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Publications related to Rosetta (9,145)
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Article
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Researchers have increasingly investigated the effectiveness of commercial mobile-assisted language learning (MALL) applications (apps) such as Duolingo, Babbel, Busuu, Memrise, and Rosetta Stone, with several methodological reviews that have been published to date. However, prior reviews have often lumped together MALL studies involving commercial...
Article
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Purpose Low-dose CT (LDCT) screening effectively reduces lung adenocarcinoma (LUAD) mortality. However, accurately evaluating the malignant potential of indeterminate lung nodules remains a challenge. Carcinoembryonic antigen cell adhesion molecule 6 (CEACAM6), a potential biomarker for distinguishing benign pulmonary nodules from LUAD, may be leve...
Article
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The design of organic–peptide hybrids has the potential to combine our vast knowledge of protein design with small molecule engineering to create hybrid structures with complex functions. Here, we describe the computational design of a photoswitchable Ca ²⁺ -binding organic–peptide hybrid. The designed molecule, designated Ca ²⁺ -binding switch (Ca...
Preprint
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Comets, asteroids, and other small bodies are thought to be remnants of the original planetesimal population of the Solar System. As such, their physical, chemical, and isotopic properties hold crucial details on how and where they formed and how they evolved. Yet, placing precise constraints on the formation region of these bodies has been challen...
Article
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Violence commonly alters intimacy, inequality, and diversity. As such, it is a movement of social time defined and punished as deviant. Most violence is also punishment of some kind that responds to other behaviors defined as deviant. Donald Black’s work on conflict and social control has shown that patterns of intimacy, inequality, and diversity p...
Article
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Gas and dust outbursts are recurring phenomena on comets, offering critical insights into their subsurface activities. On comet 67P/Churyumov-Gerasimenko, two distinct outburst types have been identified: CO2-dominated ”summer fireworks” near perihelion and water-driven events often linked to cliff collapses outside the perihelion period. While CO2...
Article
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An important step of mainstream protein structure prediction is to model the 3D protein structure based on the predicted 2D inter‐residue geometric information. This folding step has been integrated into a unified neural network to allow end‐to‐end training in state‐of‐the‐art methods like AlphaFold2, but is separately implemented using the Rosetta...
Article
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This study presents a comprehensive workflow to detect low seismic amplitude gas fields in hydrocarbon exploration projects, focusing on the West Delta Deep Marine (WDDM) concession, offshore Egypt. The workflow integrates seismic spectral decomposition and machine learning algorithms to identify subtle anomalies, including low seismic amplitude ga...
Preprint
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Abstract: Protein cages represent a cutting-edge frontier in nanoscience, merging biological complexity with engineered precision to create transformative possibilities across bioengineering fields. This comprehensive review explores the intricate world of protein cage design and hierarchical assembly, focusing on recent advancements in computatio...
Preprint
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Computational tools have revolutionised the field of artificial protein cage design, enabling unprecedented precision and efficiency in molecular engineering. This comprehensive review explores the state-of-the-art computational methods employed in designing protein cages, highlighting the integration of advanced algorithms, machine learning techni...
Article
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Se presenta una hoja didáctica que comprende actividades ante grupo para asistir la labor del docente. Los ejercicios introducen a los estudiantes a los principios químicos que dirigen el plegamiento de las proteínas y debe ayudarlos a reconocer la relevancia de los avances tecnológicos que representan Rosetta y AlphaFold. Así, los alumnos podrán v...
Article
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Variable lymphocyte receptors (VLRs) are the antigen receptors of jawless vertebrates such as lamprey. VLRs are of growing biotechnological interest for their ability to bind certain antigenic targets with higher affinity than traditional immunoglobulins. However, VLRs are disulfide‐bonded proteins that are often challenging to produce requiring ge...
Article
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Bulk nitrogen is depleted in solar system objects, including the terrestrial planets, chondritic meteorites, and comets. Recently, it was suggested that cometary nitrogen may be locked up in ammonium salts—ionic solids comprising ammonia (NH 3 ) and an acid such as hydrogen cyanide (HCN)—based on Rosetta/ROSINA data from comet 67P/Churyumov–Gerasim...
Article
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Ecological assembly—the process of ecological community formation through species introductions—has recently seen exciting theoretical advancements across dynamical, informational, and probabilistic approaches. However, these theories often remain inaccessible to non‐theoreticians, and they lack a unifying lens. Here, I introduce the assembly graph...
Article
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Wood formation is the Rosetta stone of tree physiology: a traceable, integrated record of physiological and morphological status. It also produces a large and persistent annual sink for terrestrial carbon, motivating predictive understanding. Xylogenesis studies have greatly expanded our knowledge of the intra‐annual controls on wood formation, whi...
Article
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Poly(A) polymerase (PAP 1) from Escherichia coli is the primary enzyme responsible for synthesizing poly(A) tails on RNA molecules, signaling RNA degradation in bacterial cells. In vitro, PAP 1 is used to prepare libraries for RNAseq and to produce mRNA vaccines. However, E. coli PAP 1’s toxicity and instability in low-salt buffers complicate its e...
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The transition from simple to complex multicellularity involves division of labor and specialization of cell types. In animals, complex sensory-motor systems are primarily built around specialized cells of muscles and neurons, though the evolutionary origins of these and their integration remain unclear. Here, to investigate sensory-behavior coupli...
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Background Although immunoglobulin (Ig) alleles play a pivotal role in the antibody response to pathogens, research to understand their role in the humoral immune response is still limited. Methods We retrieved the germline sequences for the IGHV from the IMGT database to illustrate the amino acid polymorphism present within germline sequences of...
Article
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The Chikungunya virus (CHIKV) is a mosquito-borne virus with a long history of recurring epidemics transmitted through Aedes mosquitoes. The rapid spread of CHIKV has intensified the need for potent vaccines. Escherichia coli (E.coli), a vital part of human gut microbiota, is utilized in recombinant DNA technology for cloning. However, its high ada...
Preprint
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Highly unsaturated carbon chains, including polyynes, have been detected in many astronomical regions and planetary systems. With the success of the QUIJOTE survey of the TMC-1, the community has seen a "boom" in the number of detected carbon chains. On the other hand, the Rosetta mission revealed the release of fully saturated hydrocarbons, C$_3$H...
Article
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Aim. This study was performed to assess the impact of preparation design and material type on the fracture resistance and mode of failure of occlusal veneers after thermocycling. Material and methods. A total number of twenty extracted lower premolars were divided randomly into two main groups according to occlusal veneer preparation design; Group...
Preprint
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Inflammasomes trigger cell death upon sensing various intracellular maladies. These supra-structures relay upstream signals by sequentially assembling architecturally congruent filaments via their pyrin domains (PYDs). Interferon Inducible Protein 16 (IFI16) is an innate immune sensor that detects dysregulated nucleic acids. Once presumed as an inf...
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There is no doubt that the great victory achieved by the Egyptians over the invading British army in 1807, and the people of the city of Rosetta took on this task, as they achieved the greatest victory in the nineteenth century, when the city of Rosetta defeated the army of the great empire. This research deals with the methodology of studying the...
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Micro-propagation is a promising and effective technique for propagation of healthy virus-free potato tubers. This study aimed to produce potato mini-and micro-tubers using micro-propagation and in vitro tuberization for two potato varieties, Lady Rosetta and Spunta. Six Combinations and concentrations of benzyl aminopurine (BAP), kinetin, and indo...
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The integration of information technology (IT) in foreign language education has transformed traditional methodologies, yet challenges persist in optimising their application. Despite the proliferation of IT tools, existing research often focuses on individual platforms without providing an analysis of their specific impacts across different learni...
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In order to explore the feasibility of the new rodenticide of type D Botulinum toxin to prevent and control the population density of pests in farmland from a molecular perspective. This study aimed to analyze the feasibility of D-type botulinum toxin for the control of urban rodents from a molecular perspective, and to detect the cleavage effect o...
Article
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Context . Highly unsaturated carbon chains, including polyynes, have been detected in many astronomical regions and planetary systems. With the success of the QUIJOTE survey of the Taurus Molecular Cloud-1 (TMC-1), the community has seen a “boom” in the number of detected carbon chains. On the other hand, the Rosetta mission revealed the release of...
Article
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The recent remarkable visit of the European Space Agency’s mission to the comet 67P/Chuyumov-Gerasimenko(hereafter 67P/C-G) by the Rosetta spacecraft see Altwegg et al. (2014) returned new important data regardingthe origin of the water on Earth. The experimental data showed very clearly that the water found in the comethad a quite different ratio...
Article
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Potato (Solanum tubersosum L.) is the fourth largest food crop worldwide and is rich source of minerals, essential amino acids, vitamins, and other bioactive compounds. The present study was conducted to optimize extraction conditions for achieving maximum yield of TPC, TFC, and antioxidant potential from ethanolic extracts of tubers, whole plant p...
Article
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PEGylated liposomes can deliver anti‐cancer drugs to brain tumors, and achieve enhanced permeability and retention effects. Triggering receptor expressed on myeloid cells 2 (TREM2) is an excellent biomarker for precise therapy of glioma. The present study is aimed at designing PEGylated nanoliposomal doxorubicin (PLD) conjugated with peptides targe...
Article
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During the last three decades, an annual proliferation in the levels of heavy metals was detected in the River Nile due to sewage, industrial and agricultural wastewater discharged into the river waters. Thus, the current study was set with the aim of investigating the possible health risks associated with water use and the consumption of Oreoc...
Preprint
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Amino acid insertions and deletions (indels) are among the most common protein mutations and necessitate changes to a protein's backbone geometry. Examining how indels affect protein folding stability (and especially how indels can increase stability) can help reveal the role of backbone energetics on stability and introduce new protein engineering...
Preprint
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With the increasing complexity of modern software and the demand for high performance, energy consumption has become a critical factor for developers and researchers. While much of the research community is focused on evaluating the energy consumption of machine learning and artificial intelligence systems -- often implemented in Python -- there is...
Article
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Antibody repurposing is the process of changing a known antibody so that it binds to a mutated antigen. One of the findings to emerge from the Coronavirus Disease 2019 (COVID-19) pandemic was that it was possible to repurpose neutralizing antibodies for Severe Acute Respiratory Syndrome, a related disease, to work for COVID-19. Thus, antibody repur...
Article
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AKR1D1, a key enzyme in the aldo-keto reductase superfamily, plays a dual role in both steroid metabolism and bile acid synthesis by catalyzing the NADPH-dependent reduction of carbon-carbon double bonds, specifically converting 3-ketosteroid hormones into 5β-steroids. Positioned at the critical intersection of steroid hormone and bile acid metabol...
Article
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L'intégration de l'Intelligence Artificielle (IA) dans l'apprentissage et l'enseignement de la langue française a transformé les méthodologies traditionnelles de l'éducation linguistique. Cette étude passe en revue la littérature récente pour explorer l'impact de l'IA sur l'éducation en langue française. Les plateformes alimentées par l'IA telles q...
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Protein structure prediction from amino acid sequences has long been a fun- damental challenge in computational biology. Accurate protein structures are essential for understanding biological functions, designing drugs, and solving complex biological problems. Traditionally, experimental techniques like X-ray crystallography and cryo-electron micro...
Preprint
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As the global population ages, the prevalence of neurodegenerative disorders is fast increasing. This neurodegeneration as well as other CNS injuries cause permanent disabilities. Thus, generation of new neurons is the rosetta stone in contemporary neuroscience.Glial cells support central nervous system (CNS) homeostasis through evolutionary conser...
Preprint
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While large language models, such as GPT and BERT, have already demonstrated unprecedented skills in everything from natural language processing to domain-specific applications, there came an unexplored phenomenon we term the Rosetta Paradox. The Rosetta Paradox characterizes the counterintuitive performance inversions across domains of knowledge....
Preprint
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This paper investigates the impact of incorporating structural information into the protein-protein interaction predictions made by ESM3, a multimodal protein language model (pLM). We utilized various structural variants as inputs and compared three widely used structure acquisition pipelines: EvoEF2, Gromacs, and Rosetta Relax, to assess their eff...
Article
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Starch content is one of the major quality criteria targeted by potato breeding programs. Traditional potato breeding is a laborious duty due to the tetraploid nature and immense heterozy-gosity of potato genomes. In addition, screening for functional genetic variations in wild relatives is slow and strenuous. Moreover, genetic diversity, which is...
Article
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Legionella pneumophila is an environmentally acquired pathogen that causes respiratory disease in humans. While the discovery of L. pneumophila is relatively recent compared to other bacterial pathogens, over the past 50 years, L. pneumophila has emerged as a powerhouse for studying host-pathogen interactions. In its natural habitat of fresh water,...
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This study examines the perceptions and experiences of law and humanities students at the multidisciplinary faculty of Taza, Sidi Mohamed Ben Abdellah University, regarding English for Specific Purposes (ESP) education in Morocco. Using a mixed-methods approach, quantitative data from a survey of 130 students is complemented by qualitative insights...
Preprint
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Several deep learning-based tools for RNA 3D structure prediction have recently emerged, including DRfold, DeepFoldRNA, RhoFold, RoseTTAFoldNA, trRosettaRNA, and AlphaFold3. In this study, we systematically evaluate these six models on three datasets: RNA Puzzles, CASP15 RNA targets, and a newly generated large dataset of sequentially distinct RNAs...
Article
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Comet 67P/Churyumov–Gerasimenko (hereafter 67P) was the primary target of ESA’s Rosetta mission. Hyperspectral images acquired by the Mapping channel of the Visible and InfraRed Thermal Imaging Spectrometer aboard Rosetta can be used to derive physical and compositional surface properties by detailed spectrophotometric analyses. This calls for a pr...
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The use of Arabic language learning applications in the digital age has brought a significant change in the way the language is learned. The Arabic language plays an important role in diplomacy, economics, international relations, and religion, making it crucial to master. Digital technology, through applications like Duolingo, Rosetta Stone, and M...
Preprint
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Computational protein design is becoming increasingly helpful in the development of new protein therapeutics with enhanced efficacy, specificity, and minimal side effects, for precise modulation of biological pathways. In vascular biology, the interaction between vascular endothelial growth factor A (VEGFA) and its receptors (VEGFR1-R3) is a pivota...
Article
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Engineering nonribosomal peptide synthetases (NRPSs) has been a “holy grail” in synthetic biology due to their modular nature and limited understanding of catalytic mechanisms. Here, we reported a computational redesign of the “gate-keeper” adenylation domain of the model NRPS-like enzyme carboxylic acid reductases (CARs) by using approximate mecha...
Preprint
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The transition from x86 to ARM architecture is becoming increasingly common across various domains, primarily driven by ARM's energy efficiency and improved performance across traditional sectors. However, this ISA shift poses significant challenges, mainly due to the extensive legacy ecosystem of x86 software and lack of portability across proprie...
Article
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Humanity’s "own goal" as a consequence of strategic paralysis Insights via AI from biological cell cleavage into comprehension and communication Embodiment of insight beyond capacity for verbal articulation From 5-fold to 8-fold and 16-fold patterns -- and beyond Cognitive insights from 24-fold organization of music Transformational implications of...
Preprint
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European Space Agency's Rosetta mission is the only space mission that performed long-term monitoring of comet at close distances. Its over two years' rendezvous with comet 67P/Churyumov-Gerasimenko revealed diverse evolutionary processes of the cometary nucleus. One of the most striking events is the migration of a 30-m boulder in the southern hem...
Conference Paper
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The MOHID SOIL TOOL (MST) is a software developed to integrate EMBRAPA soil texture data with Rosetta model input parameters, aimed at enhancing the accuracy of hydrological simulations. This tool, programmed in Python 3 with a graphical interface compatible with Windows 10/11 x64 operating systems, automates the process of importing, processing, a...
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Erythropoietin (Epo), a glycosylated protein categorized as a member of the cytokine family, is responsible for the modulation of erythrogenesis. Besides this, the nonhaematopoietic effects of Epo are associated with tissue-protective activity via an antiapoptotic pathway. This function of Epo is linked with its heterodimeric form, i.e. EpoR/βcR be...
Preprint
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Methodological improvements in cryo-electron microscopy (cryoEM) have made it a useful tool in ligand-bound structure determination for biology and drug design. However, determining the conformation and identity of bound ligands is still challenging at the resolutions typical for cry-oEM. Automated methods can aid in ligand conformational modeling,...
Article
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Introduction. The importance of noroviruses in human infectious pathology and the danger of large epidemic outbreaks in organized groups determine the need to develop means of specific prevention of infection. The aim of the study was to obtain recombinant norovirus VP1 protein and analyze its immunogenic and antigenic properties . Materials and me...
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Gelsolin is an actin-binding protein that is competitively bound by lysophosphatidic acid (LPA), a possible biomarker for the early detection of ovarian cancer. Our group has previously shown the usage of gelsolin 1-3 (a fragment of gelsolin composed of the first three of its six subdomains) along with actin to detect the presence of lysophosphatid...
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Technological progress related to astronomical observatories such as the recently launched James Webb Space Telescope (JWST) allows searching for signs of life beyond our solar system, namely, in the form of unambiguous biosignature gases in exoplanetary atmospheres. The tentative assignment of a 1 σ –2.4 σ spectral feature observed with JWST in th...
Article
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Cometary comae are a mixture of gas and ice-covered dust. Processing on the surface and in the coma change the composition of ice on dust grains relative to that of the nucleus. As the ice on dust grains sublimates, the local coma composition changes. Rosetta observations of 67P/Churyumov-Gerasimenko previously reported one of the highest D/H value...
Preprint
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Science frequently benefits from teams of interdisciplinary researchers. However, most scientists don't have access to experts from multiple fields. Fortunately, large language models (LLMs) have recently shown an impressive ability to aid researchers across diverse domains by answering scientific questions. Here, we expand the capabilities of LLMs...
Article
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We examine the role of refractory organics as a major C carrier in the outer protosolar nebula and its implications for the compositions of large Kuiper Belt objects (KBOs) and CI chondrites. By utilizing Rosetta measurements of refractory organics in comet 67P/Churyumov–Gerasimenko, we show that they would make up a large fraction of the protosola...
Article
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Understanding the structures of noncoding RNAs (ncRNAs) is important for the development of RNA-based therapeutics. There are inherent challenges in employing current experimental techniques to determine the tertiary (3D) structures of RNAs with high complexity and flexibility in folding, which makes computational methods indispensable. In this stu...
Article
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The hygiene hypothesis suggests that reduced exposure to infectious agents during early childhood impairs immune development, favoring a Th2-dominant profile and increasing allergy risks, particularly in high-income countries. Helminth infections, like allergies, induce Th2 responses with CD4+ T cells producing IL-4 and IL-5. However, helminths als...
Article
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Shistosoma mansoni parasite has a complex life cycle and the host infection occurs by the active penetration of cercariae through the skin. This penetration process starts a several immune mechanisms which are different between individual who has been infected for the first time and individual who had previous contact with the parasite antigens. Am...
Conference Paper
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Background In research hospitals or academic centers, patients are actively engaged to participate in research. However, 80% of cancer patients are not treated in these institutions. This ‘invisible’ majority is under-represented in genomic research,¹ leading to bias in the therapeutic pipeline since such research genomic data are the foundation in...
Article
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Fourfold patterns of contrasting cognitive modalities Distinctive game roles with both cognitive and strategic implications Traditional articulated arrays with cognitive and strategic implications Knight-like gambit exemplifying creation or destruction Perception of Swastika variants as the epitome of polarization Representing the surprising transi...
Presentation
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After a brief motivation, I clarify some key concepts and terms, including 'RDF', 'triple', 'semantic graph', 'ontology', 'knowledge graph', and 'reasoning', before giving a short analysis of what I believe are currently the main challenges (i.e., limited cognitive interoperability) and barriers (i.e., semantic parsing burden) that prevent semantic...