Electrostatic encoding of genome organization principles within single native nucleosomes.

The eukaryotic genome, first packed into nucleosomes of about 150 bp around the histone core, is organized into euchromatin and heterochromatin, corresponding to the A and B compartments, respectively. Here, we asked if individual nucleosomes in vivo know where to go. That is, do mono-nucleosomes by themselves contain A/B compartment information, associated with transcription activity, in their biophysical properties? We purified native mono-nucleosomes to high monodispersity and used physiological concentrations of biological polyamines to determine their condensability. The chromosomal regions known to partition into A compartments have low condensability and vice versa. In silico chromatin polymer simulations using condensability as the only input showed that biophysical information needed to form compartments is all contained in single native nucleosomes and no other factors are needed. Condensability is also strongly anticorrelated with gene expression, and especially so near the promoter region and in a cell type dependent manner. Therefore, individual nucleosomes in the promoter know whether the gene is on or off, and that information is contained in their biophysical properties. Comparison with genetic and epigenetic features suggest that nucleosome condensability is a very meaningful axis onto which to project the high dimensional cellular chromatin state. Analysis of condensability using various condensing agents including those that are protein-based suggests that genome organization principle encoded into individual nucleosomes is electrostatic in nature. Polyamine depletion in mouse T cells, by either knocking out ornithine decarboxylase (ODC) or inhibiting ODC, results in hyperpolarized condensability, suggesting that when cells cannot rely on polyamines to translate biophysical properties of nucleosomes to control gene expression and 3D genome organization, they accentuate condensability contrast, which may explain dysfunction known to occur with polyamine deficiency.

Dimensional Reduction for Single-Molecule Imaging of DNA and Nucleosome Condensation by Polyamines, HP1α and Ki-67.

Macromolecules organize themselves into discrete membrane-less compartments. Mounting evidence has suggested that nucleosomes as well as DNA itself can undergo clustering or condensation to regulate genomic activity. Current in vitro condensation studies provide insight into the physical properties of condensates, such as surface tension and diffusion. However, methods that provide the resolution needed for complex kinetic studies of multicomponent condensation are desired. Here, we use a supported lipid bilayer platform in tandem with total internal reflection microscopy to observe the two-dimensional movement of DNA and nucleosomes at the single-molecule resolution. This dimensional reduction from three-dimensional studies allows us to observe the initial condensation events and dissolution of these early condensates in the presence of physiological condensing agents. Using polyamines, we observed that the initial condensation happens on a time scale of minutes while dissolution occurs within seconds upon charge inversion. Polyamine valency, DNA length, and GC content affect the threshold polyamine concentration for condensation. Protein-based nucleosome condensing agents, HP1α and Ki-67, have much lower threshold concentrations for condensation than charge-based condensing agents, with Ki-67 being the most effective, requiring as low as 100 pM for nucleosome condensation. In addition, we did not observe condensate dissolution even at the highest concentrations of HP1α and Ki-67 tested. We also introduce a two-color imaging scheme where nucleosomes of high density labeled in one color are used to demarcate condensate boundaries and identical nucleosomes of another color at low density can be tracked relative to the boundaries after Ki-67-mediated condensation. Our platform should enable the ultimate resolution of single molecules in condensation dynamics studies of chromatin components under defined physicochemical conditions.

Measurement Performance of Activity Measurements with Newer Generation of Apple Watch in Wheelchair Users with Spinal Cord Injury.

BACKGROUND: The level of physical activity (PA) of people with spinal cord injury (SCI) has an impact on long-term complications. Currently, PA is mostly assessed by interviews. Wearable activity trackers are promising tools to objectively measure PA under everyday conditions. The only off-the-shelf, wearable activity tracker with specific measures for wheelchair users is the Apple Watch. OBJECTIVES: This study analyzes the measurement performance of Apple Watch Series 4 for wheelchair users and compares it with an earlier generation of the device. METHODS: Fifteen participants with subacute SCI during their first in-patient phase followed a test course using their wheelchair. The number of wheelchair pushes was counted manually by visual inspection and with the Apple Watch. Difference between the Apple Watch and the rater was analyzed with mean absolute percent error (MAPE) and a Bland-Altman plot. To compare the measurement error of Series 4 and an older generation of the device a t-test was calculated using data for Series 1 from a former study. RESULTS: The average of differences was 12.33 pushes (n = 15), whereas participants pushed the wheelchair 138.4 times on average (range 86-271 pushes). The range of difference and the Bland-Altman plot indicate an overestimation by Apple Watch. MAPE is 9.20% and the t-test, testing for an effect of Series 4 on the percentage of error compared with Series 1, was significant with p < 0.05. CONCLUSION: Series 4 shows a significant improvement in measurement performance compared with Series 1. Series 4 can be considered as a promising data source to capture the number of wheelchair pushes on even grounds. Future research should analyze the long-term measurement performance during everyday conditions of Series 4.

[Germany-wide, Web-based ParaReg Registry for Lifelong Monitoring of People with Spinal Cord Injury: Data Model, Ethico-legal Prerequisites and Technical Implementation]. / Das deutschlandweite, webbasierte ParaReg-Register zur lebenslangen Dokumentation von Querschnittgelähmten ­ Datenmodell, rechtlich-ethische Voraussetzungen und technische Implementierung.

OBJECTIVE: In Germany, treatment paths for patients with acute spinal cord injury (SCI) differ considerably depending on intrinsic, disease-specific and extrinsic factors. Which of these factors are associated with improved outcome with fewer subsequent complications and inpatient re-admissions is not clear. The German-wide, patient-centered, web-based ParaReg registry will be implemented to improve the long-term quality of patient care and the planning of treatment paths with increased cost-effectiveness. METHODS: In the 2017-18 conceptualization phase, the data model of the registry was developed in an iterative process of the ParaReg steering committee together with the extended DMGP board and patient representatives. In ParaReg, routine social and medical data as well as internationally established neurological, functional and participation scores will be documented. The assignment of a unique patient ID allows a lifelong, cross-center documentation of inpatient stays in one of the 27 SCI centers organized in the German-speaking Medical Society for SCI (DMGP). The ParaReg data protection concept and patient information/consent are based on the Open Source Registry for Rare Diseases (OSSE) which were extended by GDPR-relevant aspects. RESULTS: In the realization phase, which started in 2019, the information technology infrastructure was implemented according to the clinical ID management module of the Technology and Methods Platform for Networked Medical Research (TMF). In parallel, the legal and ethical prerequisites for registry operation under the patronage of the DMGP were created. Recommendations of the working group data protection of the TMF were integrated into ParaReg's data protection concept. Based on the feedback from the alpha test phase with documentation of the hospitalization data of 40 patients, the ergonomics of the electronic case report forms were improved in particular for data entry on mobile devices. CONCLUSION: After completion of the monocentric alpha test phase, the multicenter data acquisition was started in 5 DMGP-SCI centers. The sustainability of ParaReg is ensured by the structural and financial support of the DMGP after expiry of the funding by the German Federal Ministry of Education and Research (BMBF).

Digital teaching as an instrument for cross-location teaching networks in medical informatics: opportunities and challenges.

The increasingly digitized healthcare system requires new skills from all those involved. In order to impart these competencies, appropriate courses must be developed at educational institutions. In view of the rapid development of new aspects of digitization, this presents a challenge; suitable teaching formats must be developed successively. The establishment of cross-location teaching networks is one way to better meet training needs and to make the necessary spectrum of educational content available. As part of the Medical Informatics Initiative, the HiGHmed consortium is establishing such a teaching network, in the field of medical informatics, which covers many topics related to the digitization of the health care system. Various problem areas in the German education system were identified that hinder the development of the teaching network. These problem areas were prioritized firstly according to the urgency of the solution from the point of view of the HiGHmed consortium and secondly according to existing competencies in the participating societies. A workshop on the four most relevant topics was organized with experts from the German Society for Medical Informatics, Biometry and Epidemiology (GMDS), the Society for Medical Education (GMA) and the HiGHmed consortium. These are: recognition of exam results from teaching modules that are offered digitally and across locations, and their integration into existing curricula; recognition of digital, cross-location teaching in the teachers' teaching load; nationwide uniform competencies for teachers, in order to be able to conduct digital teaching effectively and with comparable quality; technical infrastructure to efficiently and securely communicate and manage the recognition of exam results between educational institutions. For all subject areas, existing preliminary work was identified on the basis of working questions, and short- and long-term needs for action were formulated. Finally, a need for the redesign of a technologically supported syntactic and semantic interoperability of learning performance recording was identified.

Hospital Information Systems.

Hospital information systems (HIS) have to be considered as socio-technical systems, which consist of technical components as well as of the human aspect like hospital staff and patients. HIS strive for the optimization of information logistics, to support tasks like patient care and administration of a hospital. To systematically manage such complex systems, HIS can be analyzed on three layers: First, tasks and entity types should be considered. Entity types represent information which is used and updated by tasks like 'Patient Admission' or 'Decision Making'. Second, application components of a HIS should be analyzed, they can be either computer-based or paper-based; both of them support tasks from the first layer. Therefore, they store and exchange information. The third layer analyzes physical data processing components of a HIS, like servers, workstations or networks. The three-layered view can be used for the systematic information management of HIS on three perspectives: strategic information management plans the development of the whole HIS for the next 5 years and longer. Measures from strategic information management are implemented as projects, coordinated by the tactical information management. The operational information management ensures a continuous and reliable operation of the HIS.

eHealth and Clinical Documentation Systems.

eHealth is the use of modern information and communication technology (ICT) for trans-institutional healthcare purposes. Important subtopics of eHealth are health data sharing and telemedicine. Most of the clinical documentation to be shared is collected in patient records to support patient care. More sophisticated approaches to electronic patient records are trans-institutional or (inter-)national. Other aims for clinical documentation are quality management, reimbursement, legal issues, and medical research. Basic prerequisite for eHealth is interoperability, which can be divided into technical, semantic and process interoperability. There is a variety of international standards to support interoperability. Telemedicine is a subtopic of eHealth, which bridges spatial distance by using ICT for medical (inter-)actions. We distinguish telemedicine among healthcare professionals and telemedicine between health care professionals and patients. Both have a great potential to face the challenges of aging societies, the increasing number of chronically ill patients, multimorbidity and low number of physicians in remote areas. With ongoing digitalization more and more data are available digitally. Clinical documentation is an important source for big data analysis and artificial intelligence. The patient has an important role: Telemonitoring, wearable technologies, and smart home devices provide digital health data from daily life. These are high-quality data which can be used for medical decisions.

The HiGHmed Didactical Framework for Online Learning Modules on Medical Informatics: First Experiences.

Within the HiGHmeducation consortium various online learning modules shall be developed by members of the consortium to address the increasing need for skilled professionals in a networked and digitalized healthcare system. Transferability of these modules to other locations is one main objective for the design of online learning modules. Thus, a didactical framework for online learning modules was developed. To ensure feasibility of the framework, the participating universities were analyzed concerning availability of e-learning support structures and infrastructures including learning management systems (LMS). The analysis especially focuses on the various LMS learning tools and their suitability for the framework. The framework is the basis for 12 HiGHmeducation online learning modules of which a part has firstly been conducted in winter 2019/20 and leads to a comparable structure of the modules.

Current Use of Sensor-Based Measurements for Paraplegics: A Literature Review.

Sensors are used in many fields to measure physical phenomena, often on mobile persons. Paraplegia is a disease with a massive impact on the ability to move, so patients show changes in walking behaviour or are even wheelchair users. It is unclear how sensors can be used with paraplegics to generate valid data for research. In the ParaReg project, such data shall be integrated with a medical register. In this paper, we elaborate current approaches for sensor measurements that might serve as an additional data source for ParaReg with the help of a literature review. We queried IEEE Xplore and MEDLINE to find publications that describe the current use of sensors for patients with paraplegia. The retrieved publications were screened for eligibility by two reviewers independently. To ensure reproducibility, we conducted an initial alignment. All publications were assessed based on their abstract. Inclusions were analysed for their major topic, and we proposed categories, which were statistically described afterwards. We retrieved 685 publications in total and included 287 publications in our analysis. The categories we found are: "diagnostic sensor tools for clinical environments", "seating position analysis", "functional electrical stimulation (FES) / neuroprosthesis control", "seating position analysis", "control systems for devices" and "assessment of physical activity". "FES / neuroprosthesis control" shows most publications and the highest publication rate in history, followed by "assessment of physical activity".

Development of a Research-Based Teaching Course as Blended-Learning Format in a Medical Informatics Program.

We consider Medical Informatics programs at universities as one of the main education resources for young scientists in our field and thus present a new design for a course teaching scientific skill at the University of Heidelberg as blended-learning format. We utilize common E-learning methods and created the whole course with respect to the concept of research-based teaching. Finally, we present our lessons learned from the current activities of the course.

Enhancing oil production and harvest by combining the marine alga Nannochloropsis oceanica and the oleaginous fungus Mortierella elongata.

BACKGROUND: Although microalgal biofuels have potential advantages over conventional fossil fuels, high production costs limit their application in the market. We developed bio-flocculation and incubation methods for the marine alga, Nannochloropsis oceanica CCMP1779, and the oleaginous fungus, Mortierella elongata AG77, resulting in increased oil productivity. RESULTS: By growing separately and then combining the cells, the M. elongata mycelium could efficiently capture N. oceanica due to an intricate cellular interaction between the two species leading to bio-flocculation. Use of a high-salt culture medium induced accumulation of triacylglycerol (TAG) and enhanced the contents of polyunsaturated fatty acids (PUFAs) including arachidonic acid and docosahexaenoic acid in M. elongata. To increase TAG productivity in the alga, we developed an effective, reduced nitrogen-supply regime based on ammonium in environmental photobioreactors. Under optimized conditions, N. oceanica produced high levels of TAG that could be indirectly monitored by following chlorophyll content. Combining N. oceanica and M. elongata to initiate bio-flocculation yielded high levels of TAG and total fatty acids, with ~ 15 and 22% of total dry weight (DW), respectively, as well as high levels of PUFAs. Genetic engineering of N. oceanica for higher TAG content in nutrient-replete medium was accomplished by overexpressing DGTT5, a gene encoding the type II acyl-CoA:diacylglycerol acyltransferase 5. Combined with bio-flocculation, this approach led to increased production of TAG under nutrient-replete conditions (~ 10% of DW) compared to the wild type (~ 6% of DW). CONCLUSIONS: The combined use of M. elongata and N. oceanica with available genomes and genetic engineering tools for both species opens up new avenues to improve biofuel productivity and allows for the engineering of polyunsaturated fatty acids.

Homology threading to generate RNA polymerase structures.

Homology threading is a powerful technology for generating structural models based on homologous structures. Here we use threading to generate four complex RNA polymerase models. The models appear to be as useful as x-ray crystal structures or cryo-electron microscopy structures to support research projects.