The Necessity of Interoperability to Uncover the Full Potential of Digital Health Devices

Personalized health care can be optimized by including patient-reported outcomes. Standardized and disease-specific questionnaires have been developed and are routinely used. These patient-reported outcome questionnaires can be simple paper forms given to the patient to fill out with a pen or embedded in digital devices. Regardless of the format used, they provide a snapshot of the patient's feelings and indicate when therapies need to be adjusted. The advantage of digitizing these questionnaires is that they can be automatically analyzed, and patients can be monitored independently of doctor visits. Although the questions of most clinical patient-reported outcome questionnaires follow defined standards and are evaluated by clinical trials, these standards do not exist for data processing. Interoperable data formats and structures would benefit multilingual and cross-study data exchange. Linking questionnaires to standardized terminologies such as the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) and Logical Observation Identifiers, Names, and Codes (LOINC) would improve this interoperability. However, linking clinically validated patient-reported outcome questionnaires to clinical terms available in SNOMED CT or LOINC is not as straightforward as it sounds. Here, we report our approach to link patient-reported outcomes from health applications to SNOMED CT or LOINC codes. We highlight current difficulties in this process and outline ways to minimize them.

Digitalization of adverse event management in oncology to improve treatment outcome-A prospective study protocol

The occurrence of adverse events frequently accompanies tumor treatments. Side effects should be detected and treated as soon as possible to maintain the best possible treatment outcome. Besides the standard reporting system Common Terminology Criteria for Adverse Events (CTCAE), physicians have recognized the potential of patient-reporting systems. These are based on a more subjective description of current patient reporting symptoms. Patient-reported symptoms are essential to define the impact of a given treatment on the quality of life and the patient's wellbeing. They also act against an underreporting of side effects which are paramount to define the actual value of a treatment for the individual patient. Here, we present a study protocol for a clinical trial that assesses the potential of a smartphone application for CTCAE conform symptom reporting and tracking that is adjusted to the standard clinical reporting system rather than symptom oriented descriptive trial tools. The presented study will be implemented in two parts, both lasting over six months. The first part will assess the feasibility of the application with 30 patients non-randomly divided into three equally-sized age groups (<55years, 55-75years, >75years). In the second part 36 other patients will be randomly assigned to two groups, one reporting using the smartphone and one not. This prospective second part will compare the impact of smartphone reported adverse events regarding applied therapy doses and quality of life to those of patients receiving standard care. We aim for early detection and treatment of adverse events in oncological treatment to improve patients' safety and outcomes. For this purpose, we will capture frequent adverse events of chemotherapies, immunotherapies, or other targeted therapies with our smartphone application. The presented trial is registered at the U.S. National Library of Medicine ClinicalTrials.gov (NCT04493450) on July 30, 2020.

Optical and hidden transport properties of BaFe1.91Ni0.09As2film

Optical spectroscopy was used to study the electrodynamics and hidden transport properties of a BaFe_1.91Ni_0.09As₂thin superconducting (SC) film. We analyzed the normal state data using a Drude-Lorentz model with two Drude components: one narrow (D₁) and another broad one (D₂). In the SC state, two gaps with2Δ0(2)/kBTc=1.9-2.0 and2Δ0(1)/kBTc=4.0-4.3 are formed from the narrow component D₁while the broad component D₂remains ungapped. The calculated total DC resistivity of the film and the low-temperature scattering rate for the narrow Drude component show a hidden Fermi-liquid behavior. The change of total electron-boson coupling (λ_tot) and representative energy (Ω₀) in the normal state with respect to the SC state is typical of other iron-based materials as well as high-temperature superconducting (HTSC) cuprates.

Direct study of structural phase transformation in single crystalline bulk and thin film BaFe2As2

The ternary iron arsenide compound BaFe₂As₂ exhibits a structural phase transition from tetragonal to orthorhombic at a temperature of about 140 K. The twin lamellae arising below this transition temperature were studied in undoped single crystalline bulk and epitaxial thin film samples using electron backscatter diffraction in a scanning electron microscope equipped with a helium cryostat. Applying this technique on bulk single crystals a characteristic twin lamella size in the range of 0.1 μm up to a few μm was observed. In contrast, in epitaxially strained thin films the phase transition is not observed at temperatures above 19 K.

3D Network exploration and visualisation for lifespan data

BACKGROUND

The Ageing Factor Database AgeFactDB contains a large number of lifespan observations for ageing-related factors like genes, chemical compounds, and other factors such as dietary restriction in different organisms. These data provide quantitative information on the effect of ageing factors from genetic interventions or manipulations of lifespan. Analysis strategies beyond common static database queries are highly desirable for the inspection of complex relationships between AgeFactDB data sets. 3D visualisation can be extremely valuable for advanced data exploration.

RESULTS

Different types of networks and visualisation strategies are proposed, ranging from basic networks of individual ageing factors for a single species to complex multi-species networks. The augmentation of lifespan observation networks by annotation nodes, like gene ontology terms, is shown to facilitate and speed up data analysis. We developed a new Javascript 3D network viewer JANet that provides the proposed visualisation strategies and has a customised interface for AgeFactDB data. It enables the analysis of gene lists in combination with AgeFactDB data and the interactive visualisation of the results.

CONCLUSION

Interactive 3D network visualisation allows to supplement complex database queries by a visually guided exploration process. The JANet interface allows gaining deeper insights into lifespan data patterns not accessible by common database queries alone. These concepts can be utilised in many other research fields.

Pushing the limits of applicability of REBCO coated conductor films through fine chemical tuning and nanoengineering of inclusions

An outstanding current carrying performance (namely critical current density, Jc) over a broad temperature range of 10-77 K for magnetic fields up to 12 T is reported for films of YBa2Cu3O7-x with Ba2Y(Nb,Ta)O6 inclusion pinning centres (YBCO-BYNTO) and thicknesses in the range of 220-500 nm. Jc values of 10 MA cm-2 were measured at 30 K - 5 T and 10 K - 9 T with a corresponding maximum of the pinning force density at 10 K close to 1 TN m-3. The system is very flexible regarding properties and microstructure tuning, and the growth window for achieving a particular microstructure is wide, which is very important for industrial processing. Hence, the dependence of Jc on the magnetic field angle was readily controlled by fine tuning the pinning microstructure. Transmission electron microscopy (TEM) analysis highlighted that higher growth rates induce more splayed and denser BYNTO nanocolumns with a matching field as high as 5.2 T. Correspondingly, a strong peak at the B||c-axis is noticed when the density of vortices is lower than the nanocolumn density. YBCO-BYNTO is a very robust and reproducible composite system for high-current coated conductors over an extended range of magnetic fields and temperatures.

Selective mass enhancement close to the quantum critical point in BaFe2(As1-x P x )2

A quantum critical point (QCP) is currently being conjectured for the BaFe₂(As_1-x P _x )₂ system at the critical value x _c  ≈ 0.3. In the proximity of a QCP, all thermodynamic and transport properties are expected to scale with a single characteristic energy, given by the quantum fluctuations. Such a universal behavior has not, however, been found in the superconducting upper critical field H _c2. Here we report H _c2 data for epitaxial thin films extracted from the electrical resistance measured in very high magnetic fields up to 67 Tesla. Using a multi-band analysis we find that H _c2 is sensitive to the QCP, implying a significant charge carrier effective mass enhancement at the doping-induced QCP that is essentially band-dependent. Our results point to two qualitatively different groups of electrons in BaFe₂(As_1-x P _x )₂. The first one (possibly associated to hot spots or whole Fermi sheets) has a strong mass enhancement at the QCP, and the second one is insensitive to the QCP. The observed duality could also be present in many other quantum critical systems.

Orientation symmetry breaking in self-assembled Ce1−xGdxO2−ynanowires derived from chemical solutions

A novel approach to perform an independent study of the nucleation and coarsening of Ce_0.9Gd_0.1O_2−ynanowires is presented.

AgeFactDB--the JenAge Ageing Factor Database--towards data integration in ageing research

AgeFactDB (http://agefactdb.jenage.de) is a database aimed at the collection and integration of ageing phenotype data including lifespan information. Ageing factors are considered to be genes, chemical compounds or other factors such as dietary restriction, whose action results in a changed lifespan or another ageing phenotype. Any information related to the effects of ageing factors is called an observation and is presented on observation pages. To provide concise access to the complete information for a particular ageing factor, corresponding observations are also summarized on ageing factor pages. In a first step, ageing-related data were primarily taken from existing databases such as the Ageing Gene Database--GenAge, the Lifespan Observations Database and the Dietary Restriction Gene Database--GenDR. In addition, we have started to include new ageing-related information. Based on homology data taken from the HomoloGene Database, AgeFactDB also provides observation and ageing factor pages of genes that are homologous to known ageing-related genes. These homologues are considered as candidate or putative ageing-related genes. AgeFactDB offers a variety of search and browse options, and also allows the download of ageing factor or observation lists in TSV, CSV and XML formats.

Nanostructural control in solution-derived epitaxial Ce(1-x)Gd(x)O(2-y) films

A novel mechanism based on aliovalent doping, allowing fine tuning of the nanostructure and surface topography of solution-derived ceria films, is reported. While under reducing atmospheric conditions, non-doped ceria films are inherently polycrystalline due to an interstitial amorphous Ce(2)C(3) phase that inhibits grain growth, a high quality epitaxial film can be achieved simply by doping with Gd(3+) cations. Gd(3+) [Formula: see text] Ce(4+) substitutions within the lattice are accompanied by charge-compensating oxygen vacancies throughout the volume of the crystallites acting as an efficient vehicle to reduce the barrier for grain boundary motion caused by interstitial Ce(2)C(3). In this way, the original nanostructure is self-purified by pushing the amorphous Ce(2)C(3) phase towards the free surface of the film. Once a full epitaxial cube-on-cube oriented ceria film is obtained, its surface morphology is dictated by the interplay between faceting on low energy {110} and/or {111} pyramidal planes and truncation of those pyramids by (001) ones. The development of the latter requires the suppression of their polar character which is thought to be achieved by charge compensation between the dopand and oxygen along [Formula: see text] directions.

A comparative view at comprehensive information resources on three-dimensional structures of biological macro-molecules

The rapidly increasing amount of information on three-dimensional (3D) structures of biological macro-molecules has still an insufficient impact on genome analysis, functional genomics and proteomics as well as on many other fields in biomedicine including disease-related research. There are, however, attempts to make structural data more easily accessible to the bench biologist. As members of the world-wide Protein Data Bank (wwPDB), the RCSB Protein Data Bank (PDB), the Protein Data Bank Japan and the Macromolecular Structure Database are the primary information resources for 3D structures of proteins, nucleic acids, carbohydrates and complexes thereof. In addition, a number of secondary resources have been set up that also provide information on all currently known structures in a relatively comprehensive manner and not focusing on specific features only. They include PDBsum, the OCA browser-database for protein structure/function, the Molecular Modeling Database and the Jena Library of Biological Macromolecules--JenaLib. Both the primary and secondary resources often merge the information in the PDB files with data from other resources and offer additional analysis tools thereby adding value to the original PDB data. Here, we briefly describe these resources from a user's point of view and from a comparative perspective. It is our aim to guide researchers outside the structure biology field in getting the most out of the 3D structure resources.

Potentiation of 3-hydroxyglutarate neurotoxicity following induction of astrocytic iNOS in neonatal rat hippocampal cultures

Neuronal damage in glutaryl-CoA dehydrogenase deficiency (GDD) has previously been addressed to N-methyl-D-aspartate (NMDA) receptor-mediated neurotoxicity of the accumulating neurotoxic metabolite 3-hydroxyglutarate. However, acute encephalopathic crises in GDD patients are typically precipitated by febrile illness or even routine vaccinations, suggesting a potentiating role of inflammatory cytokines. In the present study we investigated the effect of interleukin-1beta and interferon-gamma on 3-hydroxyglutarate toxicity in rat cortical astrocyte cultures and neonatal rat hippocampal cultures. A cotreatment of both culture systems with interleukin-1beta and interferon-gamma induced the protein expression of astrocytic inducible nitric oxide synthase (iNOS), resulting in increased nitric oxide (NO) production. Cytokine pretreatment alone had no effect on cell viability but potentiated 3-hydroxyglutarate neurotoxicity. NOS inhibition by aminoguanidine and L-NAME prevented an iNOS-mediated potentiation of 3-hydroxyglutarate neurotoxicity but failed to protect neurons against 3-hydroxyglutarate alone. In contrast, superoxide dismutase/catalase as well as MK-801 prevented toxicity of 3-hydroxyglutarate alone as well as its potentiation by iNOS, supporting a central role of NMDA receptor stimulation with subsequently increased superoxide anion production. It is concluded that the potentiation of 3-hydroxyglutarate neurotoxicity is most probably due to an induction of astrocytic iNOS and concomitantly increased NO production, enabling enhanced peroxynitrite formation. Thus, we provide evidence for a neuroimmunological approach to the precipitation of acute encephalopathic crises in GDD by inflammatory cytokines.

Neuroprotective effects of NV-31, a bilobalide-derived compound: evidence for an antioxidative mechanism

In previous studies we have already shown that the extract of Ginkgo biloba, and some of its constituents, such as ginkgolide B and bilobalide, protected cultured neurons against apoptotic and excitotoxic damage and reduced the infarct volume after focal cerebral ischemia in mice and rats. In this work, we determined the neuroprotective and antioxidative effects of 4-hydroxy-4-tert-butyl-2,3,5,6-tetrahydrothiopyran-1-oxide (NV-31), a stable compound which was synthesized to mimic the pharmacological activity profile of bilobalide. In pure neuronal cultures from chick embryo telencephalon, damage was induced by serum deprivation (24 h) and exposure to staurosporine (200 nM, 24 h) which caused an increase in the percentage of apoptotic neurons from 14 (controls) to 30 and 55%, respectively. NV-31 (1-100 nM) protected dose-dependently chick neurons against both serum deprivation- and staurosporine-induced apoptosis. Similarly, NV-31 (100 nM) reduced staurosporine (300 nM, 24 h)-induced neuronal damage in mixed cultures of neurons and astrocytes from neonatal rat hippocampus. The cellular ROS content increased 6-fold 4 h after serum deprivation as well as 4 h after the exposure to staurosporine and this increase was reduced by 50% in the presence of 10 and 100 nM NV-31, respectively. In mice, a treatment with 10 and 20 mg/kg NV-31 60 min before and immediately after focal cerebral ischemia, respectively, significantly reduced the infarct area compared with vehicle-treated animals. In the present study, we show that NV-31 promotes neuronal survival and we suggest that its antioxidative property contributes to the mechanism of neuroprotection.

Retinoic acid potentiated the protective effect of NGF against staurosporine-induced apoptosis in cultured chick neurons by increasing the trkA protein expression

Nerve growth factor (NGF) has already been shown to protect neurons and PC12 cells from cell death induced by different stimuli. When chick embryonic neurons were exposed to staurosporine (200 nM, 24 hr), the percentage of apoptotic neurons increased from 15% in controls to 80%, but the treatment with NGF alone did not show any neuroprotection. In the presence of retinoic acid (RA, 5 microM), however, NGF (20 pg/ml) reduced staurosporine-induced damage to 42% apoptotic neurons compared to 58% in the presence of RA (5 icroM) alone. TrkA protein expression in chick neurons was markedly reduced by staurosporine, but was found to be increased in the presence of RA and NGF compared with the treatment with staurosporine alone. The antiapoptotic effect caused by RA and NGF was abolished by the tyrosine kinase inhibitor K-252a, as well as by anti-trkA antibodies and anti-NGF antibodies suggesting that the increase in trkA protein expression contributed to its mechanism of action. In addition, RA-enhanced 2.6-fold the NGF secretion from cultured rat cortical astrocytes and conditioned medium of RA-treated astrocytes reduced the percentage of apoptotic chick neurons after a 24 hr-incubation with staurosporine in the same manner as the external addition of RA and NGF. Increasing the endogenous synthesis of growth factors as well as the expression of their receptors by small, blood-brain barrier-permeable drugs was suggested as a promising concept for neuroprotection.

The resolvase encoded by Xanthomonas campestris transposable element ISXc5 constitutes a new subfamily closely related to DNA invertases

BACKGROUND

Conservative site-specific recombination is responsible for the resolution of cointegrates which result during the transposition of class II transposable elements. Resolution is catalysed by a transposon-encoded recombinase, resolvase, that belongs to a large family of recombinases, including DNA invertases. Resolvases and the related invertases are likely to employ similar reaction mechanisms during recombination. There are important differences, however. Resolvases require two accessory DNA binding sites within each of the two directly repeated recombination sites. Invertases instead need a host factor, Fis, and an enhancer type DNA sequence, in addition to two inversely orientated recombination sites.

RESULTS

The resolvase encoded by transposable element ISXc5 from the gram-negative phytopathogen Xanthomonas campestris shows two features which distinguish it from other known resolvases. First, it is more closely phylogenetically related to invertases than other resolvases. In particular, two functionally important regions seem highly conserved between this resolvase and members of the invertase subfamily. Second, the enzyme exhibits a large extension of its carboxy-terminal domain with unknown function. We purified ISXc5 resolvase and analysed its resolution reaction in vitro. Our biochemical and DNA topological analysis reveals that critical features of resolution are similar, if not identical, to that carried out by gammadelta resolvase. However, despite its apparent similarity to invertases, we were unable to detect recombination on standard substrates for DNA inversion, in either the presence or absence of Fis.

CONCLUSIONS

ISXc5 resolvase employs a reaction mechanism which is common to members of the resolvase family. Its position near the evolutionary borderline to invertases and its high degree of identity within two functionally important regions with members of the DNA invertase subfamily suggest that only a few replacements of critical residues may suffice to convert this resolvase into a functional, possibly Fis-dependent invertase.

How AraC interacts specifically with its target DNAs

Previous work indicates that one subunit of the AraC protein dimer binds to a DNA target araI1, of 17 base-pairs. We systematically substituted every base-pair in a synthetic araI1 target with the three possible alternatives and then tested binding of araI1 and of these 51 DNA targets to AraC by quantitative gel shift analysis in the presence of L-arabinose. We found that every substitution of the underlined bases reduces AraC binding tenfold or more: 5' TAGCATTTTTATCCATA 3'. Substitutions at other bases have little or no effect. In the absence of L-arabinose we observed a sixfold reduction of binding of AraC to araI1. We have designated the 5' AGC sequence the A-box and the 5'TCCATA sequence the B-box. We synthesised DNA targets containing either two A or two B-boxes with the natural araI1-I2 spacing. Wild-type AraC binds both targets in the presence of L-arabinose in a gel shift-experiment. In the absence of L-arabinose, AraC binds only to the double B-box. We then tested various AraC mutant proteins in the same way. S208A and H212A bind to the double B-box but not to the double A-box in the presence or absence of L-arabinose. D256A binds to the double A-box, but not to the double B-box, in the presence of L-arabinose but not in its absence. The implications of these results for the mechanism of AraC induction by L-arabinose are discussed.