Automated UMLS-Based Comparison of Medical Forms

Medical forms are very heterogeneous: on a European scale there are thousands of data items in several hundred different systems. To enable data exchange for clinical care and research purposes there is a need to develop interoperable documentation systems with harmonized forms for data capture. A prerequisite in this harmonization process is comparison of forms. So far – to our knowledge – an automated method for comparison of medical forms is not available. A form contains a list of data items with corresponding medical concepts. An automatic comparison needs data types, item names and especially item with these unique concept codes from medical terminologies. The scope of the proposed method is a comparison of these items by comparing their concept codes (coded in UMLS). Each data item is represented by item name, concept code and value domain. Two items are called identical, if item name, concept code and value domain are the same. Two items are called matching, if only concept code and value domain are the same. Two items are called similar, if their concept codes are the same, but the value domains are different. Based on these definitions an open-source implementation for automated comparison of medical forms in ODM format with UMLS-based semantic annotations was developed. It is available as package compareODM from http://cran.r-project.org. To evaluate this method, it was applied to a set of 7 real medical forms with 285 data items from a large public ODM repository with forms for different medical purposes (research, quality management, routine care). Comparison results were visualized with grid images and dendrograms. Automated comparison of semantically annotated medical forms is feasible. Dendrograms allow a view on clustered similar forms. The approach is scalable for a large set of real medical forms.     

Germline Allele-Specific Expression of DAPK1 in Chronic Lymphocytic Leukemia

We previously reported a rare germline variant (c.1-6531) that resulted in allele–specific expression (ASE) of death-associated protein kinase 1 (DAPK1) and predisposition to chronic lymphocytic leukemia (CLL). We investigated a cohort of CLL patients lacking this mutation for the presence of ASE of DAPK1. We developed a novel strategy that combines single-nucleotide primer extension (SNuPE) with MALDI-TOF mass spectrometry, and detected germline DAPK1 ASE in 17 out of 120 (14.2%) CLL patients associated with a trend towards younger age at diagnosis. ASE was absent in 63 healthy controls. Germline cells of CLL patients with ASE showed increased levels of DNA methylation in the promoter region, however, neither genetic nor further epigenetic aberrations could be identified in the DAPK1 5′ upstream regulatory region, within distinct exons or in the 3′-UTR. We identified B-lymphoid malignancy related cell line models harboring allelic imbalance and found that allele-specific methylation in DAPK1 is associated with ASE. Our data indicate that ASE at the DAPK1 gene locus is a recurrent event, mediated by epigenetic mechanisms and potentially predisposing to CLL.     

Affective communication in rodents: ultrasonic vocalizations as a tool for research on emotion and motivation

Mice and rats emit and perceive calls in the ultrasonic range, i.e., above the human hearing threshold of about 20 kHz: so-called ultrasonic vocalizations (USV). Juvenile and adult rats emit 22-kHz USV in aversive situations, such as predator exposure and fighting or during drug withdrawal, whereas 50-kHz USV occur in appetitive situations, such as rough-and-tumble play and mating or in response to drugs of abuse, e.g., amphetamine. Aversive 22-kHz USV and appetitive 50-kHz USV serve distinct communicative functions. Whereas 22-kHz USV induce freezing behavior in the receiver, 50-kHz USV lead to social approach behavior. These opposite behavioral responses are paralleled by distinct patterns of brain activation. Freezing behavior in response to 22-kHz USV is paralleled by increased neuronal activity in brain areas regulating fear and anxiety, such as the amygdala and periaqueductal gray, whereas social approach behavior elicited by 50-kHz USV is accompanied by reduced activity levels in the amygdala but enhanced activity in the nucleus accumbens, a brain area implicated in reward processing. These opposing behavioral responses, together with distinct patterns of brain activation, particularly the bidirectional tonic activation or deactivation of the amygdala elicited by 22-kHz and 50-kHz USV, respectively, concur with a wealth of behavioral and neuroimaging studies in humans involving emotionally salient stimuli, such as fearful and happy facial expressions. Affective ultrasonic communication therefore offers a translational tool for studying the neurobiology underlying socio-affective communication. This is particularly relevant for rodent models of neurodevelopmental disorders characterized by social and communication deficits, such as autism and schizophrenia.     

Reconstruction of cranial and hyobranchial muscles in the triassic temnospondyl Gerrothorax provides evidence for akinetic suction feeding

The cranial and hyobranchial muscles of the Triassic temnospondyl Gerrothorax have been reconstructed based on direct evidence (spatial limitations, ossified muscle insertion sites on skull, mandible, and hyobranchium) and on phylogenetic reasoning (with extant basal actinopterygians and caudates as bracketing taxa). The skeletal and soft‐anatomical data allow the reconstruction of the feeding strike of this bottom‐dwelling, aquatic temnospondyl. The orientation of the muscle scars on the postglenoid area of the mandible indicates that the depressor mandibulae was indeed used for lowering the mandible and not to raise the skull as supposed previously and implies that the skull including the mandible must have been lifted off the ground during prey capture. It can thus be assumed that Gerrothorax raised the head toward the prey with the jaws still closed. Analogous to the bracketing taxa, subsequent mouth opening was caused by action of the strong epaxial muscles (further elevation of the head) and the depressor mandibulae and rectus cervicis (lowering of the mandible). During mouth opening, the action of the rectus cervicis muscle also rotated the hyobranchial apparatus ventrally and caudally, thus expanding the buccal cavity and causing the inflow of water with the prey through the mouth opening. The strongly developed depressor mandibulae and rectus cervicis, and the well ossified, large quadrate‐articular joint suggest that this action occurred rapidly and that powerful suction was generated. Also, the jaw adductors were well developed and enabled a rapid mouth closure. In contrast to extant caudate larvae and most extant actinopterygians (teleosts), no cranial kinesis was possible in the Gerrothorax skull, and therefore suction feeding was not as elaborate as in these extant forms. This reconstruction may guide future studies of feeding in extinct aquatic tetrapods with ossified hyobranchial apparatus. J. Morphol., 2013. © 2012 Wiley Periodicals, Inc.     

The Tick-Tock of Language: Is Language Processing Sensitive to Circadian Rhythmicity and Elevated Sleep Pressure?

The master circadian pacemaker emits signals that trigger organ-specific oscillators and, therefore, constitutes a basic biological process that enables organisms to anticipate daily environmental changes by adjusting behavior, physiology, and gene regulation. Although circadian rhythms are well characterized on a physiological level, little is known about circadian modulations of higher cognitive functions. Thus, we investigated circadian repercussions on language performance at the level of minimal syntactic processing by means of German noun phrases in ten young healthy men under the unmasking conditions of a 40 h constant-routine protocol. Language performance for both congruent and incongruent noun phrases displayed a clear diurnal rhythm with a peak performance decrement during the biological night. The nadirs, however, differed such that worst syntactic processing of incongruent noun phrases occurred 3 h earlier (07:00 h) than that of congruent noun phrases (10:00 h). Our results indicate that language performance displays an internally generated circadian rhythmicity with optimal time for parsing language between 3 to 6 h after the habitual wake time, which usually corresponds to 10:00–13:00 h. These results may have important ramifications for establishing optimal times for shiftwork changes or testing linguistically impaired people.     

Phagocytosis of algal chloroplasts by digestive gland cells in the photosynthesis-capable slug Elysia timida (Mollusca, Opisthobranchia, Sacoglossa)

Parapodia of the sacoglossan slug Elysia timida were preserved by high-pressure cryofixation during feeding experiments and investigated with transmission electron microscopy. This slug has been known for its long-term retention of active chloroplasts and photosynthesis. We observed different stages of phagocytosis of chloroplast components from ingested algal food by slug digestive gland cells. Thylakoid stacks and stroma of chloroplasts were engulfed by the slug cells. In the slug cells thylakoids were surrounded by one membrane only. This membrane is interpreted as having been generated by the mollusk during phagocytosis. It is inferred to be eukaryotic in origin and unlikely, therefore, to be endowed with the translocons system ordinarily regulating import of algal gene-encoded plastid preproteins. Our structural findings suggest that chloroplast components in the slug cells are thylakoid stacks with chloroplast stroma only.     

Minor contribution of leaf litter to N nutrition of beech (Fagus sylvatica) seedlings in a mountainous beech forest of Southern Germany

Aims

Our aims were to characterize the fate of leaf-litter-derived nitrogen in the plant-soil-microbe system of a temperate beech forest of Southern Germany and to identify its importance for N nutrition of beech seedlings.

Methods

¹⁵N-labelled leaf litter was traced in situ into abiotic and biotic N pools in mineral soil as well as into beech seedlings and mycorrhizal root tips over three growing seasons.

Results

There was a rapid transfer of ¹⁵N into the mineral soil already 21 days after tracer application with soil microbial biomass initially representing the dominant litter-N sink. However, ¹⁵N recovery in non-extractable soil N pools strongly increased over time and subsequently became the dominant ¹⁵N sink. Recovery in plant biomass accounted for only 0.025 % of ¹⁵N excess after 876 days. After three growing seasons, ¹⁵N excess recovery was characterized by the following sequence: non-extractable soil N?>>?extractable soil N including microbial biomass?>>?plant biomass?>?ectomycorrhizal root tips.

Conclusions

After quick vertical dislocation and cycling through microbial N pools, there was a rapid stabilization of leaf-litter-derived N in non-extractable N pools of the mineral soil. Very low ¹⁵N recovery in beech seedlings suggests a high importance of other N sources such as root litter for N nutrition of beech understorey.     

Reassessment of cf. Halticosaurus orbitoangulatus from the Upper Triassic (Norian) of Germany – a pseudosuchian,not a dinosaur

The holotype of cf. Halticosaurus orbitoangulatus Huene, 1932, comprises an incomplete and macerated but associated skull of an archosaurian reptile from the middle (second) Stubensandstein (middle Löwenstein Formation; Upper Triassic: Norian) of Baden‐Württemberg, Germany. It was originally interpreted as a theropod dinosaur but more recently it has been suggested that this taxon has crocodylomorph affinities. Detailed preparation of the holotype of cf. H. orbitoangulatus has revealed much new anatomical information and permitted reassessment of its affinities. The maxilla lacks both a distinct antorbital fossa and a medial bony lamina bordering the antorbital fenestra. The lateral surface of the dentary bears a pronounced horizontal ridge. The squamosal differs from that of basal crocodylomorphs in being L‐shaped rather than arcuate in dorsal view, lacking a dorsolateral overhang, and lacking an interlocking contact with the paroccipital process as, for example, in the basal crocodylomorph Saltoposuchus connectens from the same horizon and locality. Phylogenetic analysis placed cf. H. orbitoangulatus amongst loricatan pseudosuchians (but not amongst Crocodylomorpha) rather than amongst theropod dinosaurs. The holotype of cf. H. orbitoangulatus represents a previously unrecognized taxon of loricatan pseudosuchian, which is here named Apatosuchus orbitoangulatus and set apart from other known Norian‐age non‐crocodylomorph loricatans by its apparently much smaller size. © 2013 The Linnean Society of London