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https://www.readbyqxmd.com/read/27919732/learning-from-heterogeneous-temporal-data-in-electronic-health-records
#1
Jing Zhao, Panagiotis Papapetrou, Lars Asker, Henrik Boström
Electronic health records contain large amounts of longitudinal data that are valuable for biomedical informatics research. The application of machine learning is a promising alternative to manual analysis of such data. However, the complex structure of the data, which includes clinical events that are unevenly distributed over time, poses a challenge for standard learning algorithms. Some approaches to modeling temporal data rely on extracting single values from time series; however, this leads to the loss of potentially valuable sequential information...
December 2, 2016: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/27919219/ston-exploring-biological-pathways-using-the-sbgn-standard-and-graph-databases
#2
Vasundra Touré, Alexander Mazein, Dagmar Waltemath, Irina Balaur, Mansoor Saqi, Ron Henkel, Johann Pellet, Charles Auffray
BACKGROUND: When modeling in Systems Biology and Systems Medicine, the data is often extensive, complex and heterogeneous. Graphs are a natural way of representing biological networks. Graph databases enable efficient storage and processing of the encoded biological relationships. They furthermore support queries on the structure of biological networks. RESULTS: We present the Java-based framework STON (SBGN TO Neo4j). STON imports and translates metabolic, signalling and gene regulatory pathways represented in the Systems Biology Graphical Notation into a graph-oriented format compatible with the Neo4j graph database...
December 5, 2016: BMC Bioinformatics
https://www.readbyqxmd.com/read/27917534/a-concept-analysis-of-compassionate-midwifery
#3
Diane Ménage, Elizabeth Bailey, Susan Lees, Jane Coad
AIM: To report a concept analysis of compassionate midwifery. BACKGROUND: Recently, compassion has been incorporated into United Kingdom nursing and midwifery language through strategy, policy, recruitment and education. Professional standards direct midwives to practise compassionately therefore the concept of compassionate midwifery exists, although this has yet to be explored as a concept in the UK or internationally. An understanding of what constitutes compassionate midwifery has the potential to increase midwifery knowledge and improve practice...
November 16, 2016: Journal of Advanced Nursing
https://www.readbyqxmd.com/read/27917139/the-source-of-the-symbolic-numerical-distance-and-size-effects
#4
Attila Krajcsi, Gábor Lengyel, Petia Kojouharova
Human number understanding is thought to rely on the analog number system (ANS), working according to Weber's law. We propose an alternative account, suggesting that symbolic mathematical knowledge is based on a discrete semantic system (DSS), a representation that stores values in a semantic network, similar to the mental lexicon or to a conceptual network. Here, focusing on the phenomena of numerical distance and size effects in comparison tasks, first we discuss how a DSS model could explain these numerical effects...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27917138/neural-elements-for-predictive-coding
#5
REVIEW
Stewart Shipp
Predictive coding theories of sensory brain function interpret the hierarchical construction of the cerebral cortex as a Bayesian, generative model capable of predicting the sensory data consistent with any given percept. Predictions are fed backward in the hierarchy and reciprocated by prediction error in the forward direction, acting to modify the representation of the outside world at increasing levels of abstraction, and so to optimize the nature of perception over a series of iterations. This accounts for many 'illusory' instances of perception where what is seen (heard, etc...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27916672/famous-faces-and-voices-differential-profiles-in-early-right-and-left-semantic-dementia-and-in-alzheimer-s-disease
#6
Simona Luzzi, Sara Baldinelli, Valentina Ranaldi, Katia Fabi, Viviana Cafazzo, Fabio Fringuelli, Mauro Silvestrini, Leandro Provinciali, Carlo Reverberi, Guido Gainotti
BACKGROUND: Famous face and voice recognition is reported to be impaired both in semantic dementia (SD) and in Alzheimer's Disease (AD), although more severely in the former. In AD a coexistence of perceptual impairment in face and voice processing has also been reported and this could contribute to the altered performance in complex semantic tasks. On the other hand, in SD both face and voice recognition disorders could be related to the prevalence of atrophy in the right temporal lobe (RTL)...
December 1, 2016: Neuropsychologia
https://www.readbyqxmd.com/read/27914371/kirchhoff-scattering-from-non-penetrable-targets-modeled-as-an-assembly-of-triangular-facets
#7
Ahmad T Abawi
Frequency and time domain solutions for the scattering of acoustic waves from an arbitrarily shaped target using the Kirchhoff approximation are developed. In this method, the scattering amplitude is analytically evaluated on a single triangle and scattering from a triangularly facetted target is computed by coherently summing the contributions from all the triangles that make up its surface. In the frequency domain, the solution is expressed in terms of regular (non-singular) functions, which only require the knowledge of the directions of the incident and scattered fields, the edge vectors for the triangles and position vectors to one of their vertices...
September 2016: Journal of the Acoustical Society of America
https://www.readbyqxmd.com/read/27914058/osprey-predicts-resistance-mutations-using-positive-and-negative-computational-protein-design
#8
Adegoke Ojewole, Anna Lowegard, Pablo Gainza, Stephanie M Reeve, Ivelin Georgiev, Amy C Anderson, Bruce R Donald
Drug resistance in protein targets is an increasingly common phenomenon that reduces the efficacy of both existing and new antibiotics. However, knowledge of future resistance mutations during pre-clinical phases of drug development would enable the design of novel antibiotics that are robust against not only known resistant mutants, but also against those that have not yet been clinically observed. Computational structure-based protein design (CSPD) is a transformative field that enables the prediction of protein sequences with desired biochemical properties such as binding affinity and specificity to a target...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27913588/action-categories-in-lateral-occipitotemporal-cortex-are-organized-along-sociality-and-transitivity
#9
Moritz F Wurm, Alfonso Caramazza, Angelika Lingnau
: How neural specificity for distinct conceptual knowledge categories arises is central for understanding the organization of semantic memory in the human brain. While there is a large body of research on the neural processing of distinct object categories, the organization of action categories remains largely unknown. In particular, it is unknown if different action categories follow a specific topographical organization on the cortical surface, analogously to the category-specific organization of object knowledge...
December 2, 2016: Journal of Neuroscience: the Official Journal of the Society for Neuroscience
https://www.readbyqxmd.com/read/27911184/clinical-practice-in-portuguese-sexology
#10
Violeta Alarcão, Sofia Ribeiro, Joana Almeida, Alain Giami
Few studies explore the clinicians' knowledge, attitudes and practices regarding sexuality, despite their role in the sexual health socialization process. This study focuses on Portuguese sexologists engaged into clinical practice. It aims to characterize sexologists' sex education and training and their clinical practices, including diagnostic and therapeutic approaches. This research followed the methodology of a survey undertaken in France as a part of the Euro-Sexo study. From the 91 obtained questionnaires, 51 (56%) were active in clinical practice...
December 2, 2016: Journal of Sex & Marital Therapy
https://www.readbyqxmd.com/read/27899726/a-taxonomic-analysis-of-abstraction
#11
Stephen K Reed
An important characteristic of knowledge is that it exists at multiple levels of abstraction. This article illustrates how different levels of abstraction influence perception, comprehension, categorization, memory, and thought. Theories exist for how abstraction influences each of these cognitive processes, but there are few unifying principles for discussing these theories within a common conceptual framework. My proposed taxonomy examines three senses of abstraction: (a) an abstract entity is a concept that has no material referent, (b) abstraction focuses on only some attributes of multicomponent stimuli, and (c) an abstract idea applies to many particular instances of a category...
November 2016: Perspectives on Psychological Science: a Journal of the Association for Psychological Science
https://www.readbyqxmd.com/read/27897385/reconstruction-of-biological-pathways-and-metabolic-networks-from-in-silico-labeled-metabolites
#12
Noushin Hadadi, Jasmin Hafner, Keng Cher Soh, Vassily Hatzimanikatis
Reaction atom mappings track the positional changes of all of the atoms between the substrates and the products as they undergo the biochemical transformation. However, information on atom transitions in the context of metabolic pathways is not widely available in the literature. The understanding of metabolic pathways at the atomic level is of great importance as it can deconvolute the overlapping catabolic/anabolic pathways resulting in the observed metabolic phenotype. The automated identification of atom transitions within a metabolic network is a very challenging task since the degree of complexity of metabolic networks dramatically increases when we transit from metabolite-level studies to atom-level studies...
November 29, 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/27895608/genetic-consideration-of-schizotypal-traits-a-review
#13
REVIEW
Emma E Walter, Francesca Fernandez, Mollie Snelling, Emma Barkus
Schizotypal traits are of interest and importance in their own right and also have theoretical and clinical associations with schizophrenia. These traits comprise attenuated psychotic symptoms, social withdrawal, reduced cognitive capacity, and affective dysregulation. The link between schizotypal traits and psychotic disorders has long since been debated. The status of knowledge at this point is such schizotypal traits are a risk for psychotic disorders, but in and of themselves only confer liability, with other risk factors needing to be present before a transition to psychosis occurs...
2016: Frontiers in Psychology
https://www.readbyqxmd.com/read/27895239/making-space-for-spatial-proportions
#14
Percival G Matthews, Edward M Hubbard
The three target articles presented in this special issue converged on an emerging theme: the importance of spatial proportional reasoning. They suggest that the ability to map between symbolic fractions (like 1/5) and nonsymbolic, spatial representations of their sizes or magnitudes may be especially important for building robust fractions knowledge. In this commentary, we first reflect upon where these findings stand in a larger theoretical context, largely borrowed from mathematics education research. Next, we emphasize parallels between this work and emerging work suggesting that nonsymbolic proportional reasoning may provide an intuitive foundation for understanding fraction magnitudes...
November 28, 2016: Journal of Learning Disabilities
https://www.readbyqxmd.com/read/27894676/a-multiscale-biomechanical-model-of-platelets-correlating-with-in-vitro-results
#15
Peng Zhang, Li Zhang, Marvin J Slepian, Yuefan Deng, Danny Bluestein
Using dissipative particle dynamics (DPD) combined with coarse grained molecular dynamics (CGMD) approaches, we developed a multiscale deformable platelet model to accurately describe the molecular-scale intra-platelet constituents and biomechanical properties of platelets in blood flow. Our model includes the platelet bilayer membrane, cytoplasm and an elaborate elastic cytoskeleton. Correlating numerical simulations with published in-vitro experiments, we validated the biorheology of the cytoplasm, the elastic response of membrane to external stresses, and the stiffness of the cytoskeleton actin filaments, resulting in an accurate representation of the molecular-level biomechanical microstructures of platelets...
November 11, 2016: Journal of Biomechanics
https://www.readbyqxmd.com/read/27893252/developing-knowledge-of-nonadjacent-dependencies
#16
Jennifer Culbertson, Elena Koulaguina, Nayeli Gonzalez-Gomez, Géraldine Legendre, Thierry Nazzi
Characterizing the nature of linguistic representations and how they emerge during early development is a central goal in the cognitive science of language. One area in which this development plays out is in the acquisition of dependencies-relationships between co-occurring elements in a word, phrase, or sentence. These dependencies often involve multiple levels of representation and abstraction, built up as infants gain experience with their native language. The authors used the Headturn Preference Procedure to systematically investigate the early acquisition of 1 such dependency, the agreement between a subject and verb in French, at 6 different ages between 14 and 24 months...
December 2016: Developmental Psychology
https://www.readbyqxmd.com/read/27891647/a-roadmap-for-improving-the-representation-of-photosynthesis-in-earth-system-models
#17
Alistair Rogers, Belinda E Medlyn, Jeffrey S Dukes, Gordon Bonan, Susanne von Caemmerer, Michael C Dietze, Jens Kattge, Andrew D B Leakey, Lina M Mercado, Ülo Niinemets, I Colin Prentice, Shawn P Serbin, Stephen Sitch, Danielle A Way, Sönke Zaehle
Accurate representation of photosynthesis in terrestrial biosphere models (TBMs) is essential for robust projections of global change. However, current representations vary markedly between TBMs, contributing uncertainty to projections of global carbon fluxes. Here we compared the representation of photosynthesis in seven TBMs by examining leaf and canopy level responses of photosynthetic CO2 assimilation (A) to key environmental variables: light, temperature, CO2 concentration, vapor pressure deficit and soil water content...
January 2017: New Phytologist
https://www.readbyqxmd.com/read/27888690/exploring-socioeconomic-differences-in-syntactic-development-through-the-lens-of-real-time-processing
#18
Yi Ting Huang, Kathryn Leech, Meredith L Rowe
Differences in caregiver input across socioeconomic status (SES) predict syntactic development, but the mechanisms are not well understood. Input effects may reflect the exposure needed to acquire syntactic representations during learning (e.g., does the child have the relevant structures for passive sentences?) or access this knowledge during communication (e.g., can she use the past participle to infer the meaning of passives?). Using an eye-tracking and act-out paradigm, the current study distinguishes these mechanisms by comparing the interpretation of actives and passives in 3- to 7-year-olds (n=129) from varying SES backgrounds...
November 23, 2016: Cognition
https://www.readbyqxmd.com/read/27883928/graduate-entry-nurses-initial-perspectives-on-nursing-content-analysis-of-open-ended-survey-questions
#19
Lisa McKenna, Ingrid Brooks, Rebecca Vanderheide
BACKGROUND: Graduate entry nursing courses offer individuals with prior degrees the opportunity to gain nursing qualifications and facilitate career change. While it is known that accelerated graduate entry courses are increasingly popular, the perceptions of nursing held by such individuals and the influence this has on those seeking to enter the profession are less clearly understood. OBJECTIVE: To explore graduate entry nursing students' perceptions of nursing on entering their pre-registration course...
November 12, 2016: Nurse Education Today
https://www.readbyqxmd.com/read/27878082/predicted-rarity-weighted-richness-a-new-tool-to-prioritize-sites-for-species-representation
#20
Fábio Albuquerque, Paul Beier
Lack of biodiversity data is a major impediment to prioritizing sites for species representation. Because comprehensive species data are not available in any planning area, planners often use surrogates (such as vegetation communities, or mapped occurrences of a well-inventoried taxon) to prioritize sites. We propose and demonstrate the effectiveness of predicted rarity-weighted richness (PRWR) as a surrogate in situations where species inventories may be available for a portion of the planning area. Use of PRWR as a surrogate involves several steps...
November 2016: Ecology and Evolution
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