Monitoring Flow-Forming Processes Using Design of Experiments and a Machine Learning Approach Based on Randomized-Supervised Time Series Forest and Recursive Feature Elimination.

The machines of WF Maschinenbau process metal blanks into various workpieces using so-called flow-forming processes. The quality of these workpieces depends largely on the quality of the blanks and the condition of the machine. This creates an urgent need for automated monitoring of the forming processes and the condition of the machine. Since the complexity of the flow-forming processes makes physical modeling impossible, the present work deals with data-driven modeling using machine learning algorithms. The main contributions of this work lie in showcasing the feasibility of utilizing machine learning and sensor data to monitor flow-forming processes, along with developing a practical approach for this purpose. The approach includes an experimental design capable of providing the necessary data, as well as a procedure for preprocessing the data and extracting features that capture the information needed by the machine learning models to detect defects in the blank and the machine. To make efficient use of the small number of experiments available, the experimental design is generated using Design of Experiments methods. They consist of two parts. In the first part, a pre-selection of influencing variables relevant to the forming process is performed. In the second part of the design, the selected variables are investigated in more detail. The preprocessing procedure consists of feature engineering, feature extraction and feature selection. In the feature engineering step, the data set is augmented with time series variables that are meaningful in the domain. For feature extraction, an algorithm was developed based on the mechanisms of the r-STSF, a state-of-the-art algorithm for time series classification, extending them for multivariate time series and metric target variables. This feature extraction algorithm itself can be seen as an additional contribution of this work, because it is not tied to the application domain of monitoring flow-forming processes, but can be used as a feature extraction algorithm for multivariate time series classification in general. For feature selection, a Recursive Feature Elimination is employed. With the resulting features, random forests are trained to detect several quality features of the blank and defects of the machine. The trained models achieve good prediction accuracy for most of the target variables. This shows that the application of machine learning is a promising approach for the monitoring of flow-forming processes, which requires further investigation for confirmation.

Medication event extraction in clinical notes: Contribution of the WisPerMed team to the n2c2 2022 challenge.

In this work, we describe the findings of the 'WisPerMed' team from their participation in Track 1 (Contextualized Medication Event Extraction) of the n2c2 2022 challenge. We tackle two tasks: (i) medication extraction, which involves extracting all mentions of medications from the clinical notes, and (ii) event classification, which involves classifying the medication mentions based on whether a change in the medication has been discussed. To address the long lengths of clinical texts, which often exceed the maximum token length that models based on the transformer-architecture can handle, various approaches, such as the use of ClinicalBERT with a sliding window approach and Longformer-based models, are employed. In addition, domain adaptation through masked language modeling and preprocessing steps such as sentence splitting are utilized to improve model performance. Since both tasks were treated as named entity recognition (NER) problems, a sanity check was performed in the second release to eliminate possible weaknesses in the medication detection itself. This check used the medication spans to remove false positive predictions and replace missed tokens with the highest softmax probability of the disposition types. The effectiveness of these approaches is evaluated through multiple submissions to the tasks, as well as with post-challenge results, with a focus on the DeBERTa v3 model and its disentangled attention mechanism. Results show that the DeBERTa v3 model performs well in both the NER task and the event classification task.

Static and Dynamic Accuracy and Occlusion Robustness of SteamVR Tracking 2.0 in Multi-Base Station Setups.

The tracking of objects and person position, orientation, and movement is relevant for various medical use cases, e.g., practical training of medical staff or patient rehabilitation. However, these demand high tracking accuracy and occlusion robustness. Expensive professional tracking systems fulfill these demands, however, cost-efficient and potentially adequate alternatives can be found in the gaming industry, e.g., SteamVR Tracking. This work presents an evaluation of SteamVR Tracking in its latest version 2.0 in two experimental setups, involving two and four base stations. Tracking accuracy, both static and dynamic, and occlusion robustness are investigated using a VIVE Tracker (3.0). A dynamic analysis further compares three different velocities. An error evaluation is performed using a Universal Robots UR10 robotic arm as ground-truth system under nonlaboratory conditions. Results are presented using the Root Mean Square Error. For static experiments, tracking errors in the submillimeter and subdegree range are achieved by both setups. Dynamic experiments achieved errors in the submillimeter range as well, yet tracking accuracy suffers from increasing velocity. Four base stations enable generally higher accuracy and robustness, especially in the dynamic experiments. Both setups enable adequate accuracy for diverse medical use cases. However, use cases demanding very high accuracy should primarily rely on SteamVR Tracking 2.0 with four base stations.

Nano or Not Nano? A Structured Approach for Identifying Nanomaterials According to the European Commission's Definition.

Identifying nanomaterials (NMs) according to European Union legislation is challenging, as there is an enormous variety of materials, with different physico-chemical properties. The NanoDefiner Framework and its Decision Support Flow Scheme (DSFS) allow choosing the optimal method to measure the particle size distribution by matching the material properties and the performance of the particular measurement techniques. The DSFS leads to a reliable and economic decision whether a material is an NM or not based on scientific criteria and respecting regulatory requirements. The DSFS starts beyond regulatory requirements by identifying non-NMs by a proxy approach based on their volume-specific surface area. In a second step, it identifies NMs. The DSFS is tested on real-world materials and is implemented in an e-tool. The DSFS is compared with a decision flowchart of the European Commission's (EC) Joint Research Centre (JRC), which rigorously follows the explicit criteria of the EC NM definition with the focus on identifying NMs, and non-NMs are identified by exclusion. The two approaches build on the same scientific basis and measurement methods, but start from opposite ends: the JRC Flowchart starts by identifying NMs, whereas the NanoDefiner Framework first identifies non-NMs.

Plasmons in MoS2 studied via experimental and theoretical correlation of energy loss spectra.

This paper takes a fundamental view of the electron energy loss spectra of monolayer and few layer MoS2 . The dielectric function of monolayer MoS2 is compared to the experimental spectra to give clear criteria for the nature of different signals. Kramers-Krönig analysis allows a direct extraction of the dielectric function from the experimental data. However this analysis is sensitive to slight changes in the normalisation step of the data pretreatment. Density functional theory provides simulations of the dielectric function for comparison and validation of experimental findings. Simulated and experimental spectra are compared to isolate the π and π + σ surface plasmon modes in monolayer MoS2 . Single-particle excitations obscure the plasmons in the monolayer spectrum and momentum resolved measurements give indication of indirect interband transitions that are excited due to the large convergence and collection angles used in the experiment. LAY DESCRIPTION: Two-dimensional materials offer a path forward for smaller and more efficient devices. Their optical and electronic properties give way to beat the limits set in place by Moore's Law. Plasmon are the collective oscillations of electrons and can confine light to dimensions much smaller than its wavelength. In this work we explore the plasmonic properties of MoS2 , a representational candidate from a family of 2D materials known as transition metal dichalcogenides. High resolution electron microscopy and spectroscopy provide insights in the plasmonic properties of MoS2 down to an atomic scale. Experimental results show the relationship between plasmons and interband transitions in the electron energy loss spectrum. Density functional theory provides a theoretical support for the experimental findings and provides commentary on the fundamental underlying physics.

Association of single and multiple aneurysms with tobacco abuse: an @neurIST risk analysis.

OBJECTIVE: Although several studies have suggested that the incidence of intracranial aneurysms (IAs) is higher in smokers, the higher prevalence of subarachnoid hemorrhage (SAH) in smokers remains uncertain. It is unclear whether smoking additionally contributes to the formation of multiple aneurysms and the risk of rupture. The aim of this study was to determine whether smoking is associated with IA formation, multiplicity, or rupture. METHODS: Patients from the prospective multicenter @neurIST database (n = 1410; 985 females [69.9%]) were reviewed for the presence of SAH, multiple aneurysms, and smoking status. The prevalence of smokers in the population of patients diagnosed with at least one IA was compared with that of smokers in the general population. RESULTS: The proportion of smokers was higher in patients with IAs (56.2%) than in the reference population (51.4%; p < 0.001). A significant association of smoking with the presence of an IA was found throughout group comparisons (p = 0.01). The presence of multiple IAs was also significantly associated with smoking (p = 0.003). A trend was found between duration of smoking and the presence of multiple IAs (p = 0.057). However, the proportion of smokers among patients suffering SAH was similar to that of smokers among patients diagnosed with unruptured IAs (p = 0.48). CONCLUSIONS: Smoking is strongly associated with IA formation. Once an IA is present, however, smoking does not appear to increase the risk of rupture compared with IAs in the nonsmoking population. The trend toward an association between duration of smoking and the presence of multiple IAs stresses the need for counseling patients with IAs regarding lifestyle modification.

Server-Focused Security Assessment of Mobile Health Apps for Popular Mobile Platforms.

BACKGROUND: The importance of mobile health (mHealth) apps is growing. Independent of the technologies used, mHealth apps bring more functionality into the hands of users. In the health context, mHealth apps play an important role in providing information and services to patients, offering health care professionals ways to monitor vital parameters or consult patients remotely. The importance of confidentiality in health care and the opaqueness of transport security in apps make the latter an important research subject. OBJECTIVE: This study aimed to (1) identify relevant security concerns on the server side of mHealth apps, (2) test a subset of mHealth apps regarding their vulnerability to those concerns, and (3) compare the servers used by mHealth apps with servers used in all domains. METHODS: Server security characteristics relevant to the security of mHealth apps were assessed, presented, and discussed. To evaluate servers, appropriate tools were selected. Apps from the Android and iOS app stores were selected and tested, and the results for functional and other backend servers were evaluated. RESULTS: The 60 apps tested communicate with 823 servers. Of these, 291 were categorized as functional backend servers, and 44 (44/291, 15.1%) of these received a rating below the A range (A+, A, and A-) by Qualys SSL Labs. A chi-square test was conducted against the number of servers receiving such ratings from SSL Pulse by Qualys SSL Labs. It was found that the tested servers from mHealth apps received significantly fewer ratings below the A range (P<.001). The internationally available apps from the test set performed significantly better than those only available in the German stores (alpha=.05; P=.03). Of the 60 apps, 28 (28/60, 47%) were found using at least one functional backend server that received a rating below the A range from Qualys SSL Labs, endangering confidentiality, authenticity, and integrity of the data displayed. The number of apps that used at least one entirely unsecured connection was 20 (20/60, 33%) when communicating with functional backend servers. It was also found that a majority of apps used advertising, tracking, or external content provider servers. When looking at all nonfunctional backend servers, 48 (48/60, 80%) apps used at least one server that received a rating below the A range. CONCLUSIONS: The results show that although servers in the mHealth domain perform significantly better regarding their security, there are still problems with the configuration of some. The most severe problems observed can expose patient communication with health care professionals, be exploited to display false or harmful information, or used to send data to an app facilitating further damage on the device. Following the recommendations for mHealth app developers, the most regularly observed security issues can be avoided or mitigated.

Spin excitations in solids from many-body perturbation theory.

Collective spin excitations form a fundamental class of excitations in magnetic materials. As their energy reaches down to only a few meV, they are present at all temperatures and substantially influence the properties of magnetic systems. To study the spin excitations in solids from first principles, we have developed a computational scheme based on many-body perturbation theory within the full-potential linearized augmented plane-wave (FLAPW) method. The main quantity of interest is the dynamical transverse spin susceptibility or magnetic response function, from which magnetic excitations, including single-particle spin-flip Stoner excitations and collective spin-wave modes as well as their lifetimes, can be obtained. In order to describe spin waves we include appropriate vertex corrections in the form of a multiple-scattering T matrix, which describes the coupling of electrons and holes with different spins. The electron-hole interaction incorporates the screening of the many-body system within the random-phase approximation. To reduce the numerical cost in evaluating the four-point T matrix, we exploit a transformation to maximally localized Wannier functions that takes advantage of the short spatial range of electronic correlation in the partially filled d or f orbitals of magnetic materials. The theory and the implementation are discussed in detail. In particular, we show how the magnetic response function can be evaluated for arbitrary k points. This enables the calculation of smooth dispersion curves, allowing one to study fine details in the k dependence of the spin-wave spectra. We also demonstrate how spatial and time-reversal symmetry can be exploited to accelerate substantially the computation of the four-point quantities. As an illustration, we present spin-wave spectra and dispersions for the elementary ferromagnet bcc Fe, B2-type tetragonal FeCo, and CrO2 calculated with our scheme. The results are in good agreement with available experimental data.

Systematic comparison of 3D Deep learning and classical machine learning explanations for Alzheimer's Disease detection.

Black-box deep learning (DL) models trained for the early detection of Alzheimer's Disease (AD) often lack systematic model interpretation. This work computes the activated brain regions during DL and compares those with classical Machine Learning (ML) explanations. The architectures used for DL were 3D DenseNets, EfficientNets, and Squeeze-and-Excitation (SE) networks. The classical models include Random Forests (RFs), Support Vector Machines (SVMs), eXtreme Gradient Boosting (XGBoost), Light Gradient Boosting (LightGBM), Decision Trees (DTs), and Logistic Regression (LR). For explanations, SHapley Additive exPlanations (SHAP) values, Local Interpretable Model-agnostic Explanations (LIME), Gradient-weighted Class Activation Mapping (GradCAM), GradCAM++ and permutation-based feature importance were implemented. During interpretation, correlated features were consolidated into aspects. All models were trained on the Alzheimer's Disease Neuroimaging Initiative (ADNI) dataset. The validation includes internal and external validation on the Australian Imaging and Lifestyle flagship study of Ageing (AIBL) and the Open Access Series of Imaging Studies (OASIS). DL and ML models reached similar classification performances. Regarding the brain regions, both types focus on different regions. The ML models focus on the inferior and middle temporal gyri, and the hippocampus, and amygdala regions previously associated with AD. The DL models focus on a wider range of regions including the optical chiasm, the entorhinal cortices, the left and right vessels, and the 4th ventricle which were partially associated with AD. One explanation for the differences is the input features (textures vs. volumes). Both types show reasonable similarity to a ground truth Voxel-Based Morphometry (VBM) analysis. Slightly higher similarities were measured for ML models.

ROCOv2: Radiology Objects in COntext Version 2, an Updated Multimodal Image Dataset.

Automated medical image analysis systems often require large amounts of training data with high quality labels, which are difficult and time consuming to generate. This paper introduces Radiology Object in COntext version 2 (ROCOv2), a multimodal dataset consisting of radiological images and associated medical concepts and captions extracted from the PMC Open Access subset. It is an updated version of the ROCO dataset published in 2018, and adds 35,705 new images added to PMC since 2018. It further provides manually curated concepts for imaging modalities with additional anatomical and directional concepts for X-rays. The dataset consists of 79,789 images and has been used, with minor modifications, in the concept detection and caption prediction tasks of ImageCLEFmedical Caption 2023. The dataset is suitable for training image annotation models based on image-caption pairs, or for multi-label image classification using Unified Medical Language System (UMLS) concepts provided with each image. In addition, it can serve for pre-training of medical domain models, and evaluation of deep learning models for multi-task learning.

Piximi - An Images to Discovery web tool for bioimages and beyond.

Deep learning has greatly accelerated research in biological image analysis yet it often requires programming skills and specialized tool installation. Here we present Piximi, a modern, no-programming image analysis tool leveraging deep learning. Implemented as a web application at Piximi.app, Piximi requires no installation and can be accessed by any modern web browser. Its client-only architecture preserves the security of researcher data by running all computation locally. Piximi offers four core modules: a deep learning classifier, an image annotator, measurement modules, and pre-trained deep learning segmentation modules. Piximi is interoperable with existing tools and workflows by supporting import and export of common data and model formats. The intuitive researcher interface and easy access to Piximi allows biological researchers to obtain insights into images within just a few minutes. Piximi aims to bring deep learning-powered image analysis to a broader community by eliminating barriers to entry.

Diabetic foot ulcers segmentation challenge report: Benchmark and analysis.

Monitoring the healing progress of diabetic foot ulcers is a challenging process. Accurate segmentation of foot ulcers can help podiatrists to quantitatively measure the size of wound regions to assist prediction of healing status. The main challenge in this field is the lack of publicly available manual delineation, which can be time consuming and laborious. Recently, methods based on deep learning have shown excellent results in automatic segmentation of medical images, however, they require large-scale datasets for training, and there is limited consensus on which methods perform the best. The 2022 Diabetic Foot Ulcers segmentation challenge was held in conjunction with the 2022 International Conference on Medical Image Computing and Computer Assisted Intervention, which sought to address these issues and stimulate progress in this research domain. A training set of 2000 images exhibiting diabetic foot ulcers was released with corresponding segmentation ground truth masks. Of the 72 (approved) requests from 47 countries, 26 teams used this data to develop fully automated systems to predict the true segmentation masks on a test set of 2000 images, with the corresponding ground truth segmentation masks kept private. Predictions from participating teams were scored and ranked according to their average Dice similarity coefficient of the ground truth masks and prediction masks. The winning team achieved a Dice of 0.7287 for diabetic foot ulcer segmentation. This challenge has now entered a live leaderboard stage where it serves as a challenging benchmark for diabetic foot ulcer segmentation.

Risk of rupture of small anterior communicating artery aneurysms is similar to posterior circulation aneurysms.

BACKGROUND AND PURPOSE: According to the International Study of Unruptured Intracranial Aneurysms (ISUIA), anterior circulation (AC) aneurysms of <7 mm in diameter have a minimal risk of rupture. It is general experience, however, that anterior communicating artery (AcoA) aneurysms are frequent and mostly rupture at <7 mm. The aim of the study was to assess whether AcoA aneurysms behave differently from other AC aneurysms. METHODS: Information about 932 patients newly diagnosed with intracranial aneurysms between November 1, 2006, and March 31, 2012, including aneurysm status at diagnosis, its location, size, and risk factors, was collected during the multicenter @neurIST project. For each location or location and size subgroup, the odds ratio (OR) of aneurysms being ruptured at diagnosis was calculated. RESULTS: The OR for aneurysms to be discovered ruptured was significantly higher for AcoA (OR, 3.5 [95% confidence interval, 2.6-4.5]) and posterior circulation (OR, 2.6 [95% confidence interval, 2.1-3.3]) than for AC excluding AcoA (OR, 0.5 [95% confidence interval, 0.4-0.6]). Although a threshold of 7 mm has been suggested by ISUIA as a threshold for aggressive treatment, AcoA aneurysms <7 mm were more frequently found ruptured (OR, 2.0 [95% confidence interval, 1.3-3.0]) than AC aneurysms of 7 to 12 mm diameter as defined in ISUIA. CONCLUSIONS: We found that AC aneurysms are not a homogenous group. Aneurysms between 4 and 7 mm located in AcoA or distal anterior cerebral artery present similar rupture odds to posterior circulation aneurysms. Intervention should be recommended for this high-risk lesion group.

Explainable AI in medical imaging: An overview for clinical practitioners - Saliency-based XAI approaches.

Since recent achievements of Artificial Intelligence (AI) have proven significant success and promising results throughout many fields of application during the last decade, AI has also become an essential part of medical research. The improving data availability, coupled with advances in high-performance computing and innovative algorithms, has increased AI's potential in various aspects. Because AI rapidly reshapes research and promotes the development of personalized clinical care, alongside its implementation arises an urgent need for a deep understanding of its inner workings, especially in high-stake domains. However, such systems can be highly complex and opaque, limiting the possibility of an immediate understanding of the system's decisions. Regarding the medical field, a high impact is attributed to these decisions as physicians and patients can only fully trust AI systems when reasonably communicating the origin of their results, simultaneously enabling the identification of errors and biases. Explainable AI (XAI), becoming an increasingly important field of research in recent years, promotes the formulation of explainability methods and provides a rationale allowing users to comprehend the results generated by AI systems. In this paper, we investigate the application of XAI in medical imaging, addressing a broad audience, especially healthcare professionals. The content focuses on definitions and taxonomies, standard methods and approaches, advantages, limitations, and examples representing the current state of research regarding XAI in medical imaging. This paper focuses on saliency-based XAI methods, where the explanation can be provided directly on the input data (image) and which naturally are of special importance in medical imaging.

Explainable AI in medical imaging: An overview for clinical practitioners - Beyond saliency-based XAI approaches.

Driven by recent advances in Artificial Intelligence (AI) and Computer Vision (CV), the implementation of AI systems in the medical domain increased correspondingly. This is especially true for the domain of medical imaging, in which the incorporation of AI aids several imaging-based tasks such as classification, segmentation, and registration. Moreover, AI reshapes medical research and contributes to the development of personalized clinical care. Consequently, alongside its extended implementation arises the need for an extensive understanding of AI systems and their inner workings, potentials, and limitations which the field of eXplainable AI (XAI) aims at. Because medical imaging is mainly associated with visual tasks, most explainability approaches incorporate saliency-based XAI methods. In contrast to that, in this article we would like to investigate the full potential of XAI methods in the field of medical imaging by specifically focusing on XAI techniques not relying on saliency, and providing diversified examples. We dedicate our investigation to a broad audience, but particularly healthcare professionals. Moreover, this work aims at establishing a common ground for cross-disciplinary understanding and exchange across disciplines between Deep Learning (DL) builders and healthcare professionals, which is why we aimed for a non-technical overview. Presented XAI methods are divided by a method's output representation into the following categories: Case-based explanations, textual explanations, and auxiliary explanations.

NanoDefiner Framework and e-Tool Revisited According to the European Commission's Nanomaterial Definition 2022/C 229/01.

The new recommended definition of a nanomaterial, 2022/C 229/01, adopted by the European Commission in 2022, will have a considerable impact on European Union legislation addressing chemicals, and therefore tools to implement this new definition are urgently needed. The updated NanoDefiner framework and its e-tool implementation presented here are such instruments, which help stakeholders to find out in a straightforward way whether a material is a nanomaterial or not. They are two major outcomes of the NanoDefine project, which is explicitly referred to in the new definition. This work revisits the framework and e-tool, and elaborates necessary adjustments to make these outcomes applicable for the updated recommendation. A broad set of case studies on representative materials confirms the validity of these adjustments. To further foster the sustainability and applicability of the framework and e-tool, measures for the FAIRification of expert knowledge within the e-tool's knowledge base are elaborated as well. The updated framework and e-tool are now ready to be used in line with the updated recommendation. The presented approach may serve as an example for reviewing existing guidance and tools developed for the previous definition 2011/696/EU, particularly those adopting NanoDefine project outcomes.

Optical Properties of MoSe2 Monolayer Implanted with Ultra-Low-Energy Cr Ions.

This paper explores the optical properties of an exfoliated MoSe2 monolayer implanted with Cr+ ions, accelerated to 25 eV. Photoluminescence of the implanted MoSe2 reveals an emission line from Cr-related defects that is present only under weak electron doping. Unlike band-to-band transition, the Cr-introduced emission is characterized by nonzero activation energy, long lifetimes, and weak response to the magnetic field. To rationalize the experimental results and get insights into the atomic structure of the defects, we modeled the Cr-ion irradiation process using ab initio molecular dynamics simulations followed by the electronic structure calculations of the system with defects. The experimental and theoretical results suggest that the recombination of electrons on the acceptors, which could be introduced by the Cr implantation-induced defects, with the valence band holes is the most likely origin of the low-energy emission. Our results demonstrate the potential of low-energy ion implantation as a tool to tailor the properties of two-dimensional (2D) materials by doping.

Strength of the effective Coulomb interaction at metal and insulator surfaces.

The effective on-site Coulomb interaction (Hubbard U) between localized electrons at crystal surfaces is expected to be enhanced due to the reduced coordination number and reduced subsequent screening. By means of first principles calculations employing the constrained random-phase approximation we show that this is indeed the case for simple metals and insulators but not necessarily for transition metals and insulators that exhibit pronounced surface states. In the latter case, the screening contribution from surface states as well as the influence of the band narrowing increases the electron polarization to such an extent as to overcompensate the decrease resulting from the reduced effective screening volume. The Hubbard U parameter is thus substantially reduced in some cases, e.g., by around 30% for the (100) surface of bcc Cr.

Which is the best anticoagulant for whole blood aggregometry platelet function testing? Comparison of six anticoagulants and diverse storage conditions.

Major hindrances of impedance aggregometry are caused by limited storage time and the requirement of ex vivo anticoagulation. Data on the influence of different anticoagulants and storage conditions are rare and incomplete. This study has systematically examined the influence of six different anticoagulants (sodium and lithium heparin, 20 µg/mL and 45 µg/mL r-hirudin, benzylsulfonyl-D-Arg-Pro-4-amidinobenzylamide (BAPA), and citrate) on the results of Adenosine 5'-diphosphate (ADP) and arachidonic acid (AA) induced measurements using multiple-electrode impedance aggregometer (MEA). Measurements were carried out in a time frame of 0 min up to 48 h after blood withdrawal. In addition, the influence of storage temperatures of 4°C and 37°C was evaluated. Results of ADP-induced tests significantly varied within the first 30 min in all tested anticoagulants, in citrated blood even within the first 60 min. They remained stable up to 2 h in 20 µg/mL r-hirudin and BAPA, 4 h in citrate, 8 h in 45 µg/mL r-hirudin, and lithium heparin and up to a maximum of 12 h in sodium heparin anticoagulated blood. The analysis of AA-induced tests revealed no significantly different results up to 6 h when BAPA was used, 8 h in lithium heparin, 20 µg/mL r-hirudin and citrate, 12 h in 45 µg/mL r-hirudin, and even 24 h in sodium heparin-anticoagulated samples. A storage temperature of either 4°C or 37°C in contrast to room temperature had a negative influence on the stability of results. In conclusion, sodium heparin and 45 µg/mL r-hirudin as anticoagulants guarantee the longest storage time for impedance aggregometry.

Mining biomarker information in biomedical literature.

BACKGROUND: For selection and evaluation of potential biomarkers, inclusion of already published information is of utmost importance. In spite of significant advancements in text- and data-mining techniques, the vast knowledge space of biomarkers in biomedical text has remained unexplored. Existing named entity recognition approaches are not sufficiently selective for the retrieval of biomarker information from the literature. The purpose of this study was to identify textual features that enhance the effectiveness of biomarker information retrieval for different indication areas and diverse end user perspectives. METHODS: A biomarker terminology was created and further organized into six concept classes. Performance of this terminology was optimized towards balanced selectivity and specificity. The information retrieval performance using the biomarker terminology was evaluated based on various combinations of the terminology's six classes. Further validation of these results was performed on two independent corpora representing two different neurodegenerative diseases. RESULTS: The current state of the biomarker terminology contains 119 entity classes supported by 1890 different synonyms. The result of information retrieval shows improved retrieval rate of informative abstracts, which is achieved by including clinical management terms and evidence of gene/protein alterations (e.g. gene/protein expression status or certain polymorphisms) in combination with disease and gene name recognition. When additional filtering through other classes (e.g. diagnostic or prognostic methods) is applied, the typical high number of unspecific search results is significantly reduced. The evaluation results suggest that this approach enables the automated identification of biomarker information in the literature. A demo version of the search engine SCAIView, including the biomarker retrieval, is made available to the public through http://www.scaiview.com/scaiview-academia.html. CONCLUSIONS: The approach presented in this paper demonstrates that using a dedicated biomarker terminology for automated analysis of the scientific literature maybe helpful as an aid to finding biomarker information in text. Successful extraction of candidate biomarkers information from published resources can be considered as the first step towards developing novel hypotheses. These hypotheses will be valuable for the early decision-making in the drug discovery and development process.