Search Results (24)

Background: Cholangiocarcinoma (CCA) are aggressive bile duct cancers with a poor prognosis for which there are only few established prognostic biomarkers and molecular targets available. The gene ITIH5, a known class II tumor suppressor gene (C2TSG), encodes a secreted protein of the extracellular matrix mediating tumor suppressive properties. Recently, it was surprisingly found that the ITIH5 protein is specifically upregulated in CCAs and that ITIH5 detection in blood could be an excellent liquid biopsy marker for indicating the presence of a CCA tumor in a patient. We therefore investigated whether patients with CCAs with abundant versus low ITIH5 protein expression also differ in their prognosis. Methods: To clarify this question, a large CCA cohort (n = 175) was examined using immunohistochemistry on a tissue microarray (TMA). Results: Abundant ITIH5 expression in CCA was associated with favorable survival, a low UICC stage and the absence of perineural invasion (PNI). Conclusions: ITIH5 has biomarker potential not only for the early detection of CCA from blood-based liquid biopsies but also as a prognostic tissue biomarker for risk stratification. Our results suggest that the upregulation of ITIH5 is particularly abundant in intrahepatic CCAs (iCCA). The mechanisms mediating the strong initial upregulation of ITIH5 during the oncogenic transformation of bile duct cells are still unclear. Full article

The navigation waterways to the harbors of Rostock (Warnow Estuary), Germany, and Szczecin (Oder/Szczecin Lagoon), Poland, were recently deepened. Both activities required Environmental Impact Assessments. We conducted expert- and data-based ecosystem service assessments for both case studies. Additionally, we performed 3D-ecosystem model simulations. For the Oder Lagoon, the model results show that the waterway deepening increased the burial in sediments by 807 t N/a, 112 t P/a and 4661 T C/a. However, altogether, the impacts of the deepening to 12.5 m draught on the lagoon ecosystem are minor and a model application is not necessary, but the results improve the data basis for ecosystem service assessments. Our expert-based ecosystem service approach is adaptable to the needs of coastal engineering and hydraulic projects and is both easy and quick to apply and transferable. The assessment results highlight the relevance of cultural services and can complement EIAs. Our approach can especially support the early scoping stage of an EIA. It has the potential to enhance cooperation and communication with and between stakeholders, reduce conflicts, and save time. Additionally, it could improve the compilation and addressing of stakeholder concerns, potentially reducing costs associated with unnecessary studies. Full article

Type 2 diabetes mellitus (T2D) poses a significant global health challenge and demands effective self-management strategies, including continuous blood glucose monitoring (CGM) and lifestyle adaptations. While CGM offers real-time glucose level assessment, the quest for minimizing trauma and enhancing convenience has spurred the need to explore non-invasive alternatives for monitoring vital signs in patients with T2D. Objective: This systematic review is the first that explores the current literature and critically evaluates the use and reporting of non-invasive wearable devices for monitoring vital signs in patients with T2D. Methods: Employing the PRISMA and PICOS guidelines, we conducted a comprehensive search to incorporate evidence from relevant studies, focusing on randomized controlled trials (RCTs), systematic reviews, and meta-analyses published since 2017. Of the 437 publications identified, seven were selected based on predetermined criteria. Results: The seven studies included in this review used various sensing technologies, such as heart rate monitors, accelerometers, and other wearable devices. Primary health outcomes included blood pressure measurements, heart rate, body fat percentage, and cardiorespiratory endurance. Non-invasive wearable devices demonstrated potential for aiding T2D management, albeit with variations in efficacy across studies. Conclusions: Based on the low number of studies with higher evidence levels (i.e., RCTs) that we were able to find and the significant differences in design between these studies, we conclude that further evidence is required to validate the application, efficacy, and real-world impact of these wearable devices. Emphasizing transparency in bias reporting and conducting in-depth research is crucial for fully understanding the implications and benefits of wearable devices in T2D management. Full article

Inflammatory properties are known to promote tumor progression leading to an impaired median overall survival (mOS). Various small studies have focused on a wide range of inflammation-based prognostic indicators. By using sufficient data from 1294 out of 2323 patients diagnosed with pancreatic cancer between 2009 and 2021 at our cancer center, inflammatory markers such as the neutrophil to lymphocyte ratio (NRL), the platelet to lymphocyte ratio (PLR), the lymphocyte to monocyte ratio (LMR) and the CRP to albumin ratio (CAR) were evaluated. We identified a new combined score, termed the inflammatory benchmark index (IBI). We performed univariate and multivariate overall survival analyses and identified optimal prognostic cut-off values for each parameter. In univariate analyses, advanced age (p < 0.001), gender (p < 0.001), tumor stage (p < 0.001), CA19-9 (p = 0.001), NLR (p = 0.001), LMR (p = 0.004), PLR (p = 0.004), CAR (p = 0.001) and IBI (p = 0.001) were identified as prognostic markers. In multivariate analyses advanced age (p < 0.001), gender (p = 0.001), tumor stage (p < 0.001), CA19-9 (p < 0.001), NLR (p = 0.001), LMR (p = 0.038), CAR (p < 0.001) and IBI (p < 0.001) were independent prognostic markers. These findings emphasize the impact of inflammation in pancreatic cancer, provide easily accessible prognostic values for the clinician, and may be useful as stratification parameters for trials aimed at patient inflammation or immune response. Full article

Integrative taxonomy is a fundamental part of biodiversity and combines traditional morphology with additional methods such as DNA sequencing or biochemistry. Here, we aim to establish untargeted metabolomics for use in chemotaxonomy. We used three thallose liverwort species Riccia glauca, R. sorocarpa, and R. warnstorfii (order Marchantiales, Ricciaceae) with Lunularia cruciata (order Marchantiales, Lunulariacea) as an outgroup. Liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) were integrated with DNA marker-based sequencing of the trnL-trnF region and high-resolution bioimaging. Our untargeted chemotaxonomy methodology enables us to distinguish taxa based on chemophenetic markers at different levels of complexity: (1) molecules, (2) compound classes, (3) compound superclasses, and (4) molecular descriptors. For the investigated Riccia species, we identified 71 chemophenetic markers at the molecular level, a characteristic composition in 21 compound classes, and 21 molecular descriptors largely indicating electron state, presence of chemical motifs, and hydrogen bonds. Our untargeted approach revealed many chemophenetic markers at different complexity levels that can provide more mechanistic insight into phylogenetic delimitation of species within a clade than genetic-based methods coupled with traditional morphology-based information. However, analytical and bioinformatics analysis methods still need to be better integrated to link the chemophenetic information at multiple scales. Full article

Introduction: In lateralized oral squamous cell carcinoma (OSCC) with ipsilateral cervical lymph node metastasis (CLNM), the surgical management of the unsuspicious contralateral neck remains a matter of debate. The aim of this study was to analyze this cohort and to compare the outcomes of patients with and without contralateral elective neck dissection (END). Material and Methods: A retrospective analysis of patients with lateralized OSCC, ipsilateral CLNM (pN+) and contralateral cN0-stage was performed. Patients were divided into two groups according to the surgical management of the contralateral neck: I: END; and II: no END performed. Adjuvant radiotherapy was applied bilaterally in both groups according to individual risk. Results: A total of 65 patients (group I: 16 (24.6%); group II: 49 (75.4%)) with a median follow-up of 28 months were included. Initially, there was no case of contralateral CLNM after surgery. During follow-up, 6 (9.2%) patients presented with recurrent CLNM. In 5 of these cases (7.7%), the contralateral neck (group I: 3/16 (18.8%); group II: 2/49 (4.1%)) was affected. Increased ipsilateral lymph node ratio was associated with contralateral CLNM (p = 0.07). END of the contralateral side showed no significant benefit regarding OS (p = 0.59) and RFS (p = 0.19). Conclusions: Overall, the risk for occult contralateral CLNM in patients with lateralized OSCC ipsilateral CLNM is low. Our data suggest that END should not be performed routinely in this cohort. Risk-adapted radiotherapy of the contralateral neck alone seems to be sufficient from the oncological point of view. Full article

Bryophytes are prolific producers of unique, specialized metabolites that are not found in other plants. As many of these unique natural products are potentially interesting, for example, pharmacological use, variations in the production regarding ecological or environmental conditions have not often been investigated. Here, we investigate metabolic shifts in the epiphytic Radula complanata L. (Dumort) with regard to different environmental conditions and the type of phorophyte (host tree). Plant material was harvested from three different locations in Sweden, Germany, and Canada and subjected to untargeted liquid chromatography high-resolution mass-spectrometry (UPLC/ESI-QTOF-MS) and data-dependent acquisition (DDA-MS). Using multivariate statistics, variable selection methods, in silico compound identification, and compound classification, a large amount of variation (39%) in the metabolite profiles was attributed to the type of host tree and 25% to differences in environmental conditions. We identified 55 compounds to vary significantly depending on the host tree (36 on the family level) and 23 compounds to characterize R. complanata in different environments. Taken together, we found metabolic shifts mainly in primary metabolites that were associated with the drought response to different humidity levels. The metabolic shifts were highly specific to the host tree, including mostly specialized metabolites suggesting high levels of ecological interaction. As R. complanata is a widely distributed generalist species, we found it to flexibly adapt its metabolome according to different conditions. We found metabolic composition to also mirror the constitution of the habitat, which makes it interesting for conservation measures. Full article

The Smarter Together project implemented in the three lighthouse cities (LHCs) of Lyon, Munich, and Vienna a set of co-created and integrated smart solutions for a better life in urban districts. The implemented solutions have been monitored using a novel integrated monitoring methodology (IMM) following a co-creation process involving key stakeholders of the LHCs. With focus on holistic building refurbishment and the integration of onsite renewable energy supply (RES), the three LHCs refurbished around 117,497 m² of floor area and constructed 12,446 m² of new floor area. They implemented around 833 kWp of PV, 35 kW of solar thermal and 13,122 kW of geothermal heating systems. Altogether, the realized solutions for low-energy districts in the three LHCs will annually save around 4000 MWh/a, generate 1145 MWh/a of RES and reduce around 1496 tCO₂/a of CO₂ emissions, corresponding to specific values of 37.6 kWh/m².a and 11.9 kg-CO₂/m².a for final energy saving and CO₂ emission reductions, respectively. KPI-based monitoring and evaluation of the implemented solutions provides qualitative and quantitative insight, experience and lessons learned to optimize the process of implementation and deployment of integrated solutions for holistic building refurbishment, and thus contribute to advancing sustainable urban transformation at the district level for both LHCs and FCs. Full article

Liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics experiments have become increasingly popular because of the wide range of metabolites that can be analyzed and the possibility to measure novel compounds. LC-MS instrumentation and analysis conditions can differ substantially among laboratories and experiments, thus resulting in non-standardized datasets demanding customized annotation workflows. We present an ecosystem of R packages, centered around the MetaboCoreUtils, MetaboAnnotation and CompoundDb packages that together provide a modular infrastructure for the annotation of untargeted metabolomics data. Initial annotation can be performed based on MS¹ properties such as m/z and retention times, followed by an MS²-based annotation in which experimental fragment spectra are compared against a reference library. Such reference databases can be created and managed with the CompoundDb package. The ecosystem supports data from a variety of formats, including, but not limited to, MSP, MGF, mzML, mzXML, netCDF as well as MassBank text files and SQL databases. Through its highly customizable functionality, the presented infrastructure allows to build reproducible annotation workflows tailored for and adapted to most untargeted LC-MS-based datasets. All core functionality, which supports base R data types, is exported, also facilitating its re-use in other R packages. Finally, all packages are thoroughly unit-tested and documented and are available on GitHub and through Bioconductor. Full article

Introduction: Several studies suggest an estrogen receptor alpha (ERα)-mediated influence on the pathogenesis of oral squamous cell carcinoma (OSCC), as described for other malignancies that are not considered to be primarily hormone-dependent. Recently, an association between ERα expression and improved survival in oropharyngeal squamous cell carcinoma (OPSCC) has been found. However, the prognostic relevance of ERα in OSCC has not been proven to date. Therefore, the aim of this study was to evaluate ERα expression in OSCC in a large patient cohort and analyze its influence on survival and recurrence. Material and Methods: A total of 316 patients with primary OSCC who received initial surgical therapy were included in this analysis. The expression of ERα was evaluated on tissue microarrays by immunohistochemistry in the primary tumor and/or primary lymph node metastases. The expression level was quantified by light microscopy using the immunoreactive score (IRS) for estrogen receptor detection. An IRS equal to or greater than 2 was considered positive. The 5-year overall survival (OS) and relapse-free survival (RFS) were examined by the Kaplan–Meier method and log-rank test. Results: A total of 316 patients (111 females; 205 males) with a mean age of 61.3 years (range 27–96 years) were included in this study. In 16 patients (5.1%; 6 females and 10 males), positive ERα expression was found in the primary tumor (n = 11; 11/302) or lymph node metastases (n = 5; 5/52). Patients with positive ERα expression in primary tumors/primary lymph node metastases had a significantly lower OS and RFS (p = 0.012; p = 0.0053) compared to ERα-negative patients. Sub-group analysis in relation to gender revealed a highly significant influence of ERα expression on OS and RFS in males but not in females, both for the ERα-positive primary tumor cohort (males: p = 0.0013; p < 0.0001; females: p = 0.56; p = 0.89) and the ERα-positive primary tumor/primary lymph node metastasis cohort (males: p < 0.0001; p < 0.0001; females: p = 0.95; p = 0.96). In multivariate cox regression analysis, the ERα IRS of primary tumors (dichotomized; ERα+ vs. ERα−) was an independent risk factor for OS (HR = 4.230; 95%CI 1.616–11.076; p = 0.003) and RFS (HR = 12.390; 95%CI 4.073–37.693; p < 0.001) in the male cohort. There was a significant difference (p = 0.006) of ERα positivity with regard to the localization of the primary tumor. ERα positivity in the primary tumor was significantly associated (p = 0.026) with UICC stage, with most of the cases being diagnosed in stage IV. Furthermore, there was a significantly (p = 0.049) higher rate of bone infiltration in ERα-positive patients. Conclusion: Expression of ERα is rare in OSCC; however, it is associated with a dramatic decrease in OS in male patients. Further studies are necessary to confirm our results and to evaluate the exact mechanism underlying this observation. Hence, ERα-positive OSCC patients might benefit from an ER-based therapeutic (adjuvant) approach in the future. Full article

Concurrent suboptimal supply of several nutrients requires the coordination of nutrient-specific transcriptional, phenotypic, and metabolic changes in plants in order to optimize growth and development in most agricultural and natural ecosystems. Phosphate (P_i) and iron (Fe) deficiency induce overlapping but mostly opposing transcriptional and root growth responses in Arabidopsis thaliana. On the metabolite level, P_i deficiency negatively modulates Fe deficiency-induced coumarin accumulation, which is controlled by Fe as well as P_i deficiency response regulators. Here, we report the impact of Fe availability on seedling growth under P_i limiting conditions and on P_i deficiency-induced accumulation of amino acids and organic acids, which play important roles in P_i use efficiency. Fe deficiency in P_i replete conditions hardly changed growth and metabolite profiles in roots and shoots of Arabidopsis thaliana, but partially rescued growth under conditions of P_i starvation and severely modulated P_i deficiency-induced metabolic adjustments. Analysis of T-DNA insertion lines revealed the concerted coordination of metabolic profiles by regulators of Fe (FIT, bHLH104, BRUTUS, PYE) as well as of P_i (SPX1, PHR1, PHL1, bHLH32) starvation responses. The results show the interdependency of P_i and Fe availability and the interplay between P_i and Fe starvation signaling on the generation of plant metabolite profiles. Full article

While adolescents and adults should limit high levels of sedentary behavior, university students spend large amounts of time on sedentary activities. The aim of this study was to investigate the effect of this prolonged sitting on students’ self-perceived physical, mental, and cognitive condition and to answer the question of whether simple standing breaks in lectures can help students improve these conditions and for example feel more concentrated, motivated, or less tense in class. A five-minute standing break was introduced using a designed presentation slide for one semester in five different 90-min lectures. In addition, an active break as well as an open break with no trigger were implemented in two further lectures to explicitly investigate the effects of a standing break. Before, during, and after the semester, the students were surveyed about their physical, mental, and cognitive condition (836 respondents at start, 634 during semester, and 528 at the end). To evaluate the practicality and acceptance of the standing break, lecturers were interviewed about their experience. At all survey time points, the standing break was highly accepted by the university students. About three quarters of the students felt a relaxation of the muscles in the neck and shoulder as well as in the back and the legs. More than three quarters perceived an increase in concentration, receptiveness and retentiveness, motivation, and well-being. Results of the statistical analysis indicate that a standing break as well as an active break are more effective than an open break to improve the self-perceived physical and psychological well-being of the university students. The increase in cognitive skills is reported by all groups, including the group who were offered open breaks. Hence, standing breaks in university lectures receive a high level of acceptance and practicability and have the potential to increase students’ physical, mental, and cognitive condition and contribute to students’ physical activity and health. While field research provides opportunities such as the testing of measures in the natural environment and producing real-life results relevant to the students and lecturers, it also imposes limitations as lecture settings differed, not all disturbances could be controlled, and the participation in the study might have led to social-desirability bias. For a sustainable development of a standing-friendly teaching and learning culture at universities, further interventions as well as the consideration of the topic in all processes and decisions within the universities are necessary. Since this study has taken place, student-life has changed drastically with COVID-19 measures. While this current paper is based on research conducted in 2019 and has only tested live lectures on campus, the tools tested could also be used for online lectures. Full article

In plant ecology, biochemical analyses of bryophytes and vascular plants are often conducted on dried herbarium specimen as species typically grow in distant and inaccessible locations. Here, we present an automated in silico compound classification framework to annotate metabolites using an untargeted data independent acquisition (DIA)–LC/MS–QToF-sequential windowed acquisition of all theoretical fragment ion mass spectra (SWATH) ecometabolomics analytical method. We perform a comparative investigation of the chemical diversity at the global level and the composition of metabolite families in ten different species of bryophytes using fresh samples collected on-site and dried specimen stored in a herbarium for half a year. Shannon and Pielou’s diversity indices, hierarchical clustering analysis (HCA), sparse partial least squares discriminant analysis (sPLS-DA), distance-based redundancy analysis (dbRDA), ANOVA with post-hoc Tukey honestly significant difference (HSD) test, and the Fisher’s exact test were used to determine differences in the richness and composition of metabolite families, with regard to herbarium conditions, ecological characteristics, and species. We functionally annotated metabolite families to biochemical processes related to the structural integrity of membranes and cell walls (proto-lignin, glycerophospholipids, carbohydrates), chemical defense (polyphenols, steroids), reactive oxygen species (ROS) protection (alkaloids, amino acids, flavonoids), nutrition (nitrogen- and phosphate-containing glycerophospholipids), and photosynthesis. Changes in the composition of metabolite families also explained variance related to ecological functioning like physiological adaptations of bryophytes to dry environments (proteins, peptides, flavonoids, terpenes), light availability (flavonoids, terpenes, carbohydrates), temperature (flavonoids), and biotic interactions (steroids, terpenes). The results from this study allow to construct chemical traits that can be attributed to biogeochemistry, habitat conditions, environmental changes and biotic interactions. Our classification framework accelerates the complex annotation process in metabolomics and can be used to simplify biochemical patterns. We show that compound classification is a powerful tool that allows to explore relationships in both molecular biology by “zooming in” and in ecology by “zooming out”. The insights revealed by our framework allow to construct new research hypotheses and to enable detailed follow-up studies. Full article

The central aim in ecometabolomics and chemical ecology is to pinpoint chemical features that explain molecular functioning. The greatest challenge is the identification of compounds due to the lack of constitutive reference spectra, the large number of completely unknown compounds, and bioinformatic methods to analyze the big data. In this study we present an interdisciplinary methodological framework that extends ultra-performance liquid chromatography coupled to electrospray ionization quadrupole time-of-flight mass spectrometry (UPLC/ESI-QTOF-MS) with data-dependent acquisition (DDA-MS) and the automated in silico classification of fragment peaks into compound classes. We synthesize findings from a prior study that explored the influence of seasonal variations on the chemodiversity of secondary metabolites in nine bryophyte species. Here we reuse and extend the representative dataset with DDA-MS data. Hierarchical clustering, heatmaps, dbRDA, and ANOVA with post-hoc Tukey HSD were used to determine relationships of the study factors species, seasons, and ecological characteristics. The tested bryophytes showed species-specific metabolic responses to seasonal variations (50% vs. 5% of explained variation). Marchantia polymorpha, Plagiomnium undulatum, and Polytrichum strictum were biochemically most diverse and unique. Flavonoids and sesquiterpenoids were upregulated in all bryophytes in the growing seasons. We identified ecological functioning of compound classes indicating light protection (flavonoids), biotic and pathogen interactions (sesquiterpenoids, flavonoids), low temperature and desiccation tolerance (glycosides, sesquiterpenoids, anthocyanins, lactones), and moss growth supporting anatomic structures (few methoxyphenols and cinnamic acids as part of proto-lignin constituents). The reusable bioinformatic framework of this study can differentiate species based on automated compound classification. Our study allows detailed insights into the ecological roles of biochemical constituents of bryophytes with regard to seasonal variations. We demonstrate that compound classification can be improved with adding constitutive reference spectra to existing spectral libraries. We also show that generalization on compound classes improves our understanding of molecular ecological functioning and can be used to generate new research hypotheses. Full article

Metabolomics aims to measure and characterise the complex composition of metabolites in a biological system. Metabolomics studies involve sophisticated analytical techniques such as mass spectrometry and nuclear magnetic resonance spectroscopy, and generate large amounts of high-dimensional and complex experimental data. Open source processing and analysis tools are of major interest in light of innovative, open and reproducible science. The scientific community has developed a wide range of open source software, providing freely available advanced processing and analysis approaches. The programming and statistics environment R has emerged as one of the most popular environments to process and analyse Metabolomics datasets. A major benefit of such an environment is the possibility of connecting different tools into more complex workflows. Combining reusable data processing R scripts with the experimental data thus allows for open, reproducible research. This review provides an extensive overview of existing packages in R for different steps in a typical computational metabolomics workflow, including data processing, biostatistics, metabolite annotation and identification, and biochemical network and pathway analysis. Multifunctional workflows, possible user interfaces and integration into workflow management systems are also reviewed. In total, this review summarises more than two hundred metabolomics specific packages primarily available on CRAN, Bioconductor and GitHub. Full article