivity for the prediction of MRD status before ASCT, regardless of the machine learning model. These data plead for the importance of FDG-PET/CT RF compared to clinical and laboratory parameters and also reinforced the previously made hypothesis that the prognosis of the disease in MCL patients is linked to the most aggressive contingent, within the lesion with the highest uptake.
Three-dimensional non-approximate Coulomb interaction between two trapped quantum particles
Authors: Lizama Nicolás Z. , Carrasco Sebastián C. , Rogan José , Valdivia Juan Alejandro 
Published: October 2023

AbstractThe two trapped quantum particles interacting problem is generalized to three dimensions, and the exact Coulomb potential is used. The system is solved by expanding the wavefunction in terms of the isotropic harmonic oscillator eigenfunctions and Hydrogen atom eigenfunctions independently, showing that each one results in a prime approximation for different domains of the normalized coupling constant of the relative interactions, suggesting that the combination of the basis is enough to build a well-suited base for the non-approximate problem. The results are compared to previous works that use a model of approximate finite-rage soft-core interaction model of the problem to give insights into the many-body states of strongly correlated ultracold bosons and fermions. We conclude that the proposed three-dimensional approach facilitates the distinction between bosons and fermions while the solutions given by the expansions better define the behavior of the particles for repulsive potentials. In addition, we discuss the substantial differences between our work and the previous approximate model.
An interpretable machine learning approach to study the relationship beetwen retrognathia and skull anatomy
Authors: Makaremi Masrour , Vafaei Sadr Alireza , Marcy Benoit , Chraibi Kaadoud Ikram , Mohammad-Djafari Ali , Sadoun Salomé , De Brondeau François , N’kaoua Bernard 
Published: October 2023

AbstractMandibular retrognathia (C2Rm) is one of the most common oral pathologies. Acquiring a better understanding of the points of impact of C2Rm on the entire skull is of major interest in the diagnosis, treatment, and management of this dysmorphism, but also permits us to contribute to the debate on the changes undergone by the shape of the skull during human evolution. However, conventional methods have some limits in meeting these challenges, insofar as they require defining in advance the structures to be studied, and identifying them using landmarks. In this context, our work aims to answer these questions using AI tools and, in particular, machine learning, with the objective of relaying these treatments automatically. We propose an innovative methodology coupling convolutional neural networks (CNNs) and interpretability algorithms. Applied to a set of radiographs classified into physiological versus pathological categories, our methodology made it possible to: discuss the structures impacted by retrognathia and already identified in literature; identify new structures of potential interest in medical terms; highlight the dynamic evolution of impacted structures according to the level of gravity of C2Rm; provide for insights into the evolution of human anatomy. Results were discussed in terms of the major interest of this approach in the field of orthodontics and, more generally, in the field of automated processing of medical images.
Identification of an exosome-related signature associated with prognosis and immune infiltration in breast cancer
Authors: Guo Qiaonan , Pan Kelun , Qiu Pengjun , Liu Zundong , Chen Jianpeng , Lin Jianqing 
Published: October 2023

AbstractExosomes, nanosized vesicles, play a vital role in breast cancer (BC) occurrence, development, and drug resistance. Hence, we proceeded to study the potential prognostic value of exosome-related genes and their relationship to the immune microenvironment in BC. 121 exosome-related genes were provided by the ExoBCD database, and 7 final genes were selected to construct the prognostic signature. Besides, the expression levels of the 7 exosome-related genes were validated by the experiment in BC cell lines. Based on the signature, BC patients from the training and validation cohorts were separated into low- and high-risk groups. Subsequently, the R clusterProfiler package was applied to identify the distinct enrichment pathways between high-risk groups and low-risk groups. The relevance of the tumor immune microenvironment and exosome-related gene risk score were analyzed in BC. Eventually, the different expression levels of immune checkpoint-related genes were compared between the two risk groups. Based on the risk model, the low-risk groups were identified with a higher survival rate both in the training and validation cohorts. A better overall survival was revealed in patients with higher scores evaluated by the estimation of stromal and immune cells in malignant tumor tissues using expression (ESTIMATE) algorithm. Subsequently, BC patients with lower risk scores were indicated by higher expression levels of some immune checkpoint-related genes and immune cell infiltration. Exosomes are closely associated with the prognosis and immune cell infiltration of BC. These findings may contribute to improving immunotherapy and provide a new vision for BC treatment strategies.
Attitudes and factors influencing organ donation decision-making in Damascus, Syria: a cross-sectional study
Authors: Soqia Jameel , Ataya Jamal , Alhomsi Rawan , Soqia Horiya , Kakaje Ameer , Saadoun Rakan , Hamzeh Ammar 
Published: October 2023

AbstractOrgan donation is vital to saving lives, but its success depends on people's willingness to donate organs. This descriptive cross-sectional survey aimed to investigate attitudes towards organ donation in Damascus, Syria. Understanding attitudes is crucial for the success of organ donation programs, especially in countries with similar settings. This study was a descriptive cross-sectional survey aimed at understanding patients’ attitudes towards organ donation in Damascus, Syria. Data was collected through a carefully constructed validated survey through face-to-face interviews. 600 participants were randomly interviewed, 62.8% agreed to donate their organs after death, with helping others being the primary reason. Religious beliefs were the primary reason for organ refusal in males, while for females, it was lack of knowledge and religious beliefs. However, there were no significant differences between genders or educational level and age groups in the acceptance of organ donation. The percentage of those who agree to donate their organs after death encourages taking an effective step to build an integrated donation system, not just a center. Bearing in mind that there is no correlation with age, gender or even educational level, which means that the system may include different groups of society.
Strategic sustainability practices in intercropping-based family farming systems: study on rural communities of Iran
Authors: Ataei Pouria , Mottaghi Dastenaei Afshin , Karimi Hamid , Izadi Nasim , Menatizadeh Meysam 
Published: October 2023

AbstractThis paper reports a realistic analysis of a region using Grounded Theory (GT) to provide a sustainable model for family farming systems based on the intercropping system in rural communities of Iran. Furthermore, the fuzzy analytic hierarchy process (FAHP) was applied to assign weights to the criteria and sub-criteria of intercropping and monocropping systems. According to the model, the main phenomenon was “sustainability in the family farming system based on intercropping”. In this model, the causal factors were found to include behavioral and attitudinal motivators. Micro- and macro-factors were identified as the interfering factors in family farming systems based on intercropping. Social factors, economic components, and environmental potentials were the contextual factors of this system. Finally, the consequences included the conceptual development and evolution of sustainability, socioeconomic transformation, and ecological-environmental transformation. The results of FAHP showed that the environmental criterion was ranked the first among all criteria underpinning the sustainability of the intercropping system.
Joint triplet loss with semi-hard constraint for data augmentation and disease prediction using gene expression data
Authors: Chung Yeonwoo , Lee Hyunju 
Published: October 2023

AbstractThe accurate prediction of patients with complex diseases, such as Alzheimer’s disease (AD), as well as disease stages, including early- and late-stage cancer, is challenging owing to substantial variability among patients and limited availability of clinical data. Deep metric learning has emerged as a promising approach for addressing these challenges by improving data representation. In this study, we propose a joint triplet loss model with a semi-hard constraint (JTSC) to represent data in a small number of samples. JTSC strictly selects semi-hard samples by switching anchors and positive samples during the learning process in triplet embedding and combines a triplet loss function with an angular loss function. Our results indicate that JTSC significantly improves the number of appropriately represented samples during training when applied to the gene expression data of AD and to cancer stage prediction tasks. Furthermore, we demonstrate that using an embedding vector from JTSC as an input to the classifiers for AD and cancer stage prediction significantly improves classification performance by extracting more accurate features. In conclusion, we show that feature embedding through JTSC can aid in classification when there are a small number of samples compared to a larger number of features.
The effect of lipid metabolism disorder on patients with hyperuricemia using Multi-Omics analysis
Authors: Ma Lili , Wang Jing , Ma Li , Ge Yan , Wang Xian Min 
Published: October 2023

AbstractA multiomics study was conducted to investigate how lipid metabolism disorders affect the immune system in Xinjiang patients with hyperuricemia. The serum of 60 healthy individuals and 60 patients with hyperuricemia was collected. This study used LC–MS and HPLC to analyze differential lipid metabolites and enrichment pathways. It measured levels of immune factors tumor necrosis factor-α (TNF-α), interleukin 6 (IL-6), carnitine palmitoyltransferase-1 (CPT1), transforming growth factor-β1 (TGF-β1), glucose (Glu), lactic acid (LD), interleukin 10 (IL-10), and selenoprotein 1 (SEP1) using ELISA, as well as to confirm dysregulation of lipid metabolism in hyperuricemia. 33 differential lipid metabolites were significantly upregulated in patients with hyperuricemia. These lipid metabolites were involved in arachidonic acid metabolism, glycerophospholipid metabolism, linoleic acid metabolism, glycosylphosphatidylinositol (GPI)—anchor biosynthesis, and alpha-Linolenic acid metabolism pathways. Moreover, IL-10, CPT1, IL-6, SEP1, TGF-β1, Glu, TNF-α, and LD were associated with glycerophospholipid metabolism. In patients with hyperuricemia of Han and Uyghur nationalities, along with healthy individuals, significant differences in CPT1, TGF-β1, Glu, and LD were demonstrated by ELISA (P < 0.05). Furthermore, the levels of SEP1, IL-6, TGF-β1, Glu, and LD differed considerably between groups of the same ethnicity (P < 0.05). It was found that 33 kinds of lipid metabolites were significantly different in patients with hyperuricemia, which mainly involved 5 metabolic pathways. According to the results of further studies, it is speculated that CPT1, TGF-β1, SEP1, IL-6, Glu and LD may increase fatty acid oxidation and mitochondrial oxidative phosphorylation in patients through glycerophospholipid pathway, reduce the rate of glycolysis, and other pathways to change metabolic patterns, promote different cellular functions, and thus affect the disease progression in patients with hyperuricemia.
Structural insights for selective disruption of Beclin 1 binding to Bcl-2
Authors: Pan Yun-Zu , Liang Qiren , Tomchick Diana R. , De Brabander Jef K. , Rizo Josep 
Published: October 2023

AbstractStimulation of autophagy could provide powerful therapies for multiple diseases, including cancer and neurodegeneration. An attractive drug target for this purpose is Bcl-2, which inhibits autophagy by binding to the Beclin 1 BH3-domain. However, compounds that preclude Beclin 1/Bcl-2 binding might also induce apoptosis, which is inhibited by binding of Bcl-2 to BH3-domains of pro-apoptosis factors such as Bax. Here we describe the NMR structure of Bcl-2 bound to 35, a compound that we recently found to inhibit Beclin 1/Bcl-2 binding more potently than Bax/Bcl-2 binding. The structure shows that 35 binds at one end of the BH3-binding groove of Bcl-2. Interestingly, much of the 35-binding site is not involved in binding to Bcl-2 inhibitors described previously and mediates binding to Beclin 1 but not Bax. The structure suggests potential avenues to design compounds that disrupt Beclin 1/Bcl-2 binding and stimulate autophagy without inducing apoptosis.
Eosinophilic esophagitis and duodenal food challenge – evaluation through endoscopic confocal laser endomicroscopy
Authors: Frieling Thomas , Gjini Besmir , Melchior Ilka , Hemmerlein Bernhard , Kiesslich Ralf , Kuhlbusch-Zicklam Rita 
Published: October 2023

Abstract
Background Endoscopic confocal laser endomicroscopy (eCLE) is an established technique that allows clinical evaluation of mucosal integrity by fluorescein leaking through the mucosa upon duodenal food challenge (DFC). Analysis of eCLE with DFC in eosinophilic esophagitis (EoE) would be interesting to evaluate epithelial barrier dysfunction also in other regions of the gastrointestinal tract and to characterize potential individual food allergens that trigger the esophageal inflammation.
Methods In an observational and proof of concept study we evaluated 9 patients with histologically proven EoE by eCLE and DFC. Severity of symptoms were graduated according to the validated symptom-based EoE activity index. The endoscopic appearance of the esophagus was described according to the Endoscopic Reference Score System (ERERS). Spontaneous and food induced transfer of fluorescein into duodenal lumen were detected 10 minutes following intravenously application of fluorescein and 10 minutes after DFC. Food allergens were yeast, egg, soy, milk, and wheat, respectively. Local application of sodium chloride solution 10 % to the duodenal mucosa before DFC served as a control. Patients responding to DFC received a dietary exclusion therapy according to the results of DFC.
Results We investigated 9 patients with EoE (8 men, 49.7±13.8, 36–76 years). Symptom-based EoE activity index was 79±27.4, 33–100. In all patients EoE was confirmed by histology with number of esophageal mucosal eosinophilic granulocytes > 15/HPF, (91.4±77.4, 42–263). Mean ERERS score was 4.5±1.3, 3–7. None of the patients was aware of any food intolerance. eCLE revealed one patient with spontaneous transfer of i. v. fluorescein into duodenal lumen before DFC (“leaky gut”). 40 DFC were performed in the remaining 8 patients of whom 5 patients (61 %) responded to DFC. Rank order of fluorescein leakage upon DFC was wheat and milk in 37.5 % each, soy in 25 %, and egg in 12.5 %. The patients were treated by PPI (n=9), esophageal bouginage (n=5) and/or local corticoid therapy (n=3). The 5 patients responding to DFC received an additional food exclusion dietary advice focussed on the results of DFC. All patients reported a reduction of their symptoms. EoE activity indexes of patients with positive DFC were 73.7+28.6, 33–100 before and 22.7+37.9, 0–79 four weeks after food exclusion.
Conclusion The findings of our proof of concept study suggest that eCLE with DFC may be an interesting tool to further evaluate patients with EoE. This technique has the potential to identify patients who may benefit from an additional individual dietary therapy.