bluuebunny/crossref_metadata_2025_split huggingface dataset:
Integrating Machine Learning-Enhanced Immunopeptidomics and SARS-CoV-2 Population-Scale Analyses Unveils Novel Antigenic Features for Next-Generation COVID-19 Vaccines
Authors: Caron Etienne , Kovalchik Kevin , Hamelin David , Kubiniok Peter , Bourdin Benoite , Mostefai Fatima , Poujol Raphaël , Paré Bastien , Simpson Shawn , Sidney John , Bonneil Eric , Courcelles Mathieu , Saini Sunil Kumar , Kapoor Saketh , Weitzen Maya , Grenier Jean-Christophe , Gharsallaoui Bayrem , Maréchal Loïze , Wu Zhaoguan , Savoie Christopher , Sette Alessandro , Thibault Pierre , Sirois Isabelle , Smith Martin , Decaluwe Hélène , Hussin Julie , Lavallée-Adam Mathieu 
Published: February 2024

Abstract

Next-generation T-cell-directed vaccines for COVID-19 aim to induce durable T-cell immunity against circulating and future hypermutated SARS-CoV-2 variants. Mass Spectrometry (MS)-based immunopeptidomics holds promise for guiding vaccine design, but computational challenges impede the precise and unbiased identification of conserved T-cell epitopes crucial for vaccines against rapidly mutating viruses. We introduce a computational framework and analysis platform integrating a novel machine learning algorithm, immunopeptidomics, intra-host data, epitope immunogenicity, and geo-temporal CD8+ T-cell epitope conservation analyses. Central to our approach is MHCvalidator, a novel artificial neural network algorithm enhancing MS-based immunopeptidomics sensitivity by modeling antigen presentation and sequence features. MHCvalidator identified a novel nonconventional SARS-CoV-2 T-cell epitope presented by B7 supertype molecules, originating from a +1-frameshift in a truncated Spike (S) antigen, supported by ribo-seq data. Intra-host analysis of SARS-CoV-2 proteomes from ~100,000 COVID-19 patients revealed a prevalent S antigen truncation in ~51% of cases, exposing a rich source of frameshifted viral antigens. Our framework includes EpiTrack, a new computational pipeline tracking global mutational dynamics of MHCvalidator-identified SARS-CoV-2 CD8+ epitopes from vaccine BNT162b4. While most vaccine-encoded CD8+ epitopes exhibit global conservation from January 2020 to October 2023, a highly immunodominant A*01-associated epitope, especially in hospitalized patients, undergoes substantial mutations in Delta and Omicron variants. Our approach unveils unprecedented SARS-CoV-2 T-cell epitopes, elucidates novel antigenic features, and underscores mutational dynamics of vaccine-relevant epitopes. The analysis platform is applicable to any viruses, and underscores the need for continual vigilance in T-cell vaccine development against the evolving landscape of hypermutating SARS-CoV-2 variants.
Survival and mutational analysis of small cell carcinoma in pan-cancer
Authors: Yang Chunqian , Wei Ting 
Published: February 2024

Abstract
Background:
This study aims to delve into the differences and commonalities among small cell carcinomas (SCC) originating from different sites, including extrapulmonary small cell carcinoma (EPSCC) and small cell lung carcinoma (SCLC). We focus on understanding the trends in incidence, genomic characteristics, and treatment strategies for these subtypes, addressing the gaps in our knowledge of these rare and heterogeneous diseases.
Methods:
A comprehensive approach was employed using data from Cosmic, SEER, and GDSC databases. Epidemiological data were obtained from the SEER database, genomic mutation information from the Cosmic database, and drug sensitivity data from the GDSC database. Statistical tests were applied to analyze the data, revealing epidemiological variations in SCC across different populations and regions and identifying genomic variations.
Results:
Analysis indicates a significant difference in the incidence rates of EPSCC and SCLC, with EPSCC currently accounting for 2% − 4% of all SCC diagnoses. Genomic analysis unveils both shared and unique mutational landscapes between these two subtypes, guiding future therapeutic strategies. Tailored treatment plans were formulated based on the site of origin, and analysis of the SEER database highlighted epidemiological variations in SCC, emphasizing key factors associated with survival rates.
Conclusion:
This study provides in-depth insights into the differences and commonalities among small cell carcinomas originating from different sites, offering crucial clues for precision treatment strategies. The rising incidence of EPSCC underscores its clinical significance. These findings not only expand our understanding of SCC biology but also have profound implications for improving clinical treatment outcomes for patients..
The impact of blastocyst level on singleton birthweight in fresh IVF-ET cycles in ART: a retrospective study
Authors: Shi Senlin , Zhao Boya , Shi Qiongyao , Shi Hao 
Published: February 2024

Abstract
Background:
The positive correlation between embryo quality and pregnancy outcomes has been well confirmed in many studies, but few studies have investigated the impact of embryo quality on neonatal weight, especially among neonates from freshly transplanted blastocysts.So the objective of the article was to compare the birth weights of infants from different blastocyst grades in fresh transplantation cycles and to explore related factors affecting birth weight.
Methods:
A retrospectively cohort study was performed to compare the birth weight of different blastocyst levels in fresh transplantation cycle and explore the related factors affecting the birth weight. The 1301 fresh cycles of single blastocyst transplantation and single live birth profile were retrospectively analyzed,four groups were divided according to the grade of transplanted blastocyst. There were 170 cycles in group A with AA blastocyst level, 312 cycles in group B with AB/BA blastocyst level, 559 cycles in group C with BB/CA/AC blastocyst level and 260 cycles in group D with BC/CB blastocyst level. Comparison among four groups of patients by birth weight and general conditions, fertilization rate, embryo rate, cleavage rate and D5、D6 blastocyst formation rate and other laboratory indicators were made. And then compare the birth weight of different groups which were divided by the degree of blastocyst expansion, and the classification of intracellular mass(ICM) and extracellular trophoblastic(TE).
Results:
The study shows that birth weight of group A was significantly higher than that of the other three groups (P < 0.05). And the high quality embryo rate and blastocyst rate of group A were significantly higher than those of the other three groups (P < 0.05). What’s more, the clinical pregnancy rate, implantation rate and live birth rate of high grade blastocyst were higher, but there was no significant difference in abortion rate. The birth weight of blastocyst of grade 3 and below was significantly lower than that of those with grade 3 and above (P < 0.05).The birth weight of grade A intracellular mass was significantly higher than that of B intracellular mass of blastocyst(P < 0.05). Babies born with grade B ectotrophoblast cells were significantly heavier than those born with grade C ectotrophoblast cells(P < 0.05).
Conclusion:
The authors conclude that high grade blastocyst transplantation can achieve better pregnancy outcome. Different blastocyst levels affect birth weight, and low grade blastocyst transplantation is associated with a single birth weight loss.
Ochrobactrum anthropi infection following corneal transplantation -A Case Report and Review of Literature
Authors: liu lei , Wang Chunmei , Xu Hui , hou lulu , huang rong , shi xiaoru , jia hui 
Published: February 2024

Abstract
Background
Ochrobactrum anthropi is widely distributed and primarily infects patients with compromised immune functions .Although historically considered to possess low toxicity and pathogenicity, Ochrobactrum anthropi can lead to severe purulent infection. Here, we present a case of Ochrobactrum anthropi infection following corneal transplantation surgery,examining the occurrence and outcome of such infections post-transplantation.
Case presentation:
A retrospective analysis of cases involved examinations, genetic testing for diagnosis, and subsequent treatment. Patients with fungal corneal ulcer perforation, undergoing partial penetrating keratoplasty, exhibited anterior chamber exudation and purulence post-surgery. Despite unsuccessful antifungal treatment, genetic testing of anterior chamber fluid and purulent material confirmed Ochrobactrum anthropi infection. Antimicrobial treatment specifically targeting Ochrobactrum anthropi proved efficacious.
Conclusion
Inflammatory reactions following corneal transplantation should be vigilant for multiple infections. Genetic testing of aqueous humor holds significant guiding implications for clinical diagnosis and treatment.
Enhanced NK cell proliferation by stress-induced feeder cells
Authors: Lee Donghyun , Song Myeongkwan , Kwon Soonjo 
Published: February 2024

Abstract
Natural Killer (NK) cells, integral to the innate immune system, are notable in cell therapies because for their applicability in allogeneic treatments, distinguishing them from T cells typically employed in conventional cell therapies. However, their limited half-life poses a challenge for therapy. Although attempts to leverage feeder cells are common, safer methods are needed to mitigate the associated risks.
In our study, an upregulation in the expression of 4-1BBL in Colo-205 cells under extracellular stresses such as hypoxia and cytochalasin D was observed. This enhanced binding to the 4-1BB receptors on NK cells promotes proliferation in NK cells. Elevated CD56 expression of a marker strongly linked to NK cell proliferation in co-culture further supports this process.
Applying extracellular stressors, specifically hypoxia and cytochalasin D, to Colo-205 cells successfully tailored feeder cells, significantly enhancing NK cell proliferation.
CAPZB mRNA is a novel biomarker in cervical high-grade squamous lesions or higher
Authors: Cai Xia , Huang Wanqiu , Huang Jian , Zhu Xiuxiang , Wang Lifeng , Xia Ziyin , Xu Ling 
Published: February 2024

Abstract

Objective To evaluate Capping protein (actin filament) muscle Z-line subunit β(CAPZB) messenger ribonucleic acid(mRNA) as a biomarker for distinguishing low-grade squamous intraepithelial lesion of the cervix (LSIL) and below from high-grade squamous intraepithelial lesion of the cervix (HSIL) and above. Methods We collected a total of 166 cervical exfoliated cells, which were divided into normal group, Human papillomavirus (HPV) group, LSIL group, HSIL group, and Cervical cancer (CC) group based on histopathological results. Each sample was divided into two portions, one for fluorescence in situ hybridization (FISH) detection and the other for bisulfite sequencing polymerase chain reaction (BSP) detection. Clinical information of patients was also collected. The ability of these two methods to distinguish LSIL and below from HSIL and above was compared and analyzed. ResultsCAPZBmRNA levels decreased with the increasing severity of cervical lesions, whileCAPZBdeoxyribonucleic acid (DNA) methylation levels increased with the increasing severity of cervical lesions. FISH detection ofCAPZBmRNA and BSP detection ofCAPZBDNA methylation performed best as biomarkers for distinguishing HSIL and above from LSIL and below, with area under the roc curve (AUC), sensitivity, and specificity of 0.893, 81.25%, and 80.39%, 0.794, 64.06%, and 81.37%, respectively.CAPZBmRNA performed better thanCAPZBDNA methylation as a biomarker for assessing cervical lesions. Conclusion FISH detection ofCAPZBmRNA shows potential as a novel biomarker for distinguishing HSIL and above from LSIL and below in cervical lesions.
Towards Unsupervised Animal Activity Recognition: a Deep Learning Based Clustering Algorithm for Equine Gait Classification
Authors: Waele Timo , Shahid Adnan , Peralta Daniel , Tuyttens Frank , Poorter Eli 
Published: February 2024

Abstract
Knowing the activity type is important for many types of animal research. One example is to know how often a horse is standing still, walking, trotting or cantering. To automate this process, most scientific investigations rely on supervised neural networks, necessitating a resource-intensive and time-consuming manual labeling phase. This paper investigates the potential of unsupervised deep learning for automatic equine gait classification, employing the Deep Embedded Clustering (DEC) approach. Our evaluation compares it with alternative supervised and unsupervised algorithms, along with various pre-processing techniques. Findings indicate that probabilistic-based clustering algorithms, like Gaussian Mixture Models, are more effective for scenarios with significant variance in cluster densities, as frequently encountered in the domain of animal activity recognition. The paper establishes that transforming data from the time domain to the frequency domain using the Discrete Fourier Transform (DFT) contributes to improved performance. The integration of the DEC-based clustering algorithm with DFT achieves an overall accuracy approaching 83%. The research shows that while supervised methods still outperform unsupervised ones, with proper algorithm selection and data processing, unsupervised methods yield satisfactory results without the requisite for labeled data.
Factors Influencing Germination and Seedling Emergence of Corncockle ( Agrostemma githago ) : Insights for Weed Management in Agricultural Systems
Authors: Zare Ahmad , Keshtkar Eshagh 
Published: February 2024

Abstract
Agrostemma githago, a poisonous, noxious, and competitive weed species, can threaten crop yields in various agricultural regions worldwide. Experiments were performed twice to ascertain the effect of temperature, salt stress, osmotic potential, and burial depth on the germination and seedling emergence of A. githago. Seeds germinated across various temperatures ranging between 5 and 35°C, while germination was completely inhibited at 40°C. The optimum temperature for maximum germination percentage (GP), maximum germination rate (GR), and minimum mean germination time (MGT) ranged from 17.47°C to 19.37°C. The 50% reduction in GP occurred at 27 ○C. The seeds of A. githago germinated over a wide range of osmotic potentials, from 0 to − 1.2 MPa, however, the GP decreased with increasing osmotic potential, where at − 1.2 MPa, germinability was 19%. Similarly, seeds germinated across a broad range of salinities, with a GP of 21% at 300 mM, however, no germination was observed at 350 mM. The osmotic potential and salinity concentration required to inhibit 50% of maximum GP were estimated to be -0.99 MPa and 272 mM, respectively. Thus, it is expected that A. githago can germinate in saline and arid environments. The maximum seedling emergence (99%) was observed when seeds were placed on the soil surface. In contrast, no seedling emergence was recorded when seeds were buried at depths greater than 4 cm. Accordingly, deep conventional tillage might be helpful for managing A. githago. This knowledge can be implemented for both future research and the development of effective management for A. githago.
Validation of the ND-PAE Diagnosis in Children with Heavy Prenatal Alcohol Exposure
Authors: Veziris Christina R. , Hyland Matthew T. , Kable Julie A. , Wozniak Jeffrey R. , Coles Claire D. , May Philip A. , Kalberg Wendy O. , Sowell Elizabeth R. , Jones Kenneth L. , Riley Edward P. , Mattson Sarah N. 
Published: February 2024

Abstract

This study evaluated criteria for Neurobehavioral Disorder Associated with Prenatal Alcohol Exposure (ND-PAE). Kable et al. (2022) assessed the validity of this diagnosis in a sample with low exposure to alcohol. The current study expanded this assessment to a sample with a wider age range and heavier alcohol exposure. Data were collected from participants (5-17y) with prenatal alcohol exposure (PAE) and typically developing controls at six Collaborative Initiative on Fetal Alcohol Spectrum Disorders sites using neuropsychological assessment and caregiver reports. Impairment was tested at 1SD, 1.5SD, and 2SD below the normative average and a modification of the adaptive functioning requirement was tested. Testing impairment at 1SD resulted in the highest endorsement rates in both groups. Our findings replicated the study by Kable et al. and show that current criteria captured a high rate of those with PAE and that requiring fewer adaptive functioning criteria resulted in higher sensitivity to PAE.
Evaluation of the Ovsynch and Co-synch protocols on estrus intensity and pregnancy rate in Anatolian buffalo heifers
Authors: Baştan ilktan , Korkmaz Fırat , Şahin Derya , Şimşek Seher , Yılmaz Mehmet Ali 
Published: February 2024

Abstract
This study aimed to evaluate the Ovsynch and Co-synch synchronization protocols in terms of estrus intensity and pregnancy rate in Anatolian buffalo heifers. To this end, 27 Anatolian buffalo heifers were used. For the Ovsynch synchronization protocol, GnRH (buserelin acetate, 12 μg) was administered on day 0, PGF2α (cloprostenol, 500 μg) on day 7, and GnRH (buserelin acetate, 12 μg) on day 9, and artificial insemination was performed 16-20 hours after the second GnRH application. For the Co-synch protocol, GnRH (buserelin acetate, 12 μg) was administered on day 0, PGF2α (cloprostenol, 500 μg) on day 7, and GnRH (buserelin acetate, 12 μg) along with artificial insemination on day 10. At the time of artificial insemination, estrus intensity was classified as intense, moderate, weak, or negative. Pregnancies were within 40 to 70 days after artificial insemination using pregnancy-related glycoprotein or ultrasonography examinations. Intense, moderate, weak, and negative estrus intensities were determined at rates of 20%, 20%, 26.6%, and 33.3%, respectively, in the Ovsynch group and 41.6%, 58.3%, 0%, and 0%, respectively, in the Co-synch group (P<0.05). Pregnancy rates were 30% and 75% in the Ovsynch and Cosynch groups, respectively (P<0.05). In conclusion, the Co-synch protocol was found to be more successful than the Ovsynch protocol for synchronization in Anatolian buffalo heifers. In addition, to increase the success of artificial insemination, it is recommended to perform cervix uteri monitoring and perform artificial insemination only on animals showing estrous behavior.
Molecular characterization and expression analysis of DNA methyltransferase genes during kiwifruit ripening
Authors: Fu Changchun , Han Chao , Yu Zuolong , Liu Dan , Wei Yunxiao , Han Yanchao 
Published: February 2024

Abstract
DNA methylation plays an important role in plant growth and development, fruit ripening and stress response. DNA methylation is catalyzed by DNA methyltransferase (DNMT). DNMT genes have been isolated and identified from Arabidopsis, rice, tomato, peanut and other plants, but it has not been reported in kiwifruit. In this study, 16 DNMTs were screened and identified from kiwifruit, named AcDMT1-AcDMT16 and mainly distributed in 12 chromosomes. By predicting the subcellular localization of DNMT in kiwifruit, it was found that most of DNMT were enzyme proteins located in the nucleus. Phylogenetic tree analysis showed that among the 16 kiwifruit DNMTs, 4 members belonged to the MET subfamily, 7 belonged to the CMT, and 5 belonged to the DRM, in addition, kiwifruit was closely related to tomato. Protein structure analysis showed that there were great differences in the structure of kiwifruit DNMT, most of which did not have transmembrane structure, and the domains of each subfamily were relatively conservative. qRT-PCR and correlation analysis results showed that AcDMT3, AcDMT6 and AcDMT7 were increased with the continuous fruit ripening and softening, indicating they positively regulate kiwifruit ripening, but AcDMT1, AcDMT9, AcDMT10, AcDMT12 and AcDMT13 were reverse. The results provide basic information for functional analysis and further study of DNMTs in kiwifruit.
Bulk and single-cell RNA-sequencing analyses along with abundant machine learning methods identify a novel signature in Hidradenitis Suppurativa
Authors: Lai Xiaodong , Zhang Haini , Zhang Chong , Wang Meng , Yang Yan , Chen Wanxin , Wang Baoxi , Yan Yan 
Published: February 2024

Abstract
Objective:
Hidradenitis Suppurativa (HS) underlying molecular and immunological mechanisms remain poorly understood. This study aimed to unravel key gene expression patterns, identify hub genes, and analyze immune cell infiltration in HS lesions and peripheral blood.
Methods:
Peripheral blood and skin tissues of HS datasets were sourced from the GEO database. The dataset with the larger sample size served as the training set to identify differential genes (DEGs) between HS patients and healthy controls. Hub genes were identified using the random forest (RF), LASSO logistic regression, and support vector machine-recursive feature elimination (SVM-RFE) algorithms. Additionally, CIBERSORT was employed to determine the proportions of 22 immune cell types in HS patients and to assess their correlation with the identified hub genes. Finally, the application of single-cell RNA-seq analysis serves to enhance and refine our comprehension of the cellular heterogeneity present in HS lesions.
Results:
In HS skin lesion samples, we identified reliable 200 DEGs: 141 were upregulated, and 59 were downregulated by three methods (limma, DESeq2, and edgeR). Similarly, in blood samples associated with HS, we screened132 DEGs, with 67 upregulated and 65 downregulated genes. Through an integrative approach involving three machine learning methods and subsequent validation on an independent dataset, we successfully identified AKR1B10, IGFL2, WNK2, SLAMF7, and CCR7 as potential biomarkers and therapeutic targets for HS treatment. Furthermore, immune cell infiltration analysis showed that HS is marked by dysregulations in multiple immune cells, and correlations exist between diverse immune cells, hub genes, and immune cell subsets.
Conclusion:
AKR1B10, IGFL2, WNK2, SLAMF7, and CCR7 were successfully identified. Single-cell RNA-seq analysis further refines our understanding of the cellular heterogeneity in HS lesions. These findings contribute to advancing our knowledge of HS pathogenesis and hold promise for future therapeutic interventions.
Dynamic protein-protein interactions of the potato autophagy-related StATG8 family proteins, which are also associated with WRKY transcription factor and pathogen effector in the nucleus
Authors: Huh Sung Un 
Published: February 2024

Abstract
Background
Autophagy is a cellular recycling process responsible for eliminating damaged proteins and organelles. Autophagy-related proteins (ATGs) are primarily located in the cytoplasm, playing essential roles in various stages of autophagosome formation. Among these proteins, the ATG8/Atg8/LC3/GABARAP family proteins are evolutionarily conserved and crucial for autophagy. While ATG8 is predominantly found in the nucleus and cytoplasm of cells, its function within the nucleus remains largely unknown.
Results
This study reveals that the potato StATG8 family forms homo-/hetero-dimers and selectively interacts with the transcriptional regulator WRKY, exclusive to the nucleus, and the pathogenic protein PopP2.
Conclusions
These findings represent a fundamental step toward unraveling the role of ATG8 within the nucleus.