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Knowledge representation

Sarah E Donohue, Mandy V Bartsch, Hans-Jochen Heinze, Mircea A Schoenfeld, Jens-Max Hopf
In visual search, the more one knows about a target, the faster one can find it. Surprisingly, target identification is also faster with knowledge about distractor-features. The latter is paradoxical, as it implies that to avoid the selection of an item, the item must somehow be selected to some degree. This conundrum has been termed the 'ignoring paradox,' and, to date, little is known about how the brain resolves it. Here, in data from four experiments using neuromagnetic brain recordings in male and female humans, we provide evidence that this paradox is resolved by giving distracting information priority in cortical processing...
April 24, 2018: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
Chao Zhao, Jingchi Jiang, Yi Guan, Xitong Guo, Bin He
OBJECTIVE: Electronic medical records (EMRs) contain medical knowledge that can be used for clinical decision support (CDS). Our objective is to develop a general system that can extract and represent knowledge contained in EMRs to support three CDS tasks-test recommendation, initial diagnosis, and treatment plan recommendation-given the condition of a patient. METHODS: We extracted four kinds of medical entities from records and constructed an EMR-based medical knowledge network (EMKN), in which nodes are entities and edges reflect their co-occurrence in a record...
April 22, 2018: Artificial Intelligence in Medicine
Na'Taki Osborne Jelks, Timothy L Hawthorne, Dajun Dai, Christina H Fuller, Christine Stauber
We utilized a participatory mapping approach to collect point locations, photographs, and descriptive data about select built environment stressors identified and prioritized by community residents living in the Proctor Creek Watershed, a degraded, urban watershed in Northwest Atlanta, Georgia. Residents (watershed researchers) used an indicator identification framework to select three watershed stressors that influence urban livability: standing water, illegal dumping on land and in surface water, and faulty stormwater infrastructure...
April 22, 2018: International Journal of Environmental Research and Public Health
Randi Vita, James A Overton, Christopher J Mungall, Alessandro Sette, Bjoern Peters
The Immune Epitope Database (IEDB), at, has the mission to make published experimental data relating to the recognition of immune epitopes easily available to the scientific public. By presenting curated data in a searchable database, we have liberated it from the tables and figures of journal articles, making it more accessible and usable by immunologists. Recently, the principles of Findability, Accessibility, Interoperability and Reusability have been formulated as goals that data repositories should meet to enhance the usefulness of their data holdings...
January 1, 2018: Database: the Journal of Biological Databases and Curation
Marek Ostaszewski, Stephan Gebel, Inna Kuperstein, Alexander Mazein, Andrei Zinovyev, Ugur Dogrusoz, Jan Hasenauer, Ronan M T Fleming, Nicolas Le Novère, Piotr Gawron, Thomas Ligon, Anna Niarakis, David Nickerson, Daniel Weindl, Rudi Balling, Emmanuel Barillot, Charles Auffray, Reinhard Schneider
The Disease Maps Project builds on a network of scientific and clinical groups that exchange best practices, share information and develop systems biomedicine tools. The project aims for an integrated, highly curated and user-friendly platform for disease-related knowledge. The primary focus of disease maps is on interconnected signaling, metabolic and gene regulatory network pathways represented in standard formats. The involvement of domain experts ensures that the key disease hallmarks are covered and relevant, up-to-date knowledge is adequately represented...
April 23, 2018: Briefings in Bioinformatics
Zheng Li, Noushin Omidvar, Wei Shan Chin, Esther Robb, Amanda J Morris, Luke E K Achenie, Hongliang Xin
Molecular functionalization of porphyrins opens countless new opportunities in tailoring their physicochemical properties for light-harvesting applications. However, the immense materials space spanned by a vast number of substituent ligands and chelating metal ions prohibits high-throughput screening of combinatorial libraries. In this work, machine learning algorithms equipped with the domain knowledge of chemical graph theory were employed for predicting the energy gaps of >12000 porphyrins from the Computational Materials Repository...
April 24, 2018: Journal of Physical Chemistry. A
Teresa Schubert, Caroline Reilhac, Michael McCloskey
How are reading and writing related? In this study, we address the relationship between letter identification and letter production, uncovering a link in which production information can be used to identify letters presented dynamically. By testing an individual with a deficit in letter identification, we identified a benefit which would be masked by ceiling effects in unimpaired readers. In Experiment 1 we found that letter stimuli defined by the direction of dot motion (tiny dots within letter move leftward, background dots move rightward) provided no advantage over static letters...
March 30, 2018: Cortex; a Journal Devoted to the Study of the Nervous System and Behavior
L Gwilliams, A Marantz
The field of psycho- and neuro-linguistics has long-debated the decompositional model of visual word processing: Are written words processed via the visual forms of stem and affix morphemes, or as complex wholes? Although many have now settled upon a decompositional view, it is unclear what heuristic the brain uses to generate these visual morpheme-forms in the first place. Here we conduct a magneto-encephalography study to test two hypotheses for how this may be done: i) the brain encodes representations of the morphemes that follow the morpho-syntactic rules governing constituents: A stem morpheme will be represented if the word obeys the grammatical behaviour associated with its suffix; ii) the brain only encodes stem morphemes that occur with multiple suffixes or as words in isolation...
April 20, 2018: Neuropsychologia
Mansoor Saqi, Artem Lysenko, Yi-Ke Guo, Tatsuhiko Tsunoda, Charles Auffray
Large amounts of data emerging from experiments in molecular medicine are leading to the identification of molecular signatures associated with disease subtypes. The contextualization of these patterns is important for obtaining mechanistic insight into the aberrant processes associated with a disease, and this typically involves the integration of multiple heterogeneous types of data. In this review, we discuss knowledge representations that can be useful to explore the biological context of molecular signatures, in particular three main approaches, namely, pathway mapping approaches, molecular network centric approaches and approaches that represent biological statements as knowledge graphs...
April 19, 2018: Briefings in Bioinformatics
Jenny Roth, Melanie C Steffens, Vivian L Vignoles
The present article introduces a model based on cognitive consistency principles to predict how new identities become integrated into the self-concept, with consequences for intergroup attitudes. The model specifies four concepts (self-concept, stereotypes, identification, and group compatibility) as associative connections. The model builds on two cognitive principles, balance-congruity and imbalance-dissonance, to predict identification with social groups that people currently belong to, belonged to in the past, or newly belong to...
2018: Frontiers in Psychology
Angela Thompson, Gina Bertocci, Craig Smalley
BACKGROUND: Femur fractures are a common orthopedic injury in young children. Falls account for a large portion of accidental femur fractures in young children, but there is also a high prevalence of femur fractures in child abuse, with falls often provided as false histories. Objective information regarding fracture potential in short distance fall scenarios may aid in assessing whether a child's injuries are the result of abuse or an accidental fall. Knowledge of femur loading is the first step towards understanding likelihood of fracture in a fall...
March 31, 2018: Journal of Forensic and Legal Medicine
Sujin Kim, Donghee Sinn, Sue Yeon Syn
BACKGROUND: With abundant personal health information at hand, individuals are faced with a critical challenge in evaluating the informational value of health care records to keep useful information and discard that which is determined useless. Young, healthy college students who were previously dependents of adult parents or caregivers are less likely to be concerned with disease management. Personal health information management (PHIM) is a special case of personal information management (PIM) that is associated with multiple interactions among varying stakeholders and systems...
April 20, 2018: Journal of Medical Internet Research
Matthias Ganzinger, Matthias Gietzelt, Christian Karmen, Blanca Flores, Petra Knaup
Systems medicine is a paradigm for translating in silico methods developed for modelling biological systems into the field of medicine. Such approaches rely on the integration of as many data sources as possible, both in the dimension of disease knowledge and patient data. This is a challenging task that can only be implemented in clinical routine with the help of suitable information technology from the field of Medical Informatics. For the research project "Clinically-applicable, omics-based assessment of survival, side effects, and targets in multiple myeloma" (CLIOMMICS) we developed a prototypical systems medicine application system...
2018: Studies in Health Technology and Informatics
Jose Antonio Miñarro-Giménez, Stefan Schulz
Organised repositories of published scientific literature represent a rich source for research in knowledge representation. MEDLINE, one of the largest and most popular biomedical literature databases, provides metadata for over 24 million articles each of which is indexed using the MeSH controlled vocabulary. In order to reuse MeSH annotations for knowledge construction, we processed this data and extracted the most relevant patterns of assigned descriptors over time. The patterns consist of UMLS semantic groups related to the MeSH headings together with their associated MeSH subheadings...
2018: Studies in Health Technology and Informatics
Keyuan Jiang, Tingyu Chen, Liyuan Huang, Ricardo A Calix, Gordon R Bernard
Twitter, as a microblogging social media platform, has seen increasing applications of its data for pharmacovigilance which is to monitor and promote safe uses of pharmaceutical products. Medication names are typically used as keywords to query social media data. It is known that medication names are misspelled on social media, and finding the misspellings is challenging because there exists no a priori knowledge as to how people would misspell a medication name. We developed a data-driven, relational similarity-based approach to discover misspellings of medication names...
2018: Studies in Health Technology and Informatics
Dominika Radziun, H Henrik Ehrsson
Short-term visual deprivation by blindfolding influences tactile acuity and orientation in space and, on a neural level, leads to enhanced excitability of visual and motor cortices. However, to the best of our knowledge, the possible effects of short-term visual deprivation on body representation have not been examined. In the present study, we tested two groups of 30 healthy participants with the somatic rubber hand illusion, a well-established paradigm to probe the dynamic plasticity of body representation...
April 19, 2018: Scientific Reports
Matthew J Crossley, W Todd Maddox, F Gregory Ashby
Interventions for drug abuse and other maladaptive habitual behaviors may yield temporary success but are often fragile and relapse is common. This implies that current interventions do not erase or substantially modify the representations that support the underlying addictive behavior-that is, they do not cause true unlearning. One example of an intervention that fails to induce true unlearning comes from Crossley, Ashby, and Maddox (2013, Journal of Experimental Psychology: General), who reported that a sudden shift to random feedback did not cause unlearning of category knowledge obtained through procedural systems, and they also reported results suggesting that this failure is because random feedback is noncontingent on behavior...
April 19, 2018: Journal of Experimental Psychology. Learning, Memory, and Cognition
Elena Solovieva, Toshihide Shikanai, Noriaki Fujita, Hisashi Narimatsu
BACKGROUND: Inherited mutations in glyco-related genes can affect the biosynthesis and degradation of glycans and result in severe genetic diseases and disorders. The Glyco-Disease Genes Database (GDGDB), which provides information about these diseases and disorders as well as their causative genes, has been developed by the Research Center for Medical Glycoscience (RCMG) and released in April 2010. GDGDB currently provides information on about 80 genetic diseases and disorders caused by single-gene mutations in glyco-related genes...
April 18, 2018: Journal of Biomedical Semantics
Paul Hoffman
Effective use of semantic knowledge requires a set of conceptual representations and control processes which ensure that currently relevant aspects of this knowledge are retrieved and selected. It is well-established that levels of semantic knowledge increase across the lifespan. However, the effects of ageing on semantic control processes have not been assessed. I addressed this issue by comparing the performance profiles of young and older people on a verbal comprehension test. Two sets of variables were used to predict accuracy and RT in each group: (1) the psycholinguistic properties of words probed in each trial and (2) the performance on each trial by two groups of semantically impaired neuropsychological patients...
April 17, 2018: Journal of Neuropsychology
Vasiliki Lygirou, Agnieszka Latosinska, Manousos Makridakis, William Mullen, Christian Delles, Joost P Schanstra, Jerome Zoidakis, Burkert Pieske, Harald Mischak, Antonia Vlahou
BACKGROUND: Cardiovascular disease (CVD) describes the pathological conditions of the heart and blood vessels. Despite the large number of studies on CVD and its etiology, its key modulators remain largely unknown. To this end, we performed a comprehensive proteomic analysis of blood plasma, with the scope to identify disease-associated changes after placing them in the context of existing knowledge, and generate a well characterized dataset for further use in CVD multi-omics integrative analysis...
April 17, 2018: Journal of Translational Medicine
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