RNetCDF – A Package for Reading and Writing NetCDF Datasets

This paper describes the RNetCDF package (version 1.6), an interface for reading and writing files in Unidata NetCDF format, and gives an introduction to the NetCDF file format. NetCDF is a machine independent binary file format which allows storage of different types of array based data, along with short metadata descriptions. The package presented here allows access to the most important functions of the NetCDF C-interface for reading, writing, and modifying NetCDF datasets. In this paper, we present a short overview on the NetCDF file format and show usage examples of the package.

Left posterior parietal theta burst stimulation affects gestural imitation regardless of semantic content.

OBJECTIVE Neuro-imaging studies have suggested that the ability to imitate meaningless and meaningful gestures may differentially depend on superior (SPL) and inferior (IPL) parietal lobule. Therefore, we hypothesized that imaging-guided neuro-navigated continuous theta burst stimulation (cTBS) over left SPL mainly affects meaningless and over left IPL predominantly meaningful gestures. METHODS Twelve healthy subjects participated in this study. High resolution structural MRI was used for imaging guided neuro-navigation cTBS. Participants were targeted with one train of cTBS in three experimental sessions: sham stimulation over vertex and real cTBS over left SPL and IPL, respectively. An imitation task, including 24 meaningless and 24 meaningful gestures, was performed 'offline'. RESULTS cTBS over both left IPL and SPL significantly interfered with gestural imitation. There was no differential effect of SPL and IPL cTBS on gesture type (meaningless versus meaningful). CONCLUSIONS Our findings confirm that left posterior parietal cortex plays a predominant role in gestural imitation. However, the hypothesis based on the dual route model suggesting a differential role of SPL and IPL in the processing of meaningless and meaningful gestures could not be confirmed. SIGNIFICANCE Left SPL and IPL play a common role within the posterior-parietal network in gestural imitation regardless of semantic content.

Applying Fuzzy Ontologies to Implement the Social Semantic Web

Because the knowledge in the World Wide Web is continuously expanding, Web Knowledge Aggregation, Representation and Reasoning (abbreviated as KR) is becoming increasingly important. This article demonstrates how fuzzy ontologies can be used in KR to improve the interactions between humans and computers. The gap between the Social and Semantic Web can be reduced, and a Social Semantic Web may become possible. As an illustrative example, we demonstrate how fuzzy logic and KR can enhance technologies for cognitive cities. The underlying notion of these technologies is based on connectivism, which can be improved by incorporating the results of digital humanities research.

Patient information leaflets: informing or frightening? A focus group study exploring patients' emotional reactions and subsequent behavior towards package leaflets of commonly prescribed medications in family practices.

BACKGROUND The purpose of patient information leaflets (PILs) is to inform patients about the administration, precautions and potential side effects of their prescribed medication. Despite European Commission guidelines aiming at increasing readability and comprehension of PILs little is known about the potential risk information has on patients. This article explores patients' reactions and subsequent behavior towards risk information conveyed in PILs of commonly prescribed drugs by general practitioners (GPs) for the treatment of Type 2 diabetes, hypertension or hypercholesterolemia; the most frequent cause for consultations in family practices in Germany. METHODS We conducted six focus groups comprising 35 patients which were recruited in GP practices. Transcripts were read and coded for themes; categories were created by abstracting data and further refined into a coding framework. RESULTS Three interrelated categories are presented: (i) The vast amount of side effects and drug interactions commonly described in PILs provoke various emotional reactions in patients which (ii) lead to specific patient behavior of which (iii) consulting the GP for assistance is among the most common. Findings show that current description of potential risk information caused feelings of fear and anxiety in the reader resulting in undesirable behavioral reactions. CONCLUSIONS Future PILs need to convey potential risk information in a language that is less frightening while retaining the information content required to make informed decisions about the prescribed medication. Thus, during the production process greater emphasis needs to be placed on testing the degree of emotional arousal provoked in patients when reading risk information to allow them to undertake a benefit-risk-assessment of their medication that is based on rational rather than emotional (fearful) reactions.

Recent developments and open questions in the field of semantic roles

This introductory chapter briefly introduces a few milestones in the voluminous previous literature on semantic roles, and charts the territory in which the papers of this volume aim to make a contribution. This territory is characterized by fairly disparate conceptualizations of semantic roles and their status in theories of grammar and the lexicon, as well as by diverse and probably complementary ways of deriving or identifying them based on linguistic data. Particular attention is given to the question of how selected roles appear to relate to each other, and we preliminarily address the issue of how roles, subroles, and role complexes are best thought of in general.

Event-relating to potential dementia. Semantic processing in the course of healthy and pathological aging

While most healthy elderly are able to manage their everyday activities, studies showed that there are both stable and declining abilities during healthy aging. For example, there is evidence that semantic memory processes which involve controlled retrieval mechanism decrease, whereas the automatic functioning of the semantic network remains intact. In contrast, patients with Alzheimer’s disease (AD) suffer from episodic and semantic memory impairments aggravating their daily functioning. In AD, severe episodic as well as semantic memory deficits are observable. While the hallmark symptom of episodic memory decline in AD is well investigated, the underlying mechanisms of semantic memory deterioration remain unclear. By disentangling the semantic memory impairments in AD, the present thesis aimed to improve early diagnosis and to find a biomarker for dementia. To this end, a study on healthy aging and a study with dementia patients were conducted investigating automatic and controlled semantic word retrieval. Besides the inclusion of AD patients, a group of participants diagnosed with semantic dementia (SD) – showing isolated semantic memory loss – was assessed. Automatic and controlled semantic word retrieval was measured with standard neuropsychological tests and by means of event-related potentials (ERP) recorded during the performance of a semantic priming (SP) paradigm. Special focus was directed to the N400 or N400-LPC (late positive component) complex, an ERP that is sensitive to the semantic word retrieval. In both studies, data driven topographical analyses were applied. Furthermore, in the patient study, the combination of the individual baseline cerebral blood flow (CBF) with the N400 topography of each participant was employed in order to relate altered functional electrophysiology to the pathophysiology of dementia. Results of the aging study revealed that the automatic semantic word retrieval remains stable during healthy aging, the N400-LPC complex showed a comparable topography in contrast to the young participants. Both patient groups showed automatic SP to some extent, but strikingly the ERP topographies were altered compared to healthy controls. Most importantly, the N400 was identified as a putative marker for dementia. In particular, the degree of the topographical N400 similarity was demonstrated to separate healthy elderly from demented patients. Furthermore, the marker was significantly related to baseline CBF reduction in brain areas relevant for semantic word retrieval. Summing up, the first major finding of the present thesis was that all groups showed semantic priming, but that the N400 topography differed significantly between healthy and demented elderly. The second major contribution was the identification of the N400 similarity as a putative marker for dementia. To conclude, the present thesis added evidence of preserved automatic processing during healthy aging. Moreover, a possible marker which might contribute to an improved diagnosis and lead consequently to a more effective treatment of dementia was presented and has to be further developed.

Word encoding during sleep is suggested by correlations between word-evoked up-states and post-sleep semantic priming

To test whether humans can encode words during sleep we played everyday words to men while they were napping and assessed priming from sleep played words following waking. Words were presented during non rapid eye movement (NREM) sleep. Priming was assessed using a semantic and a perceptual priming test. These tests measured differences in the proces sing of words that had been or had not been played during sleep. Synonyms to sleep played words were the targets in the semantic priming test that tapped the meaning of sleep played words. All men responded to sleep played words by producing up states in their electroencephalogram. Up states are NREM sleep specific phases of briefly increased neuronal excitability. The word evoked up states might have promoted word processing during sleep. Yet, the mean performance in the priming tests administered following sleep was at chance level, which suggests that participants as a group failed to show priming following sleep. However, performance in the two priming tests was positively correlated to each other and to the magnitude of the word evoked up states. Hence, the larger a participant’s word evoked up states, the larger his perceptual and semantic priming. Those participants who scored high on all variables must have encoded words during sleep. We conclude that some humans are able to encode words during sleep, but more research is needed to pin down the factors that modulate this ability.

Does Age Matter? Semantic Memory in Healthy Young and Elderly Adults

Background: Semantic memory processes have been well described in literature. However, the available findings are mostly based on relatively young subjects and concrete word material (e.g. tree). Comparatively little information exists about semantic memory for abstract words (e.g. mind) and possible age related changes in semantic retrieval. In this respect, we developed a paradigm that is useful to investigate the implicit (i.e. attentionindependent) access to concrete and abstract semantic memory. These processes were then compared between young and elderly healthy subjects. Methods: A well established tool for investigating semantic memory processes is the semantic priming paradigm, which consists both of semantically unrelated and related word pairs. In our behavioral task these noun-noun word pairs were further divided into concrete, abstract and matched pronounceable non-word conditions. With this premise, the young and elderly participants performed a lexical decision task: they were asked to press a choice of two buttons as an indication for whether the word pair contained a non-word or not. In order to minimize controlled (i.e. attention-dependent) retrieval strategies, a short stimulus onset asynchrony (SOA) of 150ms was set. Reaction time (RT) changes and accuracy to related and unrelated words (priming effect) in the abstract vs. concrete condition (concreteness effect) were the dependent variables of interest. Results and Discussion: Statistical analysis confirmed both a significant priming effect (i.e. shorter RTs in semantically related compared to unrelated words) and a concreteness effect (i.e. RT decrease for concrete compared to abstract words) in the young and elderly subjects. There was no age difference in accuracy. The only age effect was a commonly known general slowing in RT over all conditions. In conclusion, age is not a critical factor in the implicit access to abstract and concrete semantic memory.

Altered Electrophysiology of Semantic Word Processing in Alzheimer's Disease and Semantic Dementia

With the progressing course of Alzheimer's disease (AD), deficits in declarative memory increasingly restrict the patients' daily activities. Besides the more apparent episodic (biographical) memory impairments, the semantic (factual) memory is also affected by this neurodegenerative disorder. The episodic pathology is well explored; instead the underlying neurophysiological mechanisms of the semantic deficits remain unclear. For a profound understanding of semantic memory processes in general and in AD patients, the present study compares AD patients with healthy controls and Semantic Dementia (SD) patients, a dementia subgroup that shows isolated semantic memory impairments. We investigate the semantic memory retrieval during the recording of an electroencephalogram, while subjects perform a semantic priming task. Precisely, the task demands lexical (word/nonword) decisions on sequentially presented word pairs, consisting of semantically related or unrelated prime-target combinations. Our analysis focuses on group-dependent differences in the amplitude and topography of the event related potentials (ERP) evoked by related vs. unrelated target words. AD patients are expected to differ from healthy controls in semantic retrieval functions. The semantic storage system itself, however, is thought to remain preserved in AD, while SD patients presumably suffer from the actual loss of semantic representations.

Loose but normal: a semantic association study.

An abnormal facilitation of the spreading activation within semantic networks is thought to under-lie schizophrenics' remote associations and referential ideas. In normal subjects, elevated magical ideation (MI) has also been associated with a style of thinking similar to that of schizotypal subjects. We thus wondered whether normal subjects with a higher MI score would judge "loose associations" as being more closely related than do subjects with a lower MI score. In two experiments, we investigated whether judgments of the semantic distance between stimulus words varied as a function of MI. In the first experiment, random word pairs of two word classes, animals and fruits, were presented. Subjects had to judge the semantic distance between word pairs. In the second experiment, sets of three words were presented, consisting of a pair of indirectly related, or unrelated nouns plus a third noun. Subjects had to judge the semantic distance of the third noun to the word pair The results of both experiments showed that higher MI subjects considered unrelated words as more closely associated than did lower MI subjects. We conjecture that for normal subjects high on MI "loose associations" may not be loose after all. We also note that the tendency to link uncommon, nonobvious, percepts may not only be the basis of paranormal and paranoid ideas of reference, but also a prerequisite of creative thinking.

Semantic, perceptual and number space: relations between category width and spatial processing.

Coarse semantic encoding and broad categorization behavior are the hallmarks of the right cerebral hemisphere's contribution to language processing. We correlated 40 healthy subjects' breadth of categorization as assessed with Pettigrew's category width scale with lateral asymmetries in perceptual and representational space. Specifically, we hypothesized broader category width to be associated with larger leftward spatial biases. For the 20 men, but not the 20 women, this hypothesis was confirmed both in a lateralized tachistoscopic task with chimeric faces and a random digit generation task; the higher a male participant's score on category width, the more pronounced were his left-visual field bias in the judgement of chimeric faces and his small-number preference in digit generation ("small" is to the left of "large" in number space). Subjects' category width was unrelated to lateral displacements in a blindfolded tactile-motor rod centering task. These findings indicate that visual-spatial functions of the right hemisphere should not be considered independent of the same hemisphere's contribution to language. Linguistic and spatial cognition may be more tightly interwoven than is currently assumed.

gems: An R Package for Simulating from Disease Progression Models

Mathematical models of disease progression predict disease outcomes and are useful epidemiological tools for planners and evaluators of health interventions. The R package gems is a tool that simulates disease progression in patients and predicts the effect of different interventions on patient outcome. Disease progression is represented by a series of events (e.g., diagnosis, treatment and death), displayed in a directed acyclic graph. The vertices correspond to disease states and the directed edges represent events. The package gems allows simulations based on a generalized multistate model that can be described by a directed acyclic graph with continuous transition-specific hazard functions. The user can specify an arbitrary hazard function and its parameters. The model includes parameter uncertainty, does not need to be a Markov model, and may take the history of previous events into account. Applications are not limited to the medical field and extend to other areas where multistate simulation is of interest. We provide a technical explanation of the multistate models used by gems, explain the functions of gems and their arguments, and show a sample application.

The Martian Gas-Analytic Package for the Landing Platform Experiments of the ExoMars 2018

The paper describes the architecture of the Martian Gas Analytic Package, which is proposed for the Russian ExoMars Lander 2018.