Text mining processing pipeline for semi structured data D3.3

Unstructured and semi-structured cohort data contain relevant information about the health condition of a patient, e.g., free text describing disease diagnoses, drugs, medication reasons, which are often not available in structured formats. One of the challenges posed by medical free texts is that there can be several ways of mentioning a concept. Therefore, encoding free text into unambiguous descriptors allows us to leverage the value of the cohort data, in particular, by facilitating its findability and interoperability across cohorts in the project.Named entity recognition and normalization enable the automatic conversion of free text into standard medical concepts. Given the volume of available data shared in the CINECA project, the WP3 text mining working group has developed named entity normalization techniques to obtain standard concepts from unstructured and semi-structured fields available in the cohorts. In this deliverable, we present the methodology used to develop the different text mining tools created by the dedicated SFU, UMCG, EBI, and HES-SO/SIB groups for specific CINECA cohorts

Validity of the acute recovery and stress scale: training monitoring of the German junior national field hockey team

The aim of the present study was to examine the sensitivity of the Acute Recovery and Stress Scale (ARSS). This new psychometric questionnaire was developed to assess the physical, mental, emotional, and overall recovery and stress states of athletes. During a five-day field hockey training camp of the German Junior National Field Hockey Team (n = 25) the ARSS was administered every morning and evening. The study indicated swift reactions of the scores of the physical and general factors as well as stability of scores for the emotional factors in accordance with the training schedule. The straining effect of the camp was best reflected by the adaptations of the scales Physical Performance Capability (F (2.9, 60.3) = 10.0, p < 0.001) and Muscular Stress (F (4, 84) = 16.7, p < 0.001). The results support the ability of the ARSS to monitor recovery-stress (im-) balances in this sample. Thus, the questionnaire has shown to be a sensitive and practical tool that might be suitable for elite sport settings

Muscle mechanical properties of strength and endurance athletes and changes after one week of intensive training

The study investigates whether tensiomyography (TMG) is sensitive to differentiate between strength and endurance athletes, and to monitor fatigue after either one week of intensive strength (ST) or endurance (END) training. Fourteen strength (24.1 +/- 2.0 years) and eleven endurance athletes (25.5 +/- 4.8 years) performed an intensive training period of 6 days of ST or END, respectively. ST and END groups completed specific performance tests as well as TMG measurements of maximal radial deformation of the muscle belly (Dm), deformation time between 10% and 90% Dm (Tc), rate of deformation development until 10% Dm (V10) and 90% Dm (V90) before (baseline), after training period (post1), and after 72 h of recovery (post2). Specific performance of both groups decreased from baseline to post1 (P < 0.05) and returned to baseline values at post2 (P < 0.05). The ST group showed higher countermovement jump (P < 0.05) and shorter Tc (P < 0.05) at baseline. After training, Dm, V10, and V90 were reduced in the ST (P < 0.05) while TMG changes were less pronounced in the END. TMG could be a useful tool to differentiate between strength and endurance athletes, and to monitor fatigue and recovery especially in strength training. (C) 2016 Elsevier Ltd. All rights reserved

How does a short, interrupted recovery break affect performance and how is it assessed? A study on acute effects

A recovery process with optimal prerequisites, which is interrupted, is termed disrupted recovery. Whether this process has an influence on performance-related factors needs to be investigated. Therefore, the aim of this study was to examine how a short disturbance of a recovery phase is assessed and whether subsequent repeated sprint performance is affected by it. A quasi-experimental 2x2-factors cross-over design with 34 sport science undergraduate students (age 20.3 ± 2.1) was applied. Factors were the type of intervention (power nap vs. systematic breathing; between-subjects) and the experimental condition (disturbed vs. non-disturbed break; within-subjects). Repeated sprint performance was measured through 6x4 s sprint protocols (with 20 s breaks) before and after a 25 min recovery break on two test days. Subjective evaluation of the interventions was measured through the Short Recovery and Stress Scale and a manipulation check assessing whether participants experienced the recovery phase as efficacious and pleasant. Regarding the objective data, no significant difference between sprint performances in terms of average peak velocity (m/s) on the NMT was found. The manipulation check revealed that disturbed conditions were rated significantly lower than regular conditions in terms of appreciation, t(31) = 3.09, p = .01. Short disturbances of recovery do not seem to affect subsequent performance; nevertheless, participants assessed disturbed conditions more negative than regular conditions. In essence, the findings indicate a negligible role of short interruptions on an objective level. Subjectively, they affected the performance-related assessment of the participants and should be treated with caution

Monitoring training and recovery responses with heart rate measures during standardized warm-up in elite badminton players

Purpose To investigate short-term training and recovery-related effects on heart rate during a standardized submaximal running test. Methods Ten elite badminton players (7 females and 3 males) were monitored during a 12-week training period in preparation for the World Championships. Exercise heart rate (HRex) and perceived exertion were measured in response to a 5-min submaximal shuttle-run test during the morning session warm-up. This test was repeatedly performed on Mondays after 1–2 days of pronounced recovery (‘recovered’ state; reference condition) and on Fridays following 4 consecutive days of training (‘strained’ state). In addition, the serum concentration of creatine kinase and urea, perceived recovery–stress states, and jump performance were assessed before warm-up. Results Creatine kinase increased in the strained compared to the recovered state and the perceived recovery–stress ratings decreased and increased, respectively (range of average effects sizes: |d| = 0.93–2.90). The overall HRex was 173 bpm and the observed within-player variability (i.e., standard deviation as a coefficient of variation [CV]) was 1.3% (90% confidence interval: 1.2% to 1.5%). A linear reduction of -1.4% (-3.0% to 0.3%) was observed in HRex over the 12-week observational period. HRex was -1.5% lower (-2.2% to -0.9%) in the strained compared to the recovered state, and the standard deviation (as a CV) representing interindividual variability in this response was 0.7% (-0.6% to 1.2%). Conclusions Our findings suggest that HRex measured during a standardized warm-up can be sensitive to short-term accumulation of training load, with HRex decreasing on average in response to consecutive days of training within repeated preparatory weekly microcycles. From a practical perspective, it seems advisable to determine intra-individual recovery–strain responses by repeated testing, as HRex responses may vary substantially between and within players

Recovery-Stress Response of Blood-Based Biomarkers

The purpose of this study was to investigate blood-based biomarkers and their regulation with regard to different recovery-stress states. A total of 35 male elite athletes (13 badminton, 22 soccer players) were recruited, and two venous blood samples were taken: one in a ‘recovered’ state (REC) after a minimum of one-day rest from exercise and another one in a ‘non-recovered’ state (NOR) after a habitual loading microcycle. Overall, 23 blood-based biomarkers of different physiologic domains, which address inflammation, muscle damage, and tissue repair, were analyzed by Luminex assays. Across all athletes, only creatine kinase (CK), interleukin (IL-) 6, and IL-17A showed higher concentrations at NOR compared to REC time points. In badminton players, higher levels of CK and IL-17A at NOR were found. In contrast, a higher value for S100 calcium-binding protein A8 (S100A8) at REC was found in badminton players. Similar differences were found for BDNF in soccer players. Soccer players also showed increased levels of CK, and IL-6 at NOR compared to REC state. Several molecular markers were shown to be responsive to differing recoverystress states, but their suitability as biomarkers in training must be further validated

Can cold water immersion enhance recovery in elite Olympic weightlifters? An individualized perspective

We investigated whether cold water immersion following intensive training sessions can enhance recovery in elite Olympic weightlifters, taking into account each athlete's individual response pattern. The entire German male Olympic weightlifting national team participated in the study (n=7), ensuring collection of data from elite athletes only. Using a randomized cross-over design, the athletes went through two high intensity training microcycles consisting of five training sessions that were either followed by a cold water immersion or passive recovery. Barbell speed in a snatch pull movement, blood parameters as well as subjective ratings of general fatigue and recovery were assessed throughout the study. Physical performance at two snatch pull intensities (85% 1RM: -0.15% vs. -0.22%, P=0.94; 90% 1RM: -0.7% vs. +1.23%, P=0.25) did not differ significantly (condition x time). While questionnaires revealed a significant decline in ratings of overall recovery (

Towards an Interoperable Ecosystem of Research Cohort and Real-world Data Catalogues Enabling Multi-center Studies

Objectives : Existing individual-level human data cover large populations on many dimensions such as lifestyle, demography, laboratory measures, clinical parameters, etc. Recent years have seen large investments in data catalogues to FAIRify data descriptions to capitalise on this great promise, i.e. make catalogue contents more Findable, Accessible, Interoperable and Reusable. However, their valuable diversity also created heterogeneity, which poses challenges to optimally exploit their richness. Methods : In this opinion review, we analyse catalogues for human subject research ranging from cohort studies to surveillance, administrative and healthcare records. Results : We observe that while these catalogues are heterogeneous, have various scopes, and use different terminologies, still the underlying concepts seem potentially harmonizable. We propose a unified framework to enable catalogue data sharing, with catalogues of multi-center cohorts nested as a special case in catalogues of real-world data sources. Moreover, we list recommendations to create an integrated community of metadata catalogues and an open catalogue ecosystem to sustain these efforts and maximise impact. Conclusions : We propose to embrace the autonomy of motivated catalogue teams and invest in their collaboration via minimal standardisation efforts such as clear data licensing, persistent identifiers for linking same records between catalogues, minimal metadata ‘common data elements’ using shared ontologies, symmetric architectures for data sharing (push/pull) with clear provenance tracks to process updates and acknowledge original contributors. And most importantly, we encourage the creation of environments for collaboration and resource sharing between catalogue developers, building on international networks such as OpenAIRE and research data alliance, as well as domain specific ESFRIs such as BBMRI and ELIXIR

miRNAs and sports: tracking training status and potentially confounding diagnoses

Background: The dependency of miRNA abundance from physiological processes such as exercises remains partially understood. We set out to analyze the effect of physical exercises on miRNA profiles in blood and plasma of endurance and strength athletes in a systematic manner and correlated differentially abundant miRNAs in athletes to disease miRNAs biomarkers towards a better understanding of how physical exercise may confound disease diagnosis by miRNAs. Methods: We profiled blood and plasma of 29 athletes before and after exercise. With four samples analyzed for each individual we analyzed 116 full miRNomes. The study set-up enabled paired analyses of individuals. Affected miRNAs were investigated for known disease associations using network analysis. Results: MiRNA patterns in blood and plasma of endurance and strength athletes vary significantly with differences in blood outreaching variations in plasma. We found only moderate differences between the miRNA levels before training and the RNA levels after training as compared to the more obvious variations found between strength athletes and endurance athletes. We observed significant variations in the abundance of miR-140-3p that is a known circulating disease markers (raw and adjusted p value of 5 × 10−12 and 4 × 10−7). Similarly, the levels of miR-140-5p and miR-650, both of which have been reported as makers for a wide range of human pathologies significantly depend on the training mode. Among the most affected disease categories we found acute myocardial infarction. MiRNAs, which are up-regulated in endurance athletes inhibit VEGFA as shown by systems biology analysis of experimentally validated target genes. Conclusion: We provide evidence that the mode and the extent of training are important confounding factors for a miRNA based disease diagnosis

Neurotoxic Alkaloids: Saxitoxin and Its Analogs

Saxitoxin (STX) and its 57 analogs are a broad group of natural neurotoxic alkaloids, commonly known as the paralytic shellfish toxins (PSTs). PSTs are the causative agents of paralytic shellfish poisoning (PSP) and are mostly associated with marine dinoflagellates (eukaryotes) and freshwater cyanobacteria (prokaryotes), which form extensive blooms around the world. PST producing dinoflagellates belong to the genera Alexandrium, Gymnodinium and Pyrodinium whilst production has been identified in several cyanobacterial genera including Anabaena, Cylindrospermopsis, Aphanizomenon Planktothrix and Lyngbya. STX and its analogs can be structurally classified into several classes such as non-sulfated, mono-sulfated, di-sulfated, decarbamoylated and the recently discovered hydrophobic analogs—each with varying levels of toxicity. Biotransformation of the PSTs into other PST analogs has been identified within marine invertebrates, humans and bacteria. An improved understanding of PST transformation into less toxic analogs and degradation, both chemically or enzymatically, will be important for the development of methods for the detoxification of contaminated water supplies and of shellfish destined for consumption. Some PSTs also have demonstrated pharmaceutical potential as a long-term anesthetic in the treatment of anal fissures and for chronic tension-type headache. The recent elucidation of the saxitoxin biosynthetic gene cluster in cyanobacteria and the identification of new PST analogs will present opportunities to further explore the pharmaceutical potential of these intriguing alkaloids