bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unsupervised corneal contour extraction algorithm with shared model for dynamic deformation videos: improving accuracy and noise resistance
Authors: Tan Zuoping , Chen Xuan , Xu Qiang , Yang Can , Lin Xiaomin , Huo Yan , Alzogool Mohammad , Wang Riwei , Wang Yan 
Published: January 2024

Abstract
Background
In this study, an automatic corneal contour extraction algorithm with a shared model is developed to extract contours from dynamic corneal videos containing noise, which improves the accuracy of corneal biomechanical evaluation and clinical diagnoses. The algorithm does not require manual labeling and completes the unsupervised semantic segmentation of each frame in corneal dynamic deformation videos based on a fully convolutional deep-learning network using corneal geometry and texture information.

Results
We included 1027 corneal videos at Tianjin Eye Hospital (Nankai University Affiliated Eye Hospital) from May 2020 to November 2021. The videos were obtained by the ultra-high-speed Scheimpflug camera, and then we used the shared model mechanism to accelerate the segmentation of corneal regions in videos, effectively resist noise, determine corneal regions based on shape factors, and finally achieve automatic and accurate extraction of corneal region contours. The Intersection over Union (IoU) of the extracted and real corneal contours using this algorithm reached 95%, and the average overlap error was 0.05, implying that the extracted corneal contour overlapped almost completely with the real contour.

Conclusions
Compared to other algorithms, the method introduced in this study does not require manual annotation of corneal contour data in advance and can still extract accurate corneal contours from noisy corneal videos with good repeatability.
Serum lipidomic study of long-chain fatty acids in psoriasis patients prior to and after anti-IL-17A monoclonal antibody treatment by quantitative GC‒MS analysis with in situ extraction
Authors: Guo XiaoYu , Zhou Jianglu , Yu Hong , Cao Han , Li Xia , Hu Qing , Yu YunQiu 
Published: January 2024

Abstract
Background
Long-chain fatty acids (LCFAs) are involved in regulating multiple physiological processes as signalling molecules. Gas chromatography–mass spectrometry (GC–MS) is widely used to quantify LCFAs. However, current quantitative methods for LCFAs using GC–MS have demonstrated complicated issues. Psoriasis is a chronic inflammatory skin disease, and its pathogenesis may be related to the overproduction of interleukin-17A (IL-17A). Clinical efficacy of anti-IL-17A monoclonal antibody (mAb) treatment in psoriasis patients has been demonstrated. Recent studies suggest that LCFAs play varying roles in the pathogenesis of psoriasis. However, more comprehensive research is needed to illuminate the mechanism of LCFAs in psoriasis.

Methods
The established in situ derivatization method for analysing LCFAs with a GC–MS platform was utilized to conduct serum lipidomics analysis of healthy volunteers and psoriasis patients receiving pretherapy and posttreatment with of anti-IL-17A mAb. Imiquimod (IMQ)-treated wild type (WT) and T-cell receptor delta chain knock-out (Tcrd−/−) mice were used to investigate the correlation between IL-17A and abnormal changes in LCFAs in psoriasis patients.

Results
A rapid and sensitive in situ extraction derivatization method for quantifying LCFAs using GC–MS was established. Serum lipidomic results showed that psoriasis patients had higher levels of saturated fatty acids (SFAs) and ω-6 polyunsaturated fatty acids (PUFAs) but lower levels of monounsaturated fatty acids (MUFAs) and ω-3 PUFAs than healthy individuals, indicating impaired serum LCFA metabolism. Anti-IL-17A mAb treatment affected most of these LCFA changes. Analysis of LCFAs in IMQ-treated mice showed that LCFAs increased in the serum of WT mice, while there were no significant changes in the Tcrd−/− mice. SFAs increased in IMQ-treated WT mice, while MUFAs showed the opposite trend, and PUFAs did not change significantly.

Conclusions
This study presented a dependable method for quantifying LCFAs that enhanced sensitivity and reduced analysis time. The lipidomic analysis results showed that anti-IL-17A mAb not only ameliorated skin lesions in psoriasis patients but also affected abnormal LCFAs metabolism. Furthermore, the study indicated a potential correlation between IL-17A and abnormal LCFA metabolism in psoriasis patients, which was supported by the alterations in serum LCFAs observed in IMQ-treated WT and Tcrd−/− mice.
Triglyceride-glucose index and obstructive sleep apnea: a systematic review and meta-analysis
Authors: Behnoush Amir Hossein , Khalaji Amirmohammad , Ghondaghsaz Elina , Masrour Mahdi , Shokri Varniab Zahra , Khalaji Soheil , Cannavo Alessandro 
Published: January 2024

AbstractBackgroundObstructive sleep apnea (OSA) has a bidirectional association with metabolic syndrome, and insulin resistance (IR). The triglyceride-glucose (TyG) index could be a simply calculated marker of IR in OSA. However, its clinical application appears still limited. Hence, this systematic review and meta-analysis aimed to respond to this question by analyzing all the existing studies showing an association between OSA and the TyG index.MethodsFour online databases, including PubMed, Scopus, the Web of Science, and Embase were searched for studies evaluating the TyG index in OSA. After screening and data extraction, a random-effect meta-analysis was performed to compare the TyG index in OSA patients vs. healthy controls by calculating standardized mean difference (SMD) and 95% confidence interval (CI) and pooling the area under the curves (AUCs) for diagnosis of OSA based on this index.ResultsTen studies involving 16,726 individuals were included in the current systematic review. Meta-analysis indicated that there was a significantly higher TyG index in patients with OSA, compared with the healthy controls (SMD 0.856, 95% CI 0.579 to 1.132,P < 0.001). Also, TyG had a diagnostic ability for OSA representing a pooled AUC of 0.681 (95% CI 0.627 to 0.735). However, based on the two studies’ findings, no difference between different severities of OSA was observed. Finally, our data showed that the TyG index is a good potential predictor of adverse outcomes in these patients.ConclusionOur study revealed that the TyG index is an easy-to-measure marker of IR for assessing OSA, both in diagnosis and prognosis. Our study supports its implementation in routine practice to help clinicians in decision-making and patient stratification.
Non-transgenic, PAMAM co-delivery DNA of interactive proteins NbCRVP and NbCalB endows Nicotiana benthamiana with a stronger antiviral effect to RNA viruses
Authors: Song Liyun , Zhang Daoshun , Liu Tianbo , Jiang Changqing , Li Bin , Li Changquan , Shen Lili , Li Ying , Wang Fenglong , Jiao Yubing , Yang Jinguang 
Published: January 2024

Abstract
Background
Viral diseases continue to pose a major threat to the world’s commercial crops. The in-depth exploration and efficient utilization of resistance proteins have become crucial strategies for their control. However, current delivery methods for introducing foreign DNA suffer from host range limitations, low transformation efficiencies, tissue damage, or unavoidable DNA integration into the host genome. The nanocarriers provides a convenient channel for the DNA delivery and functional utilization of disease-resistant proteins.

Results
In this research, we identified a cysteine-rich venom protein (NbCRVP) in Nicotiana benthamiana for the first time. Virus-induced gene silencing and transient overexpression clarified that NbCRVP could inhibit the infection of tobacco mosaic virus, potato virus Y, and cucumber mosaic virus, making it a broad-spectrum antiviral protein. Yeast two-hybrid assay, co-immunoprecipitation, and bimolecular fluorescence complementation revealed that calcium-dependent lipid-binding (CaLB domain) family protein (NbCalB) interacted with NbCRVP to assist NbCRVP playing a stronger antiviral effect. Here, we demonstrated for the first time the efficient co-delivery of DNA expressing NbCRVP and NbCalB into plants using poly(amidoamine) (PAMAM) nanocarriers, achieving stronger broad-spectrum antiviral effects.

Conclusions
Our work presents a tool for species-independent transfer of two interacting protein DNA into plant cells in a specific ratio for enhanced antiviral effect without transgenic integration, which further demonstrated new strategies for nanocarrier-mediated DNA delivery of disease-resistant proteins.

Graphical abstract
Quality of life among people with eye cancer: a systematic review from 2012 to 2022
Authors: Huang Yonghui , Guo Yunfei 
Published: January 2024

AbstractBackgroundEye cancer is a serious eye disease that threatens patients’ lives. In the past decade, there have been more and more studies on eye cancer. From the recently published eye cancer literature review, it can be seen that the two most popular research hotspots are retinoblastoma (RB) and uveal melanoma (UM) [1, 2]. Although several studies have assessed QOL in different types of eye cancer patients, a study that synthesizes the factors influencing QOL in eye cancer patients is yet to be undertaken. This study aimed to review and evaluate the literature related to the QOL of RB and UM survivors, and provide a synthesis of the current evidence on the impact of the two types of eye cancer on the overall QOL of patients.MethodsEight databases (APA Psych Articles, CINAHL Complete, Health Source: Nursing/Academic Edition, MEDLINE Complete, Scopus, Cochrane Library, PubMed, and Registers (Clinicaltrials.gov.)) were searched between January 2012 and December 2022 for English, peer-reviewed quantitative original studies within this review. All publications were screened using the Preferred Reporting Items for Systematic Review and Meta-Analyses reporting guidelines. The methodological quality of the reviews was assessed using the Joanna Briggs Institute Critical Appraisal Checklists. The findings were summarised and tabulated accordingly.ResultsSeventeen articles were analysed. Among them, 14 articles on patients with UM, and three articles on patients with RB using 18 different types of measurement tools were included. Eight researchers claimed that the overall QOL of patients with eye cancer was better than or similar to that of the general healthy population. However, nine studies indicated that these patients had poorer QOL than others. Many factors affect QOL, including treatment, sex, and age.ConclusionThis systematic review identified the QOL levels and several factors that influence the QOL of ocular cancer patients worldwide, due to the variability in quality of the studies, it also showed the need for further research to assess factors affecting long-term QOL outcomes in RB and UM survivors. Simultaneously, it clarified the necessity and importance of developing standardized and complete assessment tools to compare QOL in different countries. Early interventions can be developed to improve the survivors’ QOL by identifying potential deficits in specific areas.
Vaccines: a promising therapy for myelodysplastic syndrome
Authors: Gera Kriti , Chauhan Anjali , Castillo Paul , Rahman Maryam , Mathavan Akash , Mathavan Akshay , Oganda-Rivas Elizabeth , Elliott Leighton , Wingard John R. , Sayour Elias J. 
Published: January 2024

AbstractMyelodysplastic neoplasms (MDS) define clonal hematopoietic malignancies characterized by heterogeneous mutational and clinical spectra typically seen in the elderly. Curative treatment entails allogeneic hematopoietic stem cell transplant, which is often not a feasible option due to older age and significant comorbidities. Immunotherapy has the cytotoxic capacity to elicit tumor-specific killing with long-term immunological memory. While a number of platforms have emerged, therapeutic vaccination presents as an appealing strategy for MDS given its promising safety profile and amenability for commercialization. Several preclinical and clinical trials have investigated the efficacy of vaccines in MDS; these include peptide vaccines targeting tumor antigens, whole cell-based vaccines and dendritic cell-based vaccines. These therapeutic vaccines have shown acceptable safety profiles, but consistent clinical responses remain elusive despite robust immunological reactions. Combining vaccines with immunotherapeutic agents holds promise and requires further investigation. Herein, we highlight therapeutic vaccine trials while reviewing challenges and future directions of successful vaccination strategies in MDS.
GTax: improving de novo transcriptome assembly by removing foreign RNA contamination
Authors: Alvarez Roberto Vera , Landsman David 
Published: January 2024

AbstractThe cost and complexity of generating a complete reference genome means that many organisms lack an annotated reference. An alternative is to use a de novo reference transcriptome. This technology is cost-effective but is susceptible to off-target RNA contamination. In this manuscript, we present GTax, a taxonomy-structured database of genomic sequences that can be used with BLAST to detect and remove foreign contamination in RNA sequencing samples before assembly. In addition, we use a de novo transcriptome assembly of Solanum lycopersicum (tomato) to demonstrate that removing foreign contamination in sequencing samples reduces the number of assembled chimeric transcripts.
Rare copy-number variants as modulators of common disease susceptibility
Authors: Auwerx Chiara , Jõeloo Maarja , Sadler Marie C. , Tesio Nicolò , Ojavee Sven , Clark Charlie J. , Mägi Reedik ,   Estonian Biobank Research Team, Esko Tõnu , Metspalu Andres , Milani Lili , Nelis Mari , Reymond Alexandre , Kutalik Zoltán 
Published: January 2024

Abstract
Background
Copy-number variations (CNVs) have been associated with rare and debilitating genomic disorders (GDs) but their impact on health later in life in the general population remains poorly described.

Methods
Assessing four modes of CNV action, we performed genome-wide association scans (GWASs) between the copy-number of CNV-proxy probes and 60 curated ICD-10 based clinical diagnoses in 331,522 unrelated white British UK Biobank (UKBB) participants with replication in the Estonian Biobank.

Results
We identified 73 signals involving 40 diseases, all of which indicating that CNVs increased disease risk and caused earlier onset. We estimated that 16% of these associations are indirect, acting by increasing body mass index (BMI). Signals mapped to 45 unique, non-overlapping regions, nine of which being linked to known GDs. Number and identity of genes affected by CNVs modulated their pathogenicity, with many associations being supported by colocalization with both common and rare single-nucleotide variant association signals. Dissection of association signals provided insights into the epidemiology of known gene-disease pairs (e.g., deletions in BRCA1 and LDLR increased risk for ovarian cancer and ischemic heart disease, respectively), clarified dosage mechanisms of action (e.g., both increased and decreased dosage of 17q12 impacted renal health), and identified putative causal genes (e.g., ABCC6 for kidney stones). Characterization of the pleiotropic pathological consequences of recurrent CNVs at 15q13, 16p13.11, 16p12.2, and 22q11.2 in adulthood indicated variable expressivity of these regions and the involvement of multiple genes. Finally, we show that while the total burden of rare CNVs—and especially deletions—strongly associated with disease risk, it only accounted for ~ 0.02% of the UKBB disease burden. These associations are mainly driven by CNVs at known GD CNV regions, whose pleiotropic effect on common diseases was broader than anticipated by our CNV-GWAS.

Conclusions
Our results shed light on the prominent role of rare CNVs in determining common disease susceptibility within the general population and provide actionable insights for anticipating later-onset comorbidities in carriers of recurrent CNVs.
An optimized capsule neural networks for tomato leaf disease classification
Authors: Abouelmagd Lobna M. , Shams Mahmoud Y. , Marie Hanaa Salem , Hassanien Aboul Ella 
Published: January 2024

AbstractPlant diseases have a significant impact on leaves, with each disease exhibiting specific spots characterized by unique colors and locations. Therefore, it is crucial to develop a method for detecting these diseases based on spot shape, color, and location within the leaves. While Convolutional Neural Networks (CNNs) have been widely used in deep learning applications, they suffer from limitations in capturing relative spatial and orientation relationships. This paper presents a computer vision methodology that utilizes an optimized capsule neural network (CapsNet) to detect and classify ten tomato leaf diseases using standard dataset images. To mitigate overfitting, data augmentation, and preprocessing techniques were employed during the training phase. CapsNet was chosen over CNNs due to its superior ability to capture spatial positioning within the image. The proposed CapsNet approach achieved an accuracy of 96.39% with minimal loss, relying on a 0.00001 Adam optimizer. By comparing the results with existing state-of-the-art approaches, the study demonstrates the effectiveness of CapsNet in accurately identifying and classifying tomato leaf diseases based on spot shape, color, and location. The findings highlight the potential of CapsNet as an alternative to CNNs for improving disease detection and classification in plant pathology research.
Evidence-practice gap analysis in the role of tick in brucellosis transmission: a scoping review
Authors: Ma Rui , Li Chunfu , Gao Ai , Jiang Na , Feng Xinyu , Li Jian , Hu Wei 
Published: January 2024

Abstract
Background
Brucellosis is a zoonotic affliction instigated by bacteria belonging to the genus Brucella and is characterized by a diverse range of pervasiveness, multiple transmission routes, and serious hazards. It is imperative to amalgamate the current knowledge and identify gaps pertaining to the role of ticks in brucellosis transmission.

Methods
We systematically searched China National Knowledge Infrastructure (CNKI), WanFang, Google Scholar, and PubMed on the topic published until April 23, 2022. The procedure was performed in accordance with the Systematic Reviews and Meta-Analyses extension for Scoping Reviews (PRISMA-ScR) guidelines. The selected articles were categorized across three major topic areas, and the potential data was extracted to describe evidence-practice gaps by two reviewers.

Results
The search identified 83 eligible studies for the final analyses. The results highlighted the potential capacity of ticks in brucellosis transmission as evidenced by the detection of Brucella in 16 different tick species. The pooled overall prevalence of Brucella in ticks was 33.87% (range: 0.00–87.80%). The review also revealed the capability of Brucella to circulate in parasitic ticks' different developmental stages, thus posing a potential threat to animal and human health. Empirical evidence from in vitro rodent infection experiments has revealed that ticks possess the capability to transmit Brucella to uninfected animals (range: 45.00–80.00%). Moreover, significant epidemiological associations have been found between the occurrence of brucellosis in animals and tick control in rangelands, which further suggests that ticks may serve as potential vectors for brucellosis transmission in ruminants. Notably, a mere three cases of human brucellosis resulting from potential tick bites were identified in search of global clinical case reports from 1963 to 2019.

Conclusions
It is imperative to improve the techniques used to identify Brucella in ticks, particularly by developing a novel, efficient, precise approach that can be applied in a field setting. Furthermore, due to the lack of adequate evidence of tick-borne brucellosis, it is essential to integrate various disciplines, including experimental animal science, epidemiology, molecular genetics, and others, to better understand the efficacy of tick-borne brucellosis. By amalgamating multiple disciplines, we can enhance our comprehension and proficiency in tackling tick-borne brucellosis.
Lives ‘on hold’ in Europe: an explorative review of literature on youth aspirations and futures in situations of migration and mobility
Authors: Doumas Kyriaki , Avery Helen 
Published: January 2024

AbstractThis explorative literature review aims to examine the content and methodologies of recent empirical studies on the aspirations of youth in situations of migration in Europe. The search yielded 30 peer-reviewed social science publications in English for the period 2010–2022, including both intra-European migrants ages 10–24 and youth with backgrounds from outside Europe. Contextual analysis was used to analyse the content of the reviewed studies, while a typology developed by Beckert and Suckert was used to examine features of the future appearing in the studies’ research aims, methodology and findings. The analysis broadly situated the studies within constructivist traditions, occupying a mid-position between deterministic and agency-oriented epistemologies. All the features of the future listed by Beckert and Suckert were found in the material, but the categories 'Temporal configurations of the future' and 'Space of the future' showed greater complexities. Participants in the studies lived in different European countries and the study samples comprised a wide range of ages, socioeconomic backgrounds, and status of residence. Nevertheless, barriers linked to participants' position as migrants were tangible, while the ability these young people had to envisage the future was strongly affected by uncertainties linked to migration policy and administrative decisions on their status. A mismatch could notably be observed between youth aspirations and the opportunities offered by their life situation, which led to delays in life projects and the inability to plan ahead.Critical relevance statementBy an analysis of social studies research on aspirations of youth in situations of migration in various European countries, this review highlights the need to consider implications for youth aspirations and life trajectories in both policy and practiceKey points• Young people in situations of migration have high aspirations but confront substantial barriers• Uncertainties prevent youth from long-term planning and realising life projects• Current policies create conditions that are not consistent with European values and ambitions