Ontology Categories Research Articles

Novel combinatorial therapy of oncolytic adenovirus AdV5/3-D24-ICOSL-CD40L with anti PD-1 exhibits enhanced anti-cancer efficacy through promotion of intratumoral T-cell infiltration and modulation of tumour microenvironment in mesothelioma mouse model.

Malignant mesothelioma is a rare and aggressive form of cancer. Despite improvements in cancer treatment, there are still no curative treatment modalities for advanced stage of the malignancy. The aim of this study was to evaluate the anti-tumor efficacy of a novel combinatorial therapy combining AdV5/3-D24-ICOSL-CD40L, an oncolytic vector, with an anti-PD-1 monoclonal antibody. The efficacy of the vector was confirmed in vitro in three mesothelioma cell lines - H226, Mero-82, and MSTO-211H, and subsequently the antineoplastic properties in combination with anti-PD-1 was evaluated in xenograft H226 mesothelioma BALB/c and humanized NSG mouse models. Anticancer efficacy was attributed to reduced tumour volume and increased infiltration of tumour infiltrating lymphocytes, including activated cytotoxic T-cells (GrB+CD8+). Additionally, a correlation between tumour volume and activated CD8+ tumour infiltrating lymphocytes was observed. These findings were confirmed by transcriptomic analysis carried out on resected human tumour tissue, which also revealed upregulation of CD83 and CRTAM, as well as several chemokines (CXCL3, CXCL9, CXCL11) in the tumour microenvironment. Furthermore, according to observations, the combinatorial therapy had the strongest effect on reducing mesothelin and MUC16 levels. Gene set enrichment analysis suggested that the combinatorial therapy induced changes to the expression of genes belonging to the "adaptive immune response" gene ontology category. Combinatorial therapy with oncolytic adenovirus with checkpoint inhibitors may improve anticancer efficacy and survival by targeted cancer cell destruction and triggering of immunogenic cell death. Obtained results support further assessment of the AdV5/3-D24-ICOSL-CD40L in combination with checkpoint inhibitors as a novel therapeutic perspective for mesothelioma treatment.

Adaptive Integration of Categorical and Multi-relational Ontologies with EHR Data for Medical Concept Embedding

Representation learning has been applied to Electronic Health Records (EHR) for medical concept embedding and the downstream predictive analytics tasks with promising results. Medical ontologies can also be integrated to guide the learning so the embedding space can better align with existing medical knowledge. Yet, properly carrying out the integration is non-trivial. Medical concepts that are similar according to a medical ontology may not be necessarily close in the embedding space learned from the EHR data, as medical ontologies organize medical concepts for their own specific objectives. Any integration methodology without considering the underlying inconsistency will result in sub-optimal medical concept embedding and, in turn, degrade the performance of the downstream tasks. In this article, we propose a novel representation learning framework called ADORE ( AD aptive O ntological RE presentations) that allows the medical ontologies to adapt their structures for more robust integrating with the EHR data. ADORE first learns multiple embeddings for each category in the ontology via an attention mechanism. At the same time, it supports an adaptive integration of categorical and multi-relational ontologies in the embedding space using a category-aware graph attention network. We evaluate the performance of ADORE on a number of predictive analytics tasks using two EHR datasets. Our experimental results show that the medical concept embeddings obtained by ADORE can outperform the state-of-the-art methods for all the tasks. More importantly, it can result in clinically meaningful sub-categorization of the existing ontological categories and yield attention values that can further enhance the model interpretability.

Enterprise data and semantic modelling: conceptual model of information technology incident management

Knowledge management methods and their efficient implementation across the organization determine sound and resilient management of processes. This paper studies the semantic integration of enterprise data sources essential to service management processes. Implementing a semantic layer within the enterprise architecture uses various tools, methods, and techniques. The semantic conceptual model unifies and implements intelligent integration of multiple data sources across the enterprise, achieving consistency and more accessible interpretation. Specifically, we draw our attention to incident and problem management within enterprises. We propose an ontology - a conceptual model for the incident management process. The incident ontology presented as an intelligent data integration layer component aims to achieve operational excellence. Besides, this ontology is a fundamental part of the proactive process in problem management. An ontology as a logic-based system supports integrity validation. It infers new, no explicitly modeled facts in the problem domain, thus helping experts better analyze and understand the problem. We discuss the conducted experiment results with the proposed in this article conceptual model using the enterprise knowledge graph platform. It can be perceived as a framework for a query-answering system with components, including ontology schema, data mapping, and classification methods for data graph enrichment.

The role of charme in the phenotype and function of resident cardiac mesenchymal stromal cells

Abstract Background Charme is a murine long non-coding RNA with specific expression in striated muscles, presenting a human orthologue with 45% identity. Its depletion leads to incomplete muscle differentiation. Charme-/- mice display an altered cardiac phenotype with increased wall thickness and reduced chamber dimensions due to myocyte hyperplasia. Left ventricular dilatation and reduced fractional shortening are detected in aged Charme-/- mice. Embryonic myocardial architecture reveals aberrant compaction and ventricular hypotrabeculation, resembling some congenital cardiomyopathies. Cardiac mesenchymal stromal cells (CMSCs) play key roles in tissue homeostasis and pathophysiology, by maintaining the extracellular matrix and by paracrine action on all myocardial cells. Purpose To elucidate the phenotype, paracrine function, and myofibroblast differentiation capacity of resident CMSCs in the Charme-/- mouse model. Methods CMSCs were isolated from 5-week-old wild-type (WT) and Charme-/- mice by explant culture, pooling at least 4 different hearts per culture. Results Charme-/- CMSCs showed increased features of primitive phenotypes, such as enhanced spontaneous spheroid growth (123,6±11,9 vs 51,0±6,4 spheroids/well; N=8, p<0,0001) and clonogenesis efficiency (2,7±0,5-fold; N=7, p<0,05) compared to WT cells. Charme-/- CMSCs also showed increased migration ability (Charme-/-: 68,5±2,7% vs WT: 80,2±0,7% wound area; N=2). Flow cytometry identified a reduced proportion of lin-/Sca1+/CD90+ primitive mesenchymal cells in Charme-/- versus WT CMSCs (7,4±1,6% vs 56,9±6,5%; N=6, p<0,05). Western blot analysis on Charme-/- whole cardiac tissue showed reduced collagen I and collagen I/III protein ratio compared to WT hearts (0,17±0,03 vs 0,85±0,10 normalized OD; N=4, p<0,005). Stimulation with TGFb-1 resulted in lower expression of fibroblast activation markers compared to WT CMSCs, as assessed by immunofluorescence staining for aSMA (0,49±0,05 vs 0,76±0,10 mean fluorescence intensity; N=6-12, p<0,05) and collagen I/III mRNA expression ratio (1,3±0,1 vs 2,2±0,4 2^-DCt; N=3, p<0,01). The secretome of Charme-/- CMSCs revealed a general depletion in many cardioprotective cytokines, included in the KEGG term "PI3K-Akt signalling pathway" (FDR<0,0005) and classified in Gene Ontology categories of myoblast differentiation and fusion (GO:1901739, GO:1901741, GO:0045663, GO:0045661; FDR<0,05). In line with this, the secretome of TGFb1-stimulated Charme-/- CMSCs was less effective in sustaining cardiomyocyte survival versus the WT CMSC secretome (1,70±0,03 vs 1,90±0,04 normalized OD at 48h; N=5, p<0,005). Conclusions Charme-/- CMSCs show a less mature phenotype associated to reduced collagen I presence in situ, reduced activation and differentiation upon stimulation, and impaired cardioprotective paracrine functions, suggesting a key role of Charme in the physiology of the cardiac stroma, possibly mediating in part the altered cardiac phenotype of Charme-/- mice.

Antagonistic Activity of Streptomyces alfalfae 11F against Fusarium Wilt of Watermelon and Transcriptome Analysis Provides Insights into the Synthesis of Phenazine-1-Carboxamide.

Streptomyces alfalfa strain 11F has inhibitory effects on many phytopathogenic fungi and improves the establishment and biomass yield of switchgrass. However, the antagonistic effects of strain 11F on Fusarium wilt of watermelon and its secondary metabolites that contribute to its biocontrol activity are poorly understood. We evaluated the antagonistic and growth-promoting effects of strain 11F and conducted a transcriptome analysis to identify the metabolites contributing to antifungal activity. Strain 11F had marked inhibitory effects on six fungal pathogens. The incidence of Fusarium wilt of watermelon seedlings was decreased by 46.02%, while watermelon seedling growth was promoted, as indicated by plant height (8.7%), fresh weight (23.1%), and dry weight (60.0%). Clean RNA-sequencing data were annotated with 7553 functional genes. The 2582 differentially expressed genes (DEGs) detected in the Control vs. Case 2 comparison were divided into 42 subcategories of the biological process, cellular component, and molecular function Gene Ontology categories. Seven hundred and forty functional genes (55.47% of the DEGs) were assigned to Kyoto Encyclopedia of Genes and Genomes metabolic pathways, reflecting the complexity of the strain 11F metabolic regulatory system. The expression level of the gene phzF, which encodes an enzyme essential for phenazine-1-carboxylic acid (PCA) synthesis, was downregulated 3.7-fold between the 24 h and 48 h fermentation time points, suggesting that strain 11F can produce phenazine compounds. A phenazine compound from 11F was isolated and identified as phenazine-1-carboxamide (PCN), which contributed to the antagonistic activity against Fusarium oxysporum f. sp. niveum. PCA was speculated to be the synthetic precursor of PCN. The downregulation in phzF expression might be associated with the decrease in PCA accumulation and the increase in PCN synthesis in strain 11F from 24 to 48 h. Streptomyces alfalfae 11F protects watermelon seedlings from Fusarium wilt of watermelon and promotes seedling growth. The transcriptome analysis of strain 11F provides insights into the synthesis of PCN, which has antifungal activity against F. oxysporum f. sp. niveum of watermelon.

SNOMED CT and Basic Formal Ontology – convergence or contradiction between standards? The case of “clinical finding”

Background: SNOMED CT is a large terminology system designed to represent all aspects of healthcare. Its current form and content result from decades of bottom-up evolution. Due to SNOMED CT’s formal descriptions, it can be considered an ontology. The Basic Formal Ontology (BFO) is a foundational ontology that proposes a small set of disjoint, hierarchically ordered classes, supported by relations and axioms. In contrast, as a typical top-down endeavor, BFO was designed as a foundational framework for domain ontologies in the natural sciences and related disciplines. Whereas it is mostly assumed that domain ontologies should be created as extensions of foundational ontologies, a post-hoc harmonization of consolidated domain ontologies in use, such as SNOMED CT, is known to be challenging. Methods: We explored the feasibility of harmonizing SNOMED CT with BFO, with a focus on the SNOMED CT Clinical Finding hierarchy. With more than 100,000 classes, it accounts for about one third of SNOMED CT’s content. In particular, we represented typical SNOMED CT finding/disorder concepts using description logics under BFO. Three representational patterns were created and the logical entailments analyzed. Results: Under a first scrutiny, the clinical intuition that diseases, disorders, signs and symptoms form a homogeneous ontological upper-level class appeared incompatible with BFO’s upper-level distinction into continuants and occurrents. The Clinical finding class seemed to be an umbrella for all kinds of entities of clinical interest, such as material entities, processes, states, dispositions, and qualities. This suggests the conclusion that Clinical finding would not be a suitable upper-level class from an BFO perspective. On closer inspection of the taxonomic links within this hierarchy and the implicit meaning derived thereof, it became clear that Clinical finding classes do not characterize the entity (e.g. a fracture, allergy, tumor, pain, hemorrhage, seizure, fever) in a literal sense but rather the condition of a patient having that fracture, allergy, pain etc. This gives sense to the current characteristic of the Clinical Finding hierarchy, in which complex classes are modeled as subclasses of their constituents. Most of these taxonomic links are inferred, as the consequence of the ‘role group’ design pattern, which is ubiquitous in SNOMED CT and has often been subject of controversy regarding its semantics. Conclusion: Our analyses resulted in the proposal of (i) equating SNOMED CT’s ‘role group’ property with the reflexive and transitive BFO relation ‘has occurrent part’; and (ii) reinterpreting Clinical Findings as Clinical Occurrents, i.e. temporally extended entities in an organism, having one or more occurrents as temporal parts that occur in continuants. This re-interpretation was corroborated by a manual analysis of classes under Clinical Finding, as well as the identification of similar modeling patterns in other ontologies. As a result, SNOMED CT does not require any content redesign to establish compatibility with BFO, apart from this re-interpretation, and a suggested re-labeling. Regarding the feasibility of harmonizing terminologies with principled foundational ontologies post-hoc, our results provide support to the assumption that this does not necessarily require major redesign efforts, but rather a careful analysis of the implicit assumptions of terminology curators and users.

Abstract 19018: Unraveling the Regulatory Landscape of NKX2-5 in Human Left Atrial Tissue: Implications for Atrial Fibrillation

Cardiac transcription factors are emerging as crucial modulators of atrial fibrillation (AF), with rare and common variation implicated in AF. Mutations in NKX2-5 and more recently, NFATC1 were reported in families with autosomal dominant young-onset AF. Here, we explore the landscape of NKX2-5 and NFATC1 in human left atrium, using Chromatin Immunoprecipitation Sequencing (ChIP-seq), DAVID functional annotation and HOMER motif analyses. Post-mortem human left atrial tissue samples (n=5) were obtained from the National Disease Research Interchange (NDRI) within a recovery interval of < 4 hours. Preserved microstructural integrity and normal staining patters for TNNT2 and vimentin were verified using confocal microscopy. ChIP-seq analysis revealed an average of 2.62k NKX2-5 binding peaks, with 118 genes bound in all samples. Functional analysis identified significant enrichment in gene ontology categories and pathways (Table 1), including adrenergic and PPAR signaling pathways known to participate in AF susceptibility. Using HOMER, we mapped 55 NFATC1 consensus binding sites to the NKX2-5 ChIP peaks. Two NFATC1 consensus sites localized to an NKX2-5 binding peak located upstream from MEF2A (Figure 1). Published HI-C data from human right atrium indicates the NFATC1 binding sites are adjacent to the promoter of MEF2A in 3D space, suggesting that NKX2-5 and NFATC1 co-regulate MEF2A. In murine atria, mef2A regulates genes involved in fibrosis and adhesion, processes that are crucial in the pathogenesis of atrial fibrillation. Our data, together with published literature, provide a framework for understanding transcriptional networks that may predispose to human AF.

Gene Expression and Functional Analysis in Patients with Acute and Chronic Renal Allograft Rejection

Kidney transplantation is the therapy of choice for patients with end-stage kidney disease (ESKD). Nevertheless, the main limitation for long-term graft survival is immune-mediated rejection. Some authors have proposed that differences in immune effector mechanisms are influenced by underlying molecular mechanisms; thereby, the identification of differentially expressed genes in acute or chronic rejection in non-invasive samples such as urine may be essential for the identification of potential biomarkers and biological processes associated with allograft outcomes. Our aim was to explore differences in gene expression and functional categories associated with acute and chronic kidney rejection in blood, biopsy, and urine of kidney transplant patients using RNA-Seq. RNA was isolated and sequenced implementing standard protocols. Analyses were addressed to identify differentially expressed genes (DEGs) and Functional Categories of Gene Ontology comparing between samples. Then we focused on immune genes and pathways to identify their association with the allograft. We identified a significant transcriptional similarity between biopsy and urine, in comparison with blood in acute and chronic rejection. Functional analyses suggested an enrichment of immune processes such as antigen processing and presentation, and regulation of B cell receptor signaling pathway in blood of acute and chronic rejection, respectively. Additionally, we observed an increase in expression of chemokines in biopsy and urine of both outcomes along with an increase in chemokine receptors in blood. Our findings suggest that urine is suitable for identifying potential biomarkers and biological processes related to renal allograft rejection, as it shares a significant number of regulated genes with biopsy.

Vocational pedagogy in Automotive Mechanics: Ontological dimensions and Cognitive Load Theory implications

This research explored the way ontological categories are fundamentally useful for analysing vocational pedagogy, particularly in the context of Automotive Mechanics. Two ontological traditions were found to be especially useful: mereology, with its focus on part–whole systems, and process ontology, which emphasises the dynamics of change. The convergence of ontological categories with learning science in Automotive Mechanics pedagogy is also examined, particularly the way in which cognitive load theory helps to manage the learning complexities tied to ontological automotive concepts. The research, which targeted first-year student training, employed a qualitative case study methodology encompassing three vocational education and training institutions in Eswatini that provide training in Automotive Mechanics. The data collection involved conducting interviews with lecturers, making observations in both classrooms and workshops, and recording the teaching process on video during a one-year period. Field notes and transcriptions were analysed in order to extract key themes connected to the teaching methods. These themes were identified, grouped and further condensed to isolate the most prevalent teaching practices across the institutions. Upon identifying a significant theme pertaining to parts and wholes, the researchers delved into the philosophical and theoretical aspects of part–whole relations and their role in teaching and learning processes. They discovered beneficial interconnections between mereology, process ontology, and cognitive load theory, especially the way the hierarchical structure of Automotive Mechanics pedagogy interacts with the constraints of working memory and chunking. These connections both foster in-depth pedagogic analysis and contribute to the enhancement of Automotive Mechanics pedagogy.

Identification of Crucial Genes and Regulatory Pathways in Alfalfa against Fusarium Root Rot.

Fusarium root rot, caused by Fusarium spp. in alfalfa (Medicago sativa L.), adversely impacts alfalfa by diminishing plant quality and yield, resulting in substantial losses within the industry. The most effective strategy for controlling alfalfa Fusarium root rot is planting disease-resistant varieties. Therefore, gaining a comprehensive understanding of the mechanisms underlying alfalfa's resistance to Fusarium root rot is imperative. In this study, we observed the infection process on alfalfa seedling roots infected by Fusarium acuminatum strain HM29-05, which is labeled with green fluorescent protein (GFP). Two alfalfa varieties, namely, the resistant 'Kangsai' and the susceptible 'Zhongmu No. 1', were examined to assess various physiological and biochemical activities at 0, 2, and 3 days post inoculation (dpi). Transcriptome sequencing of the inoculated resistant and susceptible alfalfa varieties were conducted, and the potential functions and signaling pathways of differentially expressed genes (DEGs) were analyzed through gene ontology (GO) classification and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis. Meanwhile, a DEG co-expression network was constructed though the weighted gene correlation network analysis (WGCNA) algorithm. Our results revealed significant alterations in soluble sugar, soluble protein, and malondialdehyde (MDA) contents in both the 'Kangsai' and 'Zhongmu No. 1' varieties following the inoculation of F. acuminatum. WGCNA analysis showed the involvement of various enzyme and transcription factor families related to plant growth and disease resistance, including cytochrome P450, MYB, ERF, NAC, and bZIP. These findings not only provided valuable data for further verification of gene functions but also served as a reference for the deeper explorations between plants and pathogens.

A model-based approach for converting CGMES power system models into operational networks

This paper presents a model-based approach for converting Common Grid Model Exchange Specification (CGMES) power system models into operational networks. The approach utilizes the Model-Driven Architecture (MDA), borrowed from software engineering, to create a Platform-Independent Model (PIM) saved in a graph database, neo4j. The PIM is then transformed into Platform-Specific Model (PSM) using cypher queries. Finally, from the PSM, a Pandapower network is generated that is used later for running power flow simulations. The Common Information Model (CIM) ontology classes, which form the metamodel behind CGMES, are loaded into the same database, connecting them to the grid instances, allowing for automatic validation and inference. The proposed approach has been successfully applied to large-scale real-world grids that include renewable energy sources.

GeoFault: A well-founded fault ontology for interoperability in geological modeling

Geological modeling currently uses various computer-based applications. Data harmonization at the semantic level using ontologies is essential to make these applications interoperable. Since geo-modeling is part of several multidisciplinary projects, interoperability requires semantic harmonization to exchange information between geological applications and integrate other domain knowledge at a general level. Therefore, domain ontologies that describe geological knowledge must be based on a sound ontological background to ensure this knowledge is integrable. Faults are essential for understanding and solving structural problems but are complex to model because the concept of fault includes a group of geological entities with a distinct ontological nature. A fault can correspond to thin, deformed rock volumes or spatial arrangements resulting from the displacement of geological blocks, but at a broader scale, geologists describe faults as surfaces or components of complex fault arrays. Our work intends to harmonize these views by presenting a domain ontology, GeoFault, resting on the Basic Formal Ontology (BFO) and the GeoCore ontology. GeoCore and GeoFault support the parametric description of geological sites as a preliminary step for quantitative and qualitative analysis. We have proposed GeoFault after systematically revising the literature and several knowledge-acquisition sessions with expert structural geologists. The ontology formalizes a vocabulary for fault “sensu stricto,” excluding ductile shear deformations. It covers the regional to outcrop scales, excluding structures at the microscopic, orogenic, and tectonics scales, and it avoids interpretive language associated with geological processes as far as possible. Extending the BFO and GeoCore ontologies allows the fault concept to be related to formal ontological classes in a consistent semantic-rich framework. The ontology artifact is implemented in OWL 2, validated by competency questions with two use cases, and tested using an in-house ontology-driven data entry application. The GeoFault ontology is publicly available and provides a solid framework for clarifying fault knowledge and a foundation for many applications.

Single-cell transcriptome analysis of the germ cells and somatic cells during mitotic quiescence stage in goats.

The mitotic quiescence of prospermatogonia is the event known to occur during genesis of the male germline and is tied to the development of the spermatogenic lineage. The regulatory mechanisms and the functional importance of this process have been demonstrated in mice; however, regulation of this process in human and domestic animal is still largely unknown. In this study, we employed single-cell RNA sequencing to identify transcriptional signatures of prospermatogonia and major somatic cell types in testes of goats at E85, E105, and E125. We identified both common and specific Gene Ontology categories, transcription factor regulatory networks, and cell-cell interactions in cell types from goat testis. We also analyzed the transcriptional dynamic changes in prospermatogonia, Sertoli cells, Leydig cells, and interstitial cells. Our datasets provide a useful resource for the study of domestic animal germline development.

Kang Youwei and Italy in the beginning of the 20th century: comprehension of the politics of the west by the traditional confucian thinker

The article deals with the theoretical treatises written by Kang Youwei (1858 — 1927) in exile and devoted to the understanding of Western social and political reality from the standpoint of a bearer of traditional Chinese culture and Neo-Confucian philosophy. First of all, these are “Travelogue to Italy” (Yidali youji, 1904) and “Impartial Words on Republicanism” (Gonghe pingyi, 1918). Kang Yuwei’s thinking is characterized by attention to the Confucian binary opposition si — gong (private — general), which he transferred to both civilizational development and international politics. In other words, the Western path of development, which consist national imperialist states based on economic, social and foreign policy competition and individualism (“private”), was opposed to the monolithic ancient China, whose society and politics are based on the principles of “community” and unity. Kang Youwei perceived the political reality of Western countries from the standpoint of traditional Chinese historiography, which was intended to serve as a base of positive and negative precedents for use by the ruler in the name of the common good and the harmonization of society. In Kang Youwei’s system of historical views, modern Italy and Germany were very important for illustrating the principle of consolidation of political entities and the merging of small and weak states into large empires. Methodologically, this was formalized as the assignment of Germany, Italy and China to the same ontological category (tong lei).

Quantitative analysis of acetylation in peste des petits ruminants virus-infected Vero cells

BackgroundPeste des petits ruminants virus (PPRV) is a highly contagious pathogen that strongly influences the productivity of small ruminants worldwide. Acetylation is an important post-translational modification involved in regulation of multiple biological functions. However, the extent and function of acetylation in host cells during PPRV infection remains unknown.MethodsDimethylation-labeling-based quantitative proteomic analysis of the acetylome of PPRV-infected Vero cells was performed.ResultsIn total, 1068 proteins with 2641 modification sites were detected in response to PPRV infection, of which 304 differentially acetylated proteins (DAcPs) with 410 acetylated sites were identified (fold change < 0.83 or > 1.2 and P < 0.05), including 109 up-regulated and 195 down-regulated proteins. Gene Ontology (GO) classification indicated that DAcPs were mostly located in the cytoplasm (43%) and participated in cellular and metabolic processes related to binding and catalytic activity. Functional enrichment indicated that the DAcPs were involved in the minichromosome maintenance complex, unfolded protein binding, helicase activity. Only protein processing in endoplasmic reticulum pathway was enriched. A protein-protein interaction (PPI) network of the identified proteins further indicated that a various chaperone and ribosome processes were modulated by acetylation.ConclusionsTo the best of our knowledge, this is the first study on acetylome in PPRV-infected host cell. Our findings establish an important baseline for future study on the roles of acetylation in the host response to PPRV replication and provide novel insights for understanding the molecular pathological mechanism of PPRV infection.

Disassembling Descola: Phenomenological Intersections in Onto-Typological Anthropology

Abstract One of the effects of the so-called ontological turn has been to take the other so seriously that radical difference has been conceptualized ontologically. This stance has given rise, in some authors, as Descola, to a typological classification. However, we would suggest the possibility of a non-onto-typological anthropology based on Marion’s phenomenology of givenness. With the phenomenology of givenness, from which phenomena are given to a gifted – and therefore secondary – subject, this new understanding of subject allows us to think of phenomena as significations much more than as representations and to replace the discontinuity of ontological categories with the continuity of hermeneutics.

Comparative Root Transcriptome Profiling and Gene Regulatory Network Analysis between Eastern and Western Carrot (Daucus carota L.) Cultivars Reveals Candidate Genes for Vascular Tissue Patterning.

Carrot (Daucus carota L.) is a highly consumed vegetable rich in carotenoids, known for their potent antioxidant, anti-inflammatory, and immune-protecting properties. While genetic and molecular studies have largely focused on wild and Western carrot cultivars (cvs), little is known about the evolutionary interactions between closely related Eastern and Western cvs. In this study, we conducted comparative transcriptome profiling of root tissues from Eastern (UHSBC-23-1) and Western (UHSBC-100) carrot cv. to better understand differentially expressed genes (DEGs) associated with storage root development and vascular cambium (VC) tissue patterning. Through reference-guided TopHat mapping, we achieved an average mapping rate of 73.87% and identified a total of 3544 DEGs (p < 0.05). Functional annotation and gene ontology classification revealed 97 functional categories, including 33 biological processes, 19 cellular components, 45 metabolic processes, and 26 KEGG pathways. Notably, Eastern cv. exhibited enrichment in cell wall, plant-pathogen interaction, and signal transduction terms, while Western cv. showed dominance in photosynthesis, metabolic process, and carbon metabolism terms. Moreover, constructed gene regulatory network (GRN) for both cvs. obtained orthologs with 1222 VC-responsive genes of Arabidopsis thaliana. In Western cv, GRN revealed VC-responsive gene clusters primarily associated with photosynthetic processes and carbon metabolism. In contrast, Eastern cv. exhibited a higher number of stress-responsive genes, and transcription factors (e.g., MYB15, WRKY46, AP2/ERF TF connected via signaling pathways with NAC036) were identified as master regulators of xylem vessel differentiation and secondary cell wall thickening. By elucidating the comparative transcriptome profiles of Eastern and Western cvs. for the first time, our study provides valuable insights into the differentially expressed genes involved in root development and VC tissue patterning. The identification of key regulatory genes and their roles in these processes represents a significant advancement in our understanding of the evolutionary relations and molecular mechanisms underlying secondary growth of carrot and regulation by vascular cambium.

Girard and Nietzsche's phenomenology of victims

In this paper I argue that Nietzsche and Girard provide, for the first time, a phenomenology and genealogical account of the victim as both an ontological and moral category. First, I lay out Girard’s mimetic theory and show how it culminates in a phenomenology of victims and victimization. I then turn to Nietzsche, in particular Girard’s consideration of Nietzsche as the most important theologian of recent past, to show that Girard’s phenomenology – of victims, violence, and scapegoating – already exists within Nietzsche’s philosophical framework, albeit with a significantly different interpretation. It is my hope to problematize the seemingly self-evident and axiomatic character of the category of the “victim” by highlighting its specific genealogy within the Judeo-Christian tradition in order to further a much broader discussion on the hermeneutics of violence in general.

UV RESISTANCE LOCUS 8-Mediated UV-B Response Is Required Alongside CRYPTOCHROME 1 forPlant Survival in Sunlight under Field Conditions.

As sessile, photoautotrophic organisms, plants are subjected to fluctuating sunlight that includes potentially detrimental ultraviolet-B (UV-B) radiation. Experiments under controlled conditions have shown that the UV-B photoreceptor UV RESISTANCE LOCUS 8 (UVR8) controls acclimation and tolerance to UV-B in Arabidopsis thaliana; however, its long-term impact on plant fitness under naturally fluctuating environments remain poorly understood. Here, we quantified the survival and reproduction of different Arabidopsis mutant genotypes under diverse field and laboratory conditions. We found that uvr8 mutants produced more fruits than wild type when grown in growth chambers under artificial low-UV-B conditions but not under natural field conditions, indicating a fitness cost in the absence of UV-B stress. Importantly, independent double mutants of UVR8 and the blue light photoreceptor gene CRYPTOCHROME 1 (CRY1) in two genetic backgrounds showed a drastic reduction in fitness in the field. Experiments with UV-B attenuation in the field and with supplemental UV-B in growth chambers demonstrated that UV-B caused the cry1 uvr8 conditional lethal phenotype. Using RNA-seq data of field-grown single and double mutants, we explicitly identified genes showing significant statistical interaction of UVR8 and CRY1 mutations in the presence of UV-B in the field. They were enriched in Gene Ontology categories related to oxidative stress, photoprotection and DNA damage repair in addition to UV-B response. Our study demonstrates the functional importance of the UVR8-mediated response across life stages in natura, which is partially redundant with that of cry1. Moreover, these data provide an integral picture of gene expression associated with plant responses under field conditions.

Pseudocercospora fijiensis Conidial Germination Is Dominated by Pathogenicity Factors and Effectors.

Conidia play a vital role in the survival and rapid spread of fungi. Many biological processes of conidia, such as adhesion, signal transduction, the regulation of oxidative stress, and autophagy, have been well studied. In contrast, the contribution of pathogenicity factors during the development of conidia in fungal phytopathogens has been poorly investigated. To date, few reports have centered on the pathogenicity functions of fungal phytopathogen conidia. Pseudocercospora fijiensis is a hemibiotrophic fungus and the causal agent of the black Sigatoka disease in bananas and plantains. Here, a conidial transcriptome of P. fijiensis was characterized computationally. Carbohydrates, amino acids, and lipid metabolisms presented the highest number of annotations in Gene Ontology. Common conidial functions were found, but interestingly, pathogenicity factors and effectors were also identified. Upon analysis of the resulting proteins against the Pathogen-Host Interaction (PHI) database, 754 hits were identified. WideEffHunter and EffHunter effector predictors identified 618 effectors, 265 of them were shared with the PHI database. A total of 1107 conidial functions devoted to pathogenesis were found after our analysis. Regarding the conidial effectorome, it was found to comprise 40 canonical and 578 non-canonical effectors. Effectorome characterization revealed that RXLR, LysM, and Y/F/WxC are the largest effector families in the P. fijiensis conidial effectorome. Gene Ontology classification suggests that they are involved in many biological processes and metabolisms, expanding our current knowledge of fungal effectors.