De-Identifying GRASCCO - A Pilot Study for the De-Identification of the German Medical Text Project (GeMTeX) Corpus.

Introduction: The German Medical Text Project (GeMTeX) is one of the largest infrastructure efforts targeting German-language clinical documents. We here introduce the architecture of the de-identification pipeline of GeMTeX.

Methods: This pipeline comprises the export of raw clinical documents from the local hospital information system, the import into the annotation platform INCEpTION, fully automatic pre-tagging with protected health information (PHI) items by the Averbis Health Discovery pipeline, a manual curation step of these pre-annotated data, and, finally, the automatic replacement of PHI items with type-conformant substitutes.

Final Report on the German Clinical Reference Corpus 3000PA.

We here report on one of the outcomes of a large-scale German research program, the Medical Informatics Initiative (MII), aiming at the development of a solid data and software infrastructure for German-language clinical natural language processing. Within this framework, we have developed 3000PA, a national clinical reference corpus composed of patient records from three clinical university sites and annotated with a multitude of semantic annotation layers (including medical named entities, semantic and temporal relations between entities, as well as certainty and negation information related to entities and relations). This non-sharable corpus has been complemented by three sharable ones (JSYNCC, GGPONC, and GRASCCO).

GRASCCO - The First Publicly Shareable, Multiply-Alienated German Clinical Text Corpus.

We describe the creation of GRASCCO, a novel German-language corpus composed of some 60 clinical documents with more than.43,000 tokens. GRASCCO is a synthetic corpus resulting from a series of alienation steps to obfuscate privacy-sensitive information contained in real clinical documents, the true origin of all GRASCCO texts.

Piloting the Update: The Use of Therapeutic Relationship for Change - A Free Energy Account.

We apply the Free Energy Principle (FEP) to cognitive behavioral therapy (CBT). FEP describes the basic functioning of the brain as a predictive organ and states that any self-organizing system that is in equilibrium with its environment must minimize its free energy. Based on an internal model of the world and the self, predictions-so-called priors-are created, which are matched with the information input.

Pseudonymization of PHI Items in German Clinical Reports.

We describe the adaptation of a non-clinical pseudonymization system, originally developed for a German email corpus, for clinical use. This tool replaces previously identified Protected Health Information (PHI) items as carriers of privacy-sensitive information (original names for people, organizations, places, etc.) with semantic type-conformant, yet, fictitious surrogates.

Optimized Identification of Advanced Chronic Kidney Disease and Absence of Kidney Disease by Combining Different Electronic Health Data Resources and by Applying Machine Learning Strategies.

Automated identification of advanced chronic kidney disease (CKD ≥ III) and of no known kidney disease (NKD) can support both clinicians and researchers. We hypothesized that identification of CKD and NKD can be improved, by combining information from different electronic health record (EHR) resources, comprising laboratory values, discharge summaries and ICD-10 billing codes, compared to using each component alone. We included EHRs from 785 elderly multimorbid patients, hospitalized between 2010 and 2015, that were divided into a training and a test (n = 156) dataset.

An Evolutionary Approach to the Annotation of Discharge Summaries.

We here describe the evolution of annotation guidelines for major clinical named entities, namely Diagnosis, Findings and Symptoms, on a corpus of approximately 1,000 German discharge letters. Due to their intrinsic opaqueness and complexity, clinical annotation tasks require continuous guideline tuning, beginning from the initial definition of crucial entities and the subsequent iterative evolution of guidelines based on empirical evidence. We describe rationales for adaptation, with focus on several metrical criteria and task-centered clinical constraints.

Annotating German Clinical Documents for De-Identification.

We devised annotation guidelines for the de-identification of German clinical documents and assembled a corpus of 1,106 discharge summaries and transfer letters with 44K annotated protected health information (PHI) items. After three iteration rounds, our annotation team finally reached an inter-annotator agreement of 0.96 on the instance level and 0.

CDA-Compliant Section Annotation of German-Language Discharge Summaries: Guideline Development, Annotation Campaign, Section Classification.

We present the outcome of an annotation effort targeting the content-sensitive segmentation of German clinical reports into sections. We recruited an annotation team of up to eight medical students to annotate a clinical text corpus on a sentence-by-sentence basis in four pre-annotation iterations and one final main annotation step. The annotation scheme we came up with adheres to categories developed for clinical documents in the HL7-CDA (Clinical Document Architecture) standard for section headings.

3000PA-Towards a National Reference Corpus of German Clinical Language.

We introduce 3000PA, a clinical document corpus composed of 3,000 EPRs from three different clinical sites, which will serve as the backbone of a national reference language resource for German clinical NLP. We outline its design principles, results from a medication annotation campaign and the evaluation of a first medication information extraction prototype using a subset of 3000PA.

Embodied Cognition and the Direct Induction of Affect as a Compliment to Cognitive Behavioural Therapy.

We make the case for the possible integration of affect experience induced via embodiment techniques with CBT for the treatment of emotional disorders in clinical settings. Theoretically we propose a possible integration of cognitive behavioural theory, neuroscience, embodied cognition and important processes of client change outcomes such as the therapeutic alliance to enhance client outcomes. We draw from evidence of bidirectional effects between embodiment modes of bottom-up (sensory-motor simulations giving rise to important basis of knowledge) and top-down (abstract mental representations of knowledge) processes such as CBT in psychotherapy.

Single vesicle biochips for ultra-miniaturized nanoscale fluidics and single molecule bioscience.

One of the major bottlenecks in the development of biochips is maintaining the structure and function of biomolecules when interfacing them with hard matter (glass, plastics, metals, etc.), a challenge that is exacerbated during miniaturization that inevitably increases the interface to volume ratio of these devices. Biochips based on immobilized vesicles circumvent this problem by encapsulating biomolecules in the protective environment of a lipid bilayer, thus minimizing interactions with hard surfaces.

Constructing size distributions of liposomes from single-object fluorescence measurements.

We describe in detail a simple technique to construct the size distribution of liposome formulations from single-object fluorescence measurements. Liposomes that are fluorescently labeled in their membrane are first immobilized on a surface at dilute densities and then imaged individually using epi-fluorescence microscopy. The integrated intensities of several thousand single liposomes are collected and evaluated within minutes by automated image processing, using the user-friendly freeware ImageJ.

Functional brain network abnormalities during verbal working memory performance in adolescents and young adults with dyslexia.

Behavioral and functional neuroimaging studies indicate deficits in verbal working memory (WM) and frontoparietal dysfunction in individuals with dyslexia. Additionally, structural brain abnormalities in dyslexics suggest a dysconnectivity of brain regions associated with phonological processing. However, little is known about the functional neuroanatomy underlying cognitive dysfunction in dyslexia.

Neural correlates of working memory performance in adolescents and young adults with dyslexia.

Behavioral studies indicate deficits in phonological working memory (WM) and executive functioning in dyslexics. However, little is known about the underlying functional neuroanatomy. In the present study, neural correlates of WM in adolescents and young adults with dyslexia were investigated using event-related functional magnetic resonance imaging (fMRI) and a parametric verbal WM task which required the manipulation of verbal material.