Femtosecond Laser-Processing of Pre-Anodized Ti-Based Bone Implants for Cell-Repellent Functionalization.

Microstructures and nanostructures can be used to reduce the adhesion of the cells on the auxiliary material. Therefore, the aim of our work was to fabricate laser-induced hierarchical microstructures and nanostructures by femtosecond laser-treatment (wavelength 1040 nm, pulse length 350 fs, repetition rates in the kHz range) to reduce the cell adhesion. Additionally, surface chemistry modification by optimized electrochemical anodization was used to further reduce the cell adhesion. For testing, flat plates and bone screws made of Ti-6Al-4V were used. Bone-forming cells (human osteoblasts from the cell line SAOS-2) were grown on the bone implants and additional test samples for two to three weeks. After the growth period, the cells were characterized by scanning electron microscopy (SEM). While earlier experiments with fibroblasts had shown that femtosecond laser-processing followed by electrochemical anodization had a significant impact on cell adhesion reduction, for osteoblasts the same conditions resulted in an activation of the cells with increased production of extracellular matrix material. Significant reduction of cell adhesion for osteoblasts was only obtained at pre-anodized surfaces. It could be demonstrated that this functionalization by means of femtosecond laser-processing can result in bone screws that hinder the adhesion of osteoblasts.

Patient Cohort Identification on Time Series Data Using the OMOP Common Data Model.

BACKGROUND: The identification of patient cohorts for recruiting patients into clinical trials requires an evaluation of study-specific inclusion and exclusion criteria. These criteria are specified depending on corresponding clinical facts. Some of these facts may not be present in the clinical source systems and need to be calculated either in advance or at cohort query runtime (so-called feasibility query). OBJECTIVES: We use the Observational Medical Outcomes Partnership (OMOP) Common Data Model (CDM) as the repository for our clinical data. However, Atlas, the graphical user interface of OMOP, does not offer the functionality to perform calculations on facts data. Therefore, we were in search for a different approach. The objective of this study is to investigate whether the Arden Syntax can be used for feasibility queries on the OMOP CDM to enable on-the-fly calculations at query runtime, to eliminate the need to precalculate data elements that are involved with researchers' criteria specification. METHODS: We implemented a service that reads the facts from the OMOP repository and provides it in a form which an Arden Syntax Medical Logic Module (MLM) can process. Then, we implemented an MLM that applies the eligibility criteria to every patient data set and outputs the list of eligible cases (i.e., performs the feasibility query). RESULTS: The study resulted in an MLM-based feasibility query that identifies cases of overventilation as an example of how an on-the-fly calculation can be realized. The algorithm is split into two MLMs to provide the reusability of the approach. CONCLUSION: We found that MLMs are a suitable technology for feasibility queries on the OMOP CDM. Our method of performing on-the-fly calculations can be employed with any OMOP instance and without touching existing infrastructure like the Extract, Transform and Load pipeline. Therefore, we think that it is a well-suited method to perform on-the-fly calculations on OMOP.

The generic Informed Consent Service gICS®: implementation and benefits of a modular consent software tool to master the challenge of electronic consent management in research.

BACKGROUND: Defining and protecting participants' rights is the aim of several ethical codices and legal regulations. According to these regulations, the Informed Consent (IC) is an inevitable element of research with human subjects. In the era of "big data medicine", aspects of IC become even more relevant since research becomes more complex rendering compliance with legal and ethical regulations increasingly difficult. METHODS: Based on literature research and practical experiences gathered by the Institute for Community Medicine (ICM), University Medicine Greifswald, requirements for digital consent management systems were identified. RESULTS: To address the requirements, the free-of-charge, open-source software "generic Informed Consent Service" (gICS®) was developed by ICM to provide a tool to facilitate and enhance usage of digital ICs for the international research community covering various scenarios. gICS facilitates IC management based on IC modularisation and supports various workflows within research, including (1) electronic depiction of paper-based consents and (2) fully electronic consents. Numerous projects applied gICS and documented over 336,000 ICs and 2400 withdrawals since 2014. DISCUSSION: Since the consent's content is a prerequisite for securing participants' rights, application of gICS is no guarantee for legal compliance. However, gICS supports fine-granular consents and accommodation of differentiated consent states, which can be directly exchanged between systems, allowing automated data processing. CONCLUSION: gICS simplifies and supports sustained IC management as a major key to successfully conduct studies and build trust in research with human subjects. Therefore, interested researchers are invited to use gICS and provide feedback for further improvements.

EHR-Independent Predictive Decision Support Architecture Based on OMOP.

BACKGROUND: The increasing availability of molecular and clinical data of cancer patients combined with novel machine learning techniques has the potential to enhance clinical decision support, example, for assessing a patient's relapse risk. While these prediction models often produce promising results, a deployment in clinical settings is rarely pursued. OBJECTIVES: In this study, we demonstrate how prediction tools can be integrated generically into a clinical setting and provide an exemplary use case for predicting relapse risk in melanoma patients. METHODS: To make the decision support architecture independent of the electronic health record (EHR) and transferable to different hospital environments, it was based on the widely used Observational Medical Outcomes Partnership (OMOP) common data model (CDM) rather than on a proprietary EHR data structure. The usability of our exemplary implementation was evaluated by means of conducting user interviews including the thinking-aloud protocol and the system usability scale (SUS) questionnaire. RESULTS: An extract-transform-load process was developed to extract relevant clinical and molecular data from their original sources and map them to OMOP. Further, the OMOP WebAPI was adapted to retrieve all data for a single patient and transfer them into the decision support Web application for enabling physicians to easily consult the prediction service including monitoring of transferred data. The evaluation of the application resulted in a SUS score of 86.7. CONCLUSION: This work proposes an EHR-independent means of integrating prediction models for deployment in clinical settings, utilizing the OMOP CDM. The usability evaluation revealed that the application is generally suitable for routine use while also illustrating small aspects for improvement.

Preserving cultural heritage: Analyzing the antifungal potential of ionic liquids tested in paper restoration.

Early industrialization and the development of cheap production processes for paper have led to an exponential accumulation of paper-based documents during the last two centuries. Archives and libraries harbor vast amounts of ancient and modern documents and have to undertake extensive endeavors to protect them from abiotic and biotic deterioration. While services for mechanical preservation such as ex post de-acidification of historic documents are already commercially available, the possibilities for long-term protection of paper-based documents against fungal attack (apart from temperature and humidity control) are very limited. Novel processes for mechanical enhancement of damaged cellulosic documents use Ionic Liquids (IL) as essential process components. With some of these ILs having azole-functionalities similar to well-known fungicides such as Clotrimazole, the possibility of antifungal activities of these ILs was proposed but has not yet been experimentally confirmed. We evaluated the potency of four ILs with potential application in paper restoration for suppression of fungal growth on five relevant paper-infesting molds. The results revealed a general antifungal activity of all ILs, which increased with the size of the non-polar group. Physiological experiments and ultimate elemental analysis allowed to determine the minimal inhibitory concentration of each IL as well as the residual IL concentration in process-treated paper. These results provide valuable guidelines for IL-applications in paper restoration processes with antifungal activity as an added benefit. With azoles remaining in the paper after the process, simultaneous repair and biotic protection in treated documents could be facilitated.

Designing a Framework of Components to Support Patient Engagement in Research.

In the context of the German Medical Informatics Initiative (MII), where data reuse and data sharing are major goals, cross-site, long-term research on patient care data can only be conducted lawfully with informed patient consent. Thus, the MII consent working group developed a template form for patient information and broad consent based on work that has been done for a former biobank project. The broad consent enables the patient to consent to the use of a wide range of the documented data including research purposes. Therefore, a user-friendly tool is needed which not only supports the storage and maintenance of the patient's consents but also allows him to easily review or withdraw his consents. Furthermore, the tool should allow the patient to review the use of his data in research projects and possible publications. This is why we developed a concept of how such a tool could be integrated into the clinical and research system landscape and implemented a prototype as a proof of concept.

Digital Patient Communication: Improving the Hospital-Patient Relationship.

Digitally engaging patients in their care processes was for many years limited to sharing care related documents (e.g. laboratory or radiology findings, discharge letters) with them through personal electronic health records. Newer concepts have led to the establishment of patient portals as patient frontends to a hospitals electronic health record. Rarely however have complete patient pathways with pre-hospitalization, inpatient stay and post-hospitalization been evaluated to identify chains of communication processes involving clinical care scenarios, as well as subsequent home monitoring scenarios. Neither have such approaches been integrated with digital communication processes related to a patients engagement in medical research projects. In order to enhance hospital-patient relationships in a holistic manner, we hypothesize that an integrated environment (e.g. patient portal) supporting shared decision making and communication in a patient´s care situation and in the same time providing communication processes for patient research engagement will optimize the patient-hospital relationship and be supportive in binding a patient to this care providing institution.

Experiences of Transforming a Complex Nephrologic Care and Research Database into i2b2 Using the IDRT Tools.

The secondary use of data from electronic medical records has become an important factor to determine and to identify various causes of disease. For this reason, applications like informatics for integrating biology and the bedside (i2b2) offer a GUI-based front end to select patient cohorts. To make use of those tools, however, clinical data need to be extracted from the Electronic Health Record (EHR) system and integrated into the data schema of i2b2. We used TBase, a documentation system for nephrologic transplantations, as a source system and applied the Integrated Data Repository Toolkit (IDRT) for the Extract, Transform, and Load (ETL) process to load the data into i2b2. Since i2b2 uses an entity-attribute-value (EAV) schema, which is a fundamentally different way of modeling data in comparison to a standard relational schema in TBase, we evaluated if (a) the data relationship of the source system entities can still be represented in the i2b2 schema and if (b) the IDRT is a suitable solution for loading the data of a comprehensive data schema like TBase into i2b2. For that reason, we identified entities in the TBase data schema which were relevant for answering questions on cohort identification. By doing so, we found out that the entities had different structures that needed to be handled differently for the ETL process. Furthermore, the use of IDRT revealed shortcomings with regard to large input data and specific data structures that are part of most modern EHR systems. However, this project also showed that our way of modeling the TBase data in i2b2 has been proven to be successful in terms of answering the most common questions of clinicians on cohort identification.

Selective L4 Dorsal Root Ganglion Stimulation Evokes Pain Relief and Changes of Inflammatory Markers: Part I Profiling of Saliva and Serum Molecular Patterns.

OBJECTIVES: Complex regional pain syndrome (CRPS) and associated comorbidities have been linked to a pro-inflammatory state driven by different mediators. Targeted dorsal root ganglion stimulation (DRGSTIM ) suppressed pain levels and improved functional capacity in intractable CRPS. However, clinical trials assessing the impact of DRG stimulation on the neuroimmune axis are lacking. METHODS: This study enrolled 24 subjects (12 refractory CRPS patients plus suitably matched healthy controls) and performed immunoassays of inflammatory mediators in saliva and serum along with score-based assessments of pain, mood, and sleep quality at baseline and after three months of selective L4-DRGSTIM . RESULTS: After three-month L4-DRGSTIM CRPS associated pain significantly decreased. In addition, disturbed sleep and mood improved post-DRGSTIM , although statistically not significant. Significantly increased serum values of pro-inflammatory markers were detected pre- and post L4-DRGSTIM for high-mobility group box 1, tumor-necrosis factor α, interleukin (IL) 6, and leptin. IL-1ß was significantly elevated pre-L4 DRGSTIM , but not posttreatment. Elevated anti-inflammatory IL-10 significantly decreased after three months in serum, while saliva oxytocin concentrations increased in CRPS subjects after L4-DRGSTIM (p = 0.65). No severe implantation and stimulation associated adverse events were recorded. CONCLUSIONS: Selective L4-DRGSTIM improved neuropathic pain and functional impairment in CRPS as previously reported. CRPS patients displayed a pro-inflammatory molecular pattern in serum. Serum anti-inflammatory IL-10 significantly declined, while saliva oxytocin nonsignificantly increased after L4-DRGSTIM . An evidence-based relational interpretation of our study is limited due to the uncontrolled study design. However, molecular profiling of biofluids (saliva, serum) represents a novel and experimental field in applied neuromodulation, which warrant further investigations to unveil mechanisms of neuroimmune modulation.

Two Years of tranSMART in a University Hospital for Translational Research and Education.

BACKGROUND: For translational research, software platforms such as tranSMART with an integrated view of both clinical and omics data have gained more and more attention in the last years. OBJECTIVES: We wanted to examine the success and failures of tranSMART in the fields of translational research and education by looking at the examples of six use cases at our hospital. We wanted to point out suitable scenarios and user groups as well as still existing challenges and limitations. METHODS: We sum up the experience we made with our use cases with a focus on lessons learned. RESULTS: tranSMART was successfully established by a bottom-up approach at our university hospital and has been running for more than two years now. It has been used in four translational research projects as well as in education in the context of lectures and bachelor/master theses. CONCLUSION: tranSMART can be a very useful tool for translational research and education. But it should be used with both care and statistical knowledge to avoid wrong conclusions. Some technical constraints, especially for data modeling, still limit many applications. Version control and data provenance are remaining challenges.

Semi-automated De-identification of German Content Sensitive Reports for Big Data Analytics.

Purpose Projects involving collaborations between different institutions require data security via selective de-identification of words or phrases. A semi-automated de-identification tool was developed and evaluated on different types of medical reports natively and after adapting the algorithm to the text structure. Materials and Methods A semi-automated de-identification tool was developed and evaluated for its sensitivity and specificity in detecting sensitive content in written reports. Data from 4671 pathology reports (4105 + 566 in two different formats), 2804 medical reports, 1008 operation reports, and 6223 radiology reports of 1167 patients suffering from breast cancer were de-identified. The content was itemized into four categories: direct identifiers (name, address), indirect identifiers (date of birth/operation, medical ID, etc.), medical terms, and filler words. The software was tested natively (without training) in order to establish a baseline. The reports were manually edited and the model re-trained for the next test set. After manually editing 25, 50, 100, 250, 500 and if applicable 1000 reports of each type re-training was applied. Results In the native test, 61.3 % of direct and 80.8 % of the indirect identifiers were detected. The performance (P) increased to 91.4 % (P25), 96.7 % (P50), 99.5 % (P100), 99.6 % (P250), 99.7 % (P500) and 100 % (P1000) for direct identifiers and to 93.2 % (P25), 97.9 % (P50), 97.2 % (P100), 98.9 % (P250), 99.0 % (P500) and 99.3 % (P1000) for indirect identifiers. Without training, 5.3 % of medical terms were falsely flagged as critical data. The performance increased, after training, to 4.0 % (P25), 3.6 % (P50), 4.0 % (P100), 3.7 % (P250), 4.3 % (P500), and 3.1 % (P1000). Roughly 0.1 % of filler words were falsely flagged. Conclusion Training of the developed de-identification tool continuously improved its performance. Training with roughly 100 edited reports enables reliable detection and labeling of sensitive data in different types of medical reports. Key Points: · Collaborations between different institutions require de-identification of patients' data. · Software-based de-identification of content-sensitive reports grows in importance as a result of 'Big data'. · A de-identification software was developed and tested natively and after training. · The proposed de-identification software worked quite reliably, following training with roughly 100 edited reports. · A final check of the texts by an authorized person remains necessary. Citation Format · Seuss H, Dankerl P, Ihle M et al. Semi-automated De-identification of German Content Sensitive Reports for Big Data Analytics. Fortschr Röntgenstr 2017; 189: 661 - 671.

Bion and C.G. Jung. How did the container-contained model find its thinker? The fate of a cryptomnesia.

This paper investigates the possible impact of C.G. Jung's Tavistock Lectures on Bion's concept of the living container. In the first part of the paper, the author offers clues pointing to such an essential impact, which can be found in text passages as well as in the facts of the Bion-Beckett case, up to and including Bion's first publication of 'The imaginary twin'. The author suggests that cryptomnesia is the result of repression targeting a highly cathected author's communication which functions like a deep interpretation for the recipient, whose new theory then is a return of the repressed content as well as a transformation of it. The second part of the paper investigates the fate of the assumed cryptomnesia. From this point of view Bion's concept of the container in itself appears to be the result of growth in the container-contained mode. Finally the author deals with the question whether cryptomnesia in psychoanalytical literature can frequently be seen as the result of psychic growth.

Optimizing R with SparkR on a commodity cluster for biomedical research.

BACKGROUND AND OBJECTIVES: Medical researchers are challenged today by the enormous amount of data collected in healthcare. Analysis methods such as genome-wide association studies (GWAS) are often computationally intensive and thus require enormous resources to be performed in a reasonable amount of time. While dedicated clusters and public clouds may deliver the desired performance, their use requires upfront financial efforts or anonymous data, which is often not possible for preliminary or occasional tasks. We explored the possibilities to build a private, flexible cluster for processing scripts in R based on commodity, non-dedicated hardware of our department. METHODS: For this, a GWAS-calculation in R on a single desktop computer, a Message Passing Interface (MPI)-cluster, and a SparkR-cluster were compared with regards to the performance, scalability, quality, and simplicity. RESULTS: The original script had a projected runtime of three years on a single desktop computer. Optimizing the script in R already yielded a significant reduction in computing time (2 weeks). By using R-MPI and SparkR, we were able to parallelize the computation and reduce the time to less than three hours (2.6 h) on already available, standard office computers. While MPI is a proven approach in high-performance clusters, it requires rather static, dedicated nodes. SparkR and its Hadoop siblings allow for a dynamic, elastic environment with automated failure handling. SparkR also scales better with the number of nodes in the cluster than MPI due to optimized data communication. CONCLUSION: R is a popular environment for clinical data analysis. The new SparkR solution offers elastic resources and allows supporting big data analysis using R even on non-dedicated resources with minimal change to the original code. To unleash the full potential, additional efforts should be invested to customize and improve the algorithms, especially with regards to data distribution.

Intersubjectivity and the creation of meaning in the analytic process.

By means of a clinical illustration, the author describes how the intersubjective exchanges involved in an analytic process facilitate the representation of affects and memories which have been buried in the unconscious or indeed have never been available to consciousness. As a result of projective identificatory processes in the analytic relationship, in this example the analyst falls into a situation of helplessness which connects with his own traumatic experiences. Then he gets into a formal regression of the ego and responds with a so-to-speak hallucinatory reaction-an internal image which enables him to keep the analytic process on track and, later on, to construct an early traumatic experience of the analysand.

Case-based visualization of a patient cohort using SEER epidemiologic data.

Data from cancer registries can be used to track the epidemiology of cancer and can potentially serve to guide individual diagnostic and treatment decisions. Even though some cancer registry datasets have been made publicly available for scientific and clinical use, few applications have so far provided direct access to these data from within the patient context of an electronic patient record. The goal of this project was to implement a proof-of-concept integration of the public SEER (Surveillance, Epidemiology and End Results) cancer registry dataset with a digital breast cancer tumor board at a German university hospital and to determine its utility in the clinical settings. The integration was successfully established, using data from routine documentation to provide dynamic visualizations of cohort composition and Kaplan-Meier survival plots. Evaluation feedback was favorable regarding the concept and implementation, but highlighted that important data elements, e.g. receptor status data, were missing in the SEER dataset, limiting clinical value of the system.

The selective poly(ADP)ribose-polymerase 1 inhibitor INO1001 reduces spinal cord injury during porcine aortic cross-clamping-induced ischemia/reperfusion injury.

OBJECTIVE: It is well-established that poly(ADP)ribose-polymerase (PARP) assumes major importance during ischemic brain damage, and the selective PARP-1 inhibitor PJ34 reduced spinal cord damage in murine aortic occlusion-induced ischemia/reperfusion injury. We investigated the effect of the PARP-1 inhibitor INO1001 on aortic-occlusion-related porcine spinal cord injury. DESIGN AND SETTING: Prospective, randomized, controlled experimental study in an animal laboratory. PATIENTS AND PARTICIPANTS: Ten anesthetized, mechanically ventilated, and instrumented pigs. INTERVENTIONS: Animals underwent 45 min of thoracic aortic cross-clamping after receiving vehicle (n=5) or intravenous INO1001 (n=5, total dose 4 mg/kg administered both before clamping and during reperfusion). During reperfusion continuous intravenous norepinephrine was incrementally adjusted to maintain blood pressure at or above 80% of the preclamping level. Plasma INO1001 levels were analyzed by HPLC. After 4[Symbol: see text]h of reperfusion spinal cord biopsy samples were analyzed for neuronal damage (hematoxyline-eosine and Nissl staining), expression of the cyclin-dependent kinase inhibitor genes p21 and p27 (immunohistochemistry), and apoptosis (terminal deoxynucleotidyl transferase mediated nick end labeling assay). MEASUREMENTS AND RESULTS: Plasma INO1001 levels were 0.8-2.3 and 0.30-0.76 mM before and after clamping, respectively. While 3-5% of the spinal cord neurons were irreversibly damaged in the INO1001 animals, the neuronal cell injury was three times higher in the control group. Neither p21 and p27 expression nor apoptosis showed any intergroup difference. CONCLUSIONS: The selective PARP-1 inhibitor INO1001 markedly reduced aortic occlusion-induced spinal cord injury. Given the close correlation reported in the literature between morphological damage and impaired spinal cord function, INO1001 may improve spinal cord recovery after thoracic aortic cross-clamping.

Experimental validation of noninvasive referencing in navigated procedures on long bones.

Navigation procedures in orthopedic surgery require fixation of reference markers to the anatomic region of interest. Inadequate fixation might lead to micromotion or loosening of the reference marker, consequently causing registration failures or errors in navigation. Osseous rigid fixation is usually achieved by minimally invasive Schanz screws or pins. The goal of this study was to evaluate a non invasive external fixation device, a headband so far used in cranial navigation, as an alternative invasive fixation technique to reference markers in the femur. A common navigation system with an adapted trauma software application was used to track the positions of the soft tissue-attached headband relative to an invasive reference marker on the femur during manipulations of the thigh. Relative translative and rotational movements of the headband were measured during defined movements of the hip and knee and manipulations of the headband itself. The results revealed high translative and rotational movements, up to 6 mm and 3 degrees , respectively, due to minor manipulations of the affected lower extremity. Noninvasive soft tissue fixation with a headband does not allow rigid fixation for accurate navigated registration or operative procedures at the femur. Necessary intraoperative movements or manipulations would cause substantial registration failures. Invasive fixation techniques with screws or pins are still the method of choice.

Phase transformations in a model mesenchymal tissue.

Connective tissues, the most abundant tissue type of the mature mammalian body, consist of cells suspended in complex microenvironments known as extracellular matrices (ECMs). In the immature connective tissues (mesenchymes) encountered in developmental biology and tissue engineering applications, the ECMs contain varying amounts of randomly arranged fibers, and the physical state of the ECM changes as the fibers secreted by the cells undergo fibril and fiber assembly and organize into networks. In vitro composites consisting of assembling solutions of type I collagen, containing suspended polystyrene latex beads ( approximately 6 microm in diameter) with collagen-binding surface properties, provide a simplified model for certain physical aspects of developing mesenchymes. In particular, assembly-dependent topological (i.e., connectivity) transitions within the ECM could change a tissue from one in which cell-sized particles (e.g., latex beads or cells) are mechanically unlinked to one in which the particles are part of a mechanical continuum. Any particle-induced alterations in fiber organization would imply that cells could similarly establish physically distinct microdomains within tissues. Here we show that the presence of beads above a critical number density accelerates the sol-gel transition that takes place during the assembly of collagen into a globally interconnected network of fibers. The presence of this suprathreshold number of beads also dramatically changes the viscoelastic properties of the collagen matrix, but only when the initial concentration of soluble collagen is itself above a critical value. Our studies provide a starting point for the analysis of phase transformations of more complex biomaterials including developing and healing tissues as well as tissue substitutes containing living cells.

Architecture and material properties of diatom shells provide effective mechanical protection.

Diatoms are the major contributors to phytoplankton blooms in lakes and in the sea and hence are central in aquatic ecosystems and the global carbon cycle. All free-living diatoms differ from other phytoplankton groups in having silicified cell walls in the form of two 'shells' (the frustule) of manifold shape and intricate architecture whose function and role, if any, in contributing to the evolutionary success of diatoms is under debate. We explored the defence potential of the frustules as armour against predators by measuring their strength. Real and virtual loading tests (using calibrated glass microneedles and finite element analysis) were performed on centric and pennate diatom cells. Here we show that the frustules are remarkably strong by virtue of their architecture and the material properties of the diatom silica. We conclude that diatom frustules have evolved as mechanical protection for the cells because exceptional force is required to break them. The evolutionary arms race between diatoms and their specialized predators will have had considerable influence in structuring pelagic food webs and biogeochemical cycles.