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In 2007, the European Parliament established the Directive 2007/2/EC for the Infrastructure for Spatial Information in the European Community (INSPIRE). The goal of this Directive was to implement specific technical rules for the interoperability and harmonization of spatial data-sets and services based on the Spatial Data Infrastructures (SDI) of each Member State. This article describes the results of a survey for the use of Geoinformatics and the maturity level of the INSPIRE Directive within Member States and European Free Trade Association (EFTA) countries. The survey contacted between March 2017 and December 2017. An online survey was sent through mail to the Geographic Information System (GIS) technical staff of the Statistical Institutes (SI) of the EU and EFTA countries. In total, 17 EU countries and 2 EFTA countries responded to the invitation for the survey. The analysis of the responses in this questionnaire demonstrated that the state of implementation of INSPIRE still displays dissimilar levels of maturity across the SIs, while the degree of using geospatial technologies differs from service to service.

There is a trend of significantly more people to be employed in the agro-food sector in Southern Europe lately, mainly due to the changes occurred in the E.U. economy the last years. However, there is definitely a challenge that has to be met in order to obtain competitive agricultural products, and has to do with the management of natural resources (soil, water and energy). Eleagro (developed by GeoAnalysis S.A.) is developing a tool for remote crop monitoring with the use of Unmanned Aerial Vehicles (UAVs) and satellites, aiming at using these technologies for precision agriculture management. Remote sensing is advantageous over traditional methods of plant and soil sampling, because it offers the potential for quick area mapping of soil and plant properties and allows for quantification of crop variation (e.g. nutrient deficiency or sufficiency, pest and disease attacks and infestations, water stress and faulty irrigation equipment detection and weed infestation). Remote sensing in agriculture is predicted to be in the near future the main methodology of data acquisition from agricultural field parcels, due to the physical evolution of satellite technology providing better spatial resolution and lower cost image acquisition. The creation of crop information with the use of remote sensing techniques is expected to aid in the connection between the crop management knowledge obtained through long experimentation and the spatial analysis of the problems that need to be managed. Thus, treatments available at the disposal of the growers have to be targeted towards specific management zones in the field and should not be broadcasted uniformly over the whole area, increasing the cost of plant protection and damaging the environment. The same principle applies for plant nutrition. GeoAnalysis S.A. also, along with crop monitoring, is developing pest management techniques, using natural or bio-physical means for the reduction of the agro-ecosystem pathogenesis. The present work has assessed thermal imagery and plant analysis as tools for early detection of Verticillium wilt, in accordance with an 11-point calibration scale, which was based on visual observation of the disease symptoms. [ABSTRACT FROM AUTHOR]

Targeted proteomics methods have been greatly improved and refined over the last decade and are becoming increasingly the method of choice in protein and peptide quantitative assays. Despite the tremendous progress, targeted proteomics assays still suffer from inadequate sensitivity for lower abundant proteins and throughput, especially in complex biological samples. These attributes are essential for establishing targeted proteomics methods at the forefront of clinical use. Here, we report an assay utilizing the SureQuant internal standard-triggered targeted method on a latest generation mass spectrometer coupled with an EvoSep One liquid chromatography platform, which displays high sensitivity and a high throughput of 100 samples per day. We demonstrate the robustness of this method by quantifying proteins spanning six orders of magnitude in human wound fluid exudates, a biological fluid that exhibits sample complexity and composition similar to plasma. Among the targets quantified were low-abundance proteins such at tumor necrosis factor A and interleukin 1-β, highlighting the value of this method in the quantification of trace amounts of invaluable biomarkers that were until recently hardly accessible by targeted proteomics methods. Taken together, this method extends the toolkit of targeted proteomics assays and will help to drive forward mass spectrometry-based proteomics biomarker quantification., Competing Interests: Conflicts of Interest H. S. is a full-time employee of HARTMANN. The other authors declare no competing interests., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

Recently, there has been a major push toward the development of next-generation treatments against snakebite envenoming. However, unlike current antivenoms that rely on animal-derived polyclonal antibodies, most of these novel approaches are reliant on an in-depth understanding of the over 2000 known snake venom toxins. Indeed, by identifying similarities (i.e., conserved epitopes) across these different toxins, it is possible to design cross-reactive treatments, such as broadly-neutralising antibodies, that target these similarities. Therefore, in this project, we built an automated pipeline that generates sequence and structural distance matrices and homology trees across all available snake venom toxin sequences and structures. To facilitate analysis, we also developed a user-friendly and high-throughput visualisation tool, coined "Venom TOxin CluStering" (V-ToCs). This tool allows researchers to easily investigate sequence and structure patterns in snake venom toxins for a wide array of purposes, such as elucidating toxin evolution, and will also hopefully help guide the discovery and development of increasingly broadly-neutralising antivenoms in the near future., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 The Authors. Published by Elsevier Ltd.. All rights reserved.)

The geospatial dataset presented in this manuscript, represents elements of the historical, natural, political and cultural environment of Cyprus, as it was recorded by British officials during the early years (1878-1883) of their administration on the island. The data were derived from Horatio Herbert Kitchener's map of Cyprus, published in 1885 in 15 sheets, at a scale of 1:63 360 (1 inch to 1 mile), which is considered a milestone in the cartography of the island. The geospatial layers were extracted my manual on-screen digitization of the geographic features depicted on the georeferenced seamless mosaic created by the individual sheets (Chalkias et al., 2023). The database consists of the following vector layers: (a) road network, (b) hydrographic network, (c) administration boundaries as well as land cover/use in raster format and covers the entire area of the island (9 247 km 2 ). In addition, the locations and the population attributes recorded in the census of 1881, have been added to the database as well. Historical maps and censuses are a valuable and the most common source of geospatial data used in historical research, when space and the spatial distribution of phenomena, are considered a critical parameter. However, among other, the availability of historical geospatial data, is recognized as a limitation to the further development of Historical GIS. Therefore, this dataset aims to contribute to this need., (© 2024 The Authors.)

Introduction: Influenza A virus (IAV) infection is a global respiratory disease, which annually leads to 3-5 million cases of severe illness, resulting in 290,000-650,000 deaths. Additionally, during the past century, four global IAV pandemics have claimed millions of human lives. The epithelial lining of the trachea plays a vital role during IAV infection, both as point of viral entry and replication as well as in the antiviral immune response. Tracheal tissue is generally inaccessible from human patients, which makes animal models crucial for the study of the tracheal host immune response., Method: In this study, pigs were inoculated with swine- or human-adapted H1N1 IAV to gain insight into how host adaptation of IAV shapes the innate immune response during infection. In-depth multi-omics analysis (global proteomics and RNA sequencing) of the host response in upper and lower tracheal tissue was conducted, and results were validated by microfluidic qPCR. Additionally, a subset of samples was selected for histopathological examination., Results: A classical innate antiviral immune response was induced in both upper and lower trachea after infection with either swine- or human-adapted IAV with upregulation of genes and higher abundance of proteins associated with viral infection and recognition, accompanied by a significant induction of interferon stimulated genes with corresponding higher proteins concentrations. Infection with the swine-adapted virus induced a much stronger immune response compared to infection with a human-adapted IAV strain in the lower trachea, which could be a consequence of a higher viral load and a higher degree of inflammation., Discussion: Central components of the JAK-STAT pathway, apoptosis, pyrimidine metabolism, and the cytoskeleton were significantly altered depending on infection with swine- or human-adapted virus and might be relevant mechanisms in relation to antiviral immunity against putative zoonotic IAV. Based on our findings, we hypothesize that during host adaptation, IAV evolve to modulate important host cell elements to favor viral infectivity and replication., Competing Interests: Author YZ was employed by company BGI-Qingdao. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest., (Copyright © 2024 Laybourn, Hellemann Polhaus, Kristensen, Lyngfeldt Henriksen, Zhang, Brogaard, Larsen, Trebbien, Larsen, Kalogeropoulos, auf dem Keller and Skovgaard.)

Extracellular proteolysis critically regulates cellular and tissue responses and is often dysregulated in human diseases. The crosstalk between proteolytic processing and other major post-translational modifications (PTMs) is emerging as an important regulatory mechanism to modulate protease activity and maintain cellular and tissue homeostasis. Here, we focus on matrix metalloproteinase (MMP)-mediated cleavages and N-acetylgalactosamine (GalNAc)-type of O-glycosylation, two major PTMs of proteins in the extracellular space. We investigated the influence of truncated O-glycan trees, also referred to as Tn antigen, following the inactivation of C1GALT1-specific chaperone 1 (COSMC) on the general and MMP9-specific proteolytic processing in MDA-MB-231 breast cancer cells. Quantitative assessment of the proteome and N-terminome using terminal amine isotopic labelling of substrates (TAILS) technology revealed enhanced proteolysis by MMP9 within the extracellular proteomes of MDA-MB-231 cells expressing Tn antigen. In addition, we detected substantial modifications in the proteome and discovered novel ectodomain shedding events regulated by the truncation of O-glycans. These results highlight the critical role of mature O-glycosylation in fine-tuning proteolytic processing and proteome homeostasis by modulating protein susceptibility to proteolytic degradation. These data suggest a complex interplay between proteolysis and O-GalNAc glycosylation, possibly affecting cancer phenotypes., (© 2024 The Author(s). Protein Science published by Wiley Periodicals LLC on behalf of The Protein Society.)

Intestinal edema is a common manifestation of numerous gastrointestinal diseases and is characterized by the accumulation of fluid in the interstitial space of the intestinal wall. Technical advances in laser capture microdissection and low-biomass proteomics now allow us to specifically characterize the intestinal edema proteome. Using advanced proteomics, we identify peptides derived from antimicrobial factors with high signal intensity, but also highlight major contributions from the blood clotting system, extracellular matrix (ECM) and protease-protease inhibitor networks. The ECM is a complex fibrillar network of macromolecules that provides structural and mechanical support to the intestinal tissue. One abundant component of the ECM observed in Salmonella-driven intestinal edema is the glycoprotein fibronectin, recognized for its structure-function interplay regulated by mechanical forces. Using mechanosensitive staining of fibronectin fibers reveals that they are tensed in the edema, despite the high abundance of proteases able to cleave fibronectin. In contrast, fibronectin fibers increasingly relax in other cecal tissue areas as the infection progresses. Co-staining for fibrin(ogen) indicates the formation of a provisional matrix in the edema, similar to what is observed in response to skin injury, while collagen staining reveals a sparse and disrupted collagen fiber network. These observations plus the absence of low tensional fibronectin fibers and the additional finding of a high number of protease inhibitors in the edema proteome could indicate a critical role of stretched fibronectin fibers in maintaining tissue integrity in the severely inflamed cecum. Understanding these processes may also provide valuable functional diagnostic markers of intestinal disease progression in the future., (© 2024 The Authors. The FEBS Journal published by John Wiley & Sons Ltd on behalf of Federation of European Biochemical Societies.)

Positional proteomics methodologies have transformed protease research, and have brought mass spectrometry (MS)-based degradomics studies to the forefront of protease characterization and system-wide interrogation of protease signaling. Considerable advancements in both sensitivity and throughput of liquid chromatography (LC)-MS/MS instrumentation enable the generation of enormous positional proteomics datasets of natural and protein termini and neo-termini of cleaved protease substrates. However, concomitant progress has not been observed to the same extent in data analysis and post-processing steps, arguably constituting the largest bottleneck in positional proteomics workflows. Here, we present a computational tool, CLIPPER 2.0, that builds on prior algorithms developed for MS-based protein termini analysis, facilitating peptide-level annotation and data analysis. CLIPPER 2.0 can be used with several sample preparation workflows and proteomics search algorithms and enables fast and automated database information retrieval, statistical and network analysis, as well as visualization of terminomic datasets. We demonstrate the applicability of our tool by analyzing GluC and MMP9 cleavages in HeLa lysates. CLIPPER 2.0 is available at https://github.com/UadKLab/CLIPPER-2.0., Competing Interests: Conflict of interest The authors declare that they have no conflicts of interest., (Copyright © 2024 The Authors. Published by Elsevier Inc. All rights reserved.)

The Craspase CRISPR-Cas effector consists of the RNA-guided ribonuclease gRAMP and the protease TPR-CHAT, coupling target RNA recognition to protease activation. The natural substrate of Craspase is Csx30, a protein cleaved in two fragments that subsequently activates downstream antiviral pathways. Here, we determined the protease substrate specificity of Craspase from Candidatus "Jettenia caeni" ( Jc -Craspase). We find that Jc -Craspase cleaves Jc -Csx30 in a target RNA-dependent fashion in A|S, which is different from the sites found in two other studied Craspases (L|D and M|K for Candidatus "Scalindua brodae" and Desulfonema ishimotonii , respectively). The fact that Craspase cleaves a nonconserved site across orthologs indicates the evolution of specific protein interactions between Craspase and its respective Csx30 target protein. The Craspase family thus represents a panel of proteases with different substrate specificities, which we exploited for the development of a readout for multiplexed RNA detection.

Coronary artery disease (CAD) constitutes a leading cause of morbidity and mortality worldwide. Percutaneous coronary intervention (PCI) is indicated in a significant proportion of CAD patients, either to improve prognosis or to relieve symptoms not responding to optimal medical therapy. Thus the annual number of patients undergoing PCI in a given geographical area could serve as a surrogate marker of the total CAD burden there. The aim of this study was to analyze the potential, spatial patterns of PCItreated CAD patients in Crete. We evaluated data from all patients subjected to PCI at the island's sole reference centre for cardiac catheterization within a 4-year study period (2013-2016). The analysis focused on regional variations of yearly PCI rates, as well as on the effect of several clinical parameters on the severity of the coronary artery stenosis treated with PCI across Crete. A spatial database within the ArcGIS environment was created and an analysis carried out based on global and local regression using ordinary least squares (OLS) and geographically weighted regression (GWR), respectively. The results revealed significant inter-municipality variation in PCI rates and thus potentially CAD burden, while the degree and direction of correlation between key clinical factors to coronary stenosis severity demonstrated specific geographical patterns. These preliminary results could set the basis for future research, with the ultimate aim to facilitate efficient healthcare strategies planning.

The aim was to investigate the long-term effects of a single episode of immature Status Epilepticus (SE) on the excitability of the septal and temporal hippocampus in vitro, by studying the relationship between interictal-like epileptiform discharges (IEDs) and high-frequency oscillations (HFOs; Ripples, Rs and Fast Ripples, FRs). A pentylenetetrazol-induced Status Epilepticus-(SE)-like generalized seizure was induced at postnatal day 20 in 22 male and female juvenile rats, sacrificed >40 days later to prepare hippocampal slices. Spontaneous IEDs induced by Mg 2+ -free ACSF were recorded from the CA3 area of temporal (T) or septal (S) slices. Recordings were band-pass filtered off-line revealing Rs and FRs and a series of measurements were conducted, with mean values compared with those obtained from age-matched controls (CTRs). In CTR S (vs T) slices, we recorded longer R & FR durations, a longer HFO-IED temporal overlap, higher FR peak power and more frequent FR initiation preceding IEDs (% events). Post-SE, in T slices all types of events duration (IED, R, FR) and the time lag between their onsets (R-IED, FR-IED, R-FR) increased, while FR/R peak power decreased; in S slices, the IED 1st population spike and the FR amplitudes, the R and FR peak power and the (percent) events where Rs or FRs preceded IEDs all decreased. The CA3 IED-HFO relationship offers insights to the septal-to-temporal synchronization patterns; its post-juvenile-SE changes indicate permanent modifications in the septotemporal excitability gradient. Moreover, these findings are in line to region-specific regulation of various currents post-SE, as reported in literature., (Copyright © 2024 IBRO. Published by Elsevier Inc. All rights reserved.)

Protein structure determination is a critical aspect of biological research, enabling us to understand protein function and potential applications. Recent advances in deep learning and artificial intelligence have led to the development of several protein structure prediction tools, such as AlphaFold2 and ColabFold. However, their performance has primarily been evaluated on well-characterised proteins and their ability to predict sturtctures of proteins lacking experimental structures, such as many snake venom toxins, has been less scrutinised. In this study, we evaluated three modelling tools on their prediction of over 1000 snake venom toxin structures for which no experimental structures exist. Our findings show that AlphaFold2 (AF2) performed the best across all assessed parameters. We also observed that ColabFold (CF) only scored slightly worse than AF2, while being computationally less intensive. All tools struggled with regions of intrinsic disorder, such as loops and propeptide regions, and performed well in predicting the structure of functional domains. Overall, our study highlights the importance of exercising caution when working with proteins with no experimental structures available, particularly those that are large and contain flexible regions. Nonetheless, leveraging computational structure prediction tools can provide valuable insights into the modelling of protein interactions with different targets and reveal potential binding sites, active sites, and conformational changes, as well as into the design of potential molecular binders for reagent, diagnostic, or therapeutic purposes., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Endogenous and bacterial proteases play important roles in wound healing and infection. Analysis of alterations in the low-molecular-weight peptidome by individual enzymes could therefore provide insight into proteolytic events occurring in wounds and may aid in the discovery of biomarkers. Using liquid chromatography with tandem mass spectrometry, we characterized the peptidome of plasma and acute wound fluids digested ex vivo with human (neutrophil elastase and cathepsin G) and bacterial proteases ( Pseudomonas aeruginosa LasB and Staphyloccocus aureus V8). We identified over 100 protein targets for each enzyme and characterized enzyme specific peptides and cleavage patterns. Moreover, we found unique peptide regions in V8 digested samples that were also present in dressing extracts from S. aureus infected wounds. Finally, the work indicates that peptidomic analysis of qualitative differences of proteolytic activity of individual enzymes may aid in the discovery of potential diagnostic biomarkers for wound healing status., Competing Interests: The authors declare no competing interests., (© 2024 The Author(s).)

The paper proposes a novel model assessment paradigm aiming to address shortcoming of posterior predictive p -values, which provide the default metric of fit for Bayesian structural equation modelling (BSEM). The model framework presented in the paper focuses on the approximate zero approach (Psychological Methods, 17, 2012, 313), which involves formulating certain parameters (such as factor loadings) to be approximately zero through the use of informative priors, instead of explicitly setting them to zero. The introduced model assessment procedure monitors the out-of-sample predictive performance of the fitted model, and together with a list of guidelines we provide, one can investigate whether the hypothesised model is supported by the data. We incorporate scoring rules and cross-validation to supplement existing model assessment metrics for BSEM. The proposed tools can be applied to models for both continuous and binary data. The modelling of categorical and non-normally distributed continuous data is facilitated with the introduction of an item-individual random effect. We study the performance of the proposed methodology via simulation experiments as well as real data on the 'Big-5' personality scale and the Fagerstrom test for nicotine dependence., (© 2023 The Authors. British Journal of Mathematical and Statistical Psychology published by John Wiley & Sons Ltd on behalf of British Psychological Society.)

Terminal amine isotopic labeling of substrates (TAILS) is a sensitive and robust quantitative mass spectrometry (MS)-based proteomics method used for the characterization of physiological or proteolytically processed protein N-termini, as well as other N-terminal posttranslational modifications (PTMs). TAILS is a well-established, high-throughput, negative enrichment workflow that enables system-wide exploration of N-terminomes independent of sample complexity. TAILS makes use of amine reactivity of free N-termini and a highly efficient aldehyde-functionalized polymer to deplete internal peptides generated after proteolytic digestion during sample preparation. Thereby, it enriches for natural N-termini, allowing for unbiased and complete investigation of differential proteolysis, protease substrate discovery, and analysis of N-terminal PTMs. In this chapter, we provide a state-of-the-art protocol, with detailed steps in all parts of the TAILS sample preparation, MS analysis, and post-processing of acquired data., (© 2023. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.)

Venous leg ulcers represent a clinical challenge and impair the quality of life of patients. This study examines impaired wound healing in venous leg ulcers at the molecular level. Protein expression patterns for biomarkers were analysed in venous leg ulcer wound fluids from 57 patients treated with a protease-modulating polyacrylate wound dressing for 12 weeks, and compared with exudates from 10 acute split-thickness wounds. Wound healing improved in the venous leg ulcer wounds: 61.4% of the 57 patients with venous leg ulcer achieved a relative wound area reduction of ≥ 40%, and 50.9% of the total 57 patients achieved a relative wound area reduction of ≥ 60%. Within the first 14 days, abundances of S100A8, S100A9, neutrophil elastase, matrix metalloproteinase-2, and fibronectin in venous leg ulcer exudates decreased significantly and remained stable, yet higher than in acute wounds. Interleukin-1β, tumour necrosis factor alpha, and matrix metalloproteinase-9 abundance ranges were similar in venous leg ulcers and acute wound fluids. Collagen (I) α1 abundance was higher in venous leg ulcer wound fluids and was not significantly regulated. Overall, significant biomarker changes occurred in the first 14 days before a clinically robust healing response in the venous leg ulcer cohort.

Snakebite envenoming was reintroduced as a Category A Neglected Tropical Disease by the World Health Organization in 2017. Since then, increased attention has been directed towards this affliction and towards the development of a deeper understanding of how snake venoms exert their toxic effects and how antivenoms can counter them. However, most of our in vivo generated knowledge stems from the use of animal models which do not always accurately reflect how the pathogenic effects of snake venoms manifest in humans. Moreover, animal experiments are associated with pain, distress, and eventually animal sacrifice due to the toxic nature of snake venoms. Related to this, the implementation of the 3Rs principle (Replacement, Reduction, and Refinement) in the use of experimental animals in snakebite envenoming research is recommended by the World Health Organization. Therefore, more humane experimental designs and new in vitro/ex vivo alternatives for experimental animals are sought after. Here, we report the use of an organotypic model of human skin to further elucidate the pathophysiology of the dermonecrotic effects caused by the venom of the black-necked spitting cobra, Naja nigricollis, in humans. The goal of this study is to expand the repertoire of available models that can be used to study the local tissue damages induced by cytotoxic venoms., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)

Objective: To investigate the effect of generating mechanism on the relationship between interictal-like epileptiform discharges (IEDs) and the underlying High Frequency Oscillations (HFOs; Ripples, R, and Fast Ripples, FR)., Methods: Synchronous spontaneous IEDs were recorded from the CA1 area of hippocampal slices from adult rats, perfused by Mg 2+ -free ACSF (n = 41slices/14 animals) or 4-aminopyridine (50 μM, n = 37slices/16 animals); IED filtering revealed Rs and FRs and several metrics were calculated and compared (amplitude, duration, relative onset, time lag, % overlap, peak frequency, peak power, FR/R)., Results: Longer IEDs and higher 1st Population Spike (PS) amplitude in Mg 2+ -free ACSF (vs 4-AP; P < .001, P < .001) correlated with longer duration and higher amplitude Rs (P < .0001, P = .001) and longer duration FRs (P < .001). In both media, Rs and FRs appeared before IED onset with Rs preceding FRs; R- and FR-IED lag (P = .008, P = .01) as well as R-FR lag (P = .04) were significantly longer in Mg 2+ -free ACSF vs in 4-AP. R peak frequency and power were higher in Mg 2+ -free ACSF, while no such differences were observed in FRs. Inter-model differences were mostly reflected in Rs, not FRs, suggesting that mechanisms unique to R generation are more active in Mg 2+ -free ACSF vs in 4-AP. FRs appeared to contribute equally to IEDs irrespective of generating mechanism., Significance: Several of the metrics used, particularly those regarding the timing between HFOs and IEDs, appear to correlate with the synchronizing mechanism and we propose that they may be useful when investigating antiepileptic substance effects on neuronal network activity., (© 2022 The Authors. Epilepsia Open published by Wiley Periodicals LLC on behalf of International League Against Epilepsy.)

Competing Interests: Conflicts of Interest H.S. is a full-time employee of Paul Hartmann AG. The other authors declare to have no conflict of interests., (Copyright © 2022 The Authors. Published by Elsevier Inc. All rights reserved.)