HEnRY: a DZIF LIMS tool for the collection and documentation of biomaterials in multicentre studies.

BACKGROUND: Well-characterized biomaterials of high quality have great potential for acceleration and quality improvement in translational biomedical research. To improve accessibility of local sample collections, efforts have been made to create central biomaterial banks and catalogues. Available technical solutions for creating professional local sample catalogues and connecting them to central systems are cost intensive and/or technically complex to implement. Therefore, the Translational Thematic Unit HIV of the German Center for Infection Research (DZIF) developed a Laboratory Information and Management System (LIMS) called HIV Engaged Research Technology (HEnRY) for implementation into the Translational Platform HIV (TP-HIV) at the DZIF and other research networks. RESULTS: HEnRY is developed at the University Hospital of Cologne. It is an advanced LIMS to manage processing and storage of samples and aliquots of different sample types. Features include: monitoring of stored samples and associated information data selection via query tools or Structured Query Language (SQL) preparation of summary documents, including scannable search lists centralized management of the practical laboratory part of multicentre studies (e.g. import of drawing schemes and sample processing steps), preparation of aliquot shipments, including associated documents to be added to shipments unique and secure identification of aliquots through use of customizable Quick Response (QR) code labels directly from HEnRY support of aliquot data transmission to central registries. In summary, HEnRY offers all features necessary for a LIMS software. In addition, the structure of HEnRY provides sufficient flexibility to allow the implementation in other research areas. CONCLUSION: HEnRY is a free biobanking tool published under the MIT license. While it was developed to support HIV research in Germany, the feature set and language options, allow much broader applications and make this a powerful free research tool.

Needs for an Integration of Specific Data Sources and Items - First Insights of a National Survey Within the German Center for Infection Research.

State-subsidized programs develop medical data integration centers in Germany. To get infection disease (ID) researchers involved in the process of data sharing, common interests and minimum data requirements were prioritized. In 06/2019 we have initiated the German Infectious Disease Data Exchange (iDEx) project. We have developed and performed an online survey to determine prioritization of requests for data integration and exchange in ID research. The survey was designed with three sub-surveys, including a ranking of 15 data categories and 184 specific data items and a query of available 51 data collecting systems. A total of 84 researchers from 17 fields of ID research participated in the survey (predominant research fields: gastrointestinal infections n=11, healthcare-associated and antibiotic-resistant infections n=10, hepatitis n=10). 48% (40/84) of participants had experience as medical doctor. The three top ranked data categories were microbiology and parasitology, experimental data, and medication (53%, 52%, and 47% of maximal points, respectively). The most relevant data items for these categories were bloodstream infections, availability of biomaterial, and medication (88%, 87%, and 94% of maximal points, respectively). The ranking of requests of data integration and exchange is diverse and depends on the chosen measure. However, there is need to promote discipline-related digitalization and data exchange.

KID--an algorithm for fast and efficient text mining used to automatically generate a database containing kinetic information of enzymes.

BACKGROUND: The amount of available biological information is rapidly increasing and the focus of biological research has moved from single components to networks and even larger projects aiming at the analysis, modelling and simulation of biological networks as well as large scale comparison of cellular properties. It is therefore essential that biological knowledge is easily accessible. However, most information is contained in the written literature in an unstructured way, so that methods for the systematic extraction of knowledge directly from the primary literature have to be deployed. DESCRIPTION: Here we present a text mining algorithm for the extraction of kinetic information such as K(M), K(i), k(cat) etc. as well as associated information such as enzyme names, EC numbers, ligands, organisms, localisations, pH and temperatures. Using this rule- and dictionary-based approach, it was possible to extract 514,394 kinetic parameters of 13 categories (K(M), K(i), k(cat), k(cat)/K(M), V(max), IC(50), S(0.5), K(d), K(a), t(1/2), pI, n(H), specific activity, V(max)/K(M)) from about 17 million PubMed abstracts and combine them with other data in the abstract. A manual verification of approx. 1,000 randomly chosen results yielded a recall between 51% and 84% and a precision ranging from 55% to 96%, depending of the category searched.The results were stored in a database and are available as "KID the KInetic Database" via the internet. CONCLUSIONS: The presented algorithm delivers a considerable amount of information and therefore may aid to accelerate the research and the automated analysis required for today's systems biology approaches. The database obtained by analysing PubMed abstracts may be a valuable help in the field of chemical and biological kinetics. It is completely based upon text mining and therefore complements manually curated databases. The database is available at http://kid.tu-bs.de. The source code of the algorithm is provided under the GNU General Public Licence and available on request from the author.

mSpecs: a software tool for the administration and editing of mass spectral libraries in the field of metabolomics.

BACKGROUND: Metabolome analysis with GC/MS has meanwhile been established as one of the "omics" techniques. Compound identification is done by comparison of the MS data with compound libraries. Mass spectral libraries in the field of metabolomics ought to connect the relevant mass traces of the metabolites to other relevant data, e.g. formulas, chemical structures, identification numbers to other databases etc. Since existing solutions are either commercial and therefore only available for certain instruments or not capable of storing such information, there is need to provide a software tool for the management of such data. RESULTS: Here we present mSpecs, an open source software tool to manage mass spectral data in the field of metabolomics. It provides editing of mass spectra and virtually any associated information, automatic calculation of formulas and masses and is extensible by scripts. The graphical user interface is capable of common techniques such as copy/paste, undo/redo and drag and drop. It owns import and export filters for the major public file formats in order to provide compatibility to commercial instruments. CONCLUSION: mSpecs is a versatile tool for the management and editing of mass spectral libraries in the field of metabolomics. Beyond that it provides capabilities for the automatic management of libraries though its scripting functionality. mSpecs can be used on all major platforms and is licensed under the GNU General Public License and available at http://mspecs.tu-bs.de.

Impact of meteorological conditions on the incidence of acute aortic dissection.

BACKGROUND:: There is still much controversy about whether meteorological conditions influence the occurrence of acute aortic dissection (AAD). The aim of the present study was to investigate the possible correlation between atmospheric pressure, temperature, lunar cycle and the event of aortic dissection in our patient population. METHODS:: The clinical data for 348 patients with AAD (73% type Stanford A) were confronted with the meteorological data provided by the Cologne weather station over the same period. RESULTS:: There were no statistically significant differences between meteorological parameters on days of AAD events compared with control days. A logistic regression model showed that air pressure (odds ratio [OR] 1.004, 95% confidence interval [CI] 0.991-1.017, p = 0.542), air temperature (OR 0.978, 95% CI 0.949-1.008, p = 0.145), season ( p = 0.918) and month of the event ( p = 0.175) as well as presence of full moon (OR 1.579, 95% CI 0.763-3.270, p = 0.219) were not able to predict AAD events. Also, no predictive power of meteorological data and season was found on analysing their impact on different types of AAD events. CONCLUSIONS:: Our study did not reveal any dependence of atmospheric pressure, air temperature or the presence of full moon on the incidence of different types of AAD.

Impact of gender on long-term outcomes after surgical repair for acute Stanford A aortic dissection: a propensity score matched analysis.

OBJECTIVES: Previous research suggests that female gender is associated with increased mortality rates after surgery for Stanford A acute aortic dissection (AAD). However, women with AAD usually present with different clinical symptoms that may bias outcomes. Moreover, there is a lack of long-term results regarding overall mortality and freedom from major cerebrovascular events. We analysed the impact of gender on long-term outcomes after surgery for Stanford A AAD by comparing genders with similar risk profiles using propensity score matching. METHODS: A total of 240 patients operated for Stanford A AAD were included in this study. To control for selection bias and other confounders, propensity score matching was applied to gender groups. RESULTS: After propensity score matching, the gender groups were well balanced in terms of risk profiles. There were no statistically significant differences regarding duration of cardiopulmonary bypass ( P = 0.165) and duration of aortic cross-clamp time ( P = 0.111). Female patients received less fresh frozen plasma ( P = 0.021), had shorter stays in the intensive care unit ( P = 0.031), lower incidence of temporary neurological dysfunction ( P < 0.001) and lower incidence of dialysis ( P = 0.008). There were no significant differences regarding intraoperative mortality ( P = 1.000), 30-day mortality ( P = 0.271), long-term overall cumulative survival ( P = 0.954) and long-term freedom from cerebrovascular events ( P = 0.235) with up to a 9-year follow-up. CONCLUSIONS: Considering patients with similar risk profiles, female gender per se is not associated with worse long-term survival and freedom from stroke after surgical aortic repair. Moreover, female patients might even benefit from a smoother early postoperative course and lower incidence of early postoperative complications.

Axillar or Aortic Cannulation for Aortic Repair in Patients With Stanford A Dissection?

BACKGROUND: The choice of an optimal cannulation site for aortic repair in patients with Stanford A acute aortic dissection remains controversial. The aim of this study was to compare the early results and long-term outcomes of axillar and direct aortic cannulation. METHODS: A total of 235 consecutive patients who underwent surgical aortic repair with the use of axillar or direct aortic cannulation from January 2006 to April 2015 were analyzed. The primary end points were long-term overall cumulative survival and freedom from major cerebrovascular events with up to 10 years of follow-up. The secondary end points were early postoperative clinical characteristics and rates of adverse events. To control for confounders, a 1:3 propensity score matching was performed. RESULTS: After matching, there were no statistically significant differences between the two groups regarding baseline characteristics. Both groups were associated with comparable outcomes; among other things, the length of stay in the intensive care unit (ICU) (p = 0.220), mechanical ventilation (p = 0.177), total hospital stay (p = 0.243), and hospital rates of adverse events. There were no statistically significant differences (p = 0.625) in terms of freedom from major cerebrovascular events. However, both early (p = 0.009) and late (p = 0.016) overall survival were significantly poorer for patients undergoing aortic cannulation. CONCLUSIONS: The outcomes were comparable regarding early hospital outcomes and rates of adverse events. Whereas postoperative freedom from major cerebrovascular events was similar, survival over long-term follow-up was significantly poorer when direct aortic cannulation was used. More investigations are needed to enable an understanding of the underlying factors for potentially higher late mortality when direct aortic cannulation is used during a surgical procedure for acute Stanford A dissection.