Wochenende — modular and flexible alignment-based shotgun metagenome analysis

Background: Shotgun metagenome analysis provides a robust and verifiable method for comprehensive microbiome analysis of fungal, viral, archaeal and bacterial taxonomy, particularly with regard to visualization of read mapping location, normalization options, growth dynamics and functional gene repertoires. Current read classification tools use non-standard output formats, or do not fully show information on mapping location. As reference datasets are not perfect, portrayal of mapping information is critical for judging results effectively. Results: Our alignment-based pipeline, Wochenende, incorporates flexible quality control, trimming, mapping, various filters and normalization. Results are completely transparent and filters can be adjusted by the user. We observe stringent filtering of mismatches and use of mapping quality sharply reduces the number of false positives. Further modules allow genomic visualization and the calculation of growth rates, as well as integration and subsequent plotting of pipeline results as heatmaps or heat trees. Our novel normalization approach additionally allows calculation of absolute abundance profiles by comparison with reads assigned to the human host genome. Conclusion: Wochenende has the ability to find and filter alignments to all kingdoms of life using both short and long reads, and requires only good quality reference genomes. Wochenende automatically combines multiple available modules ranging from quality control and normalization to taxonomic visualization. Wochenende is available at https://github.com/MHH-RCUG/nf_wochenende

Η πρόσληψη της Σοβιετικής Ένωσης από τα Annales d'histoire économique et sociale και τα Annales d'histoire sociale κατά τον Μεσοπόλεμο

Η παρούσα διπλωματική εργασία διερευνά την πρόσληψη της επανάστασης του Οκτώβρη του 1917 στην Τσαρική Αυτοκρατορία και της Σοβιετικής Ένωσης (εφεξής Σ.Ε.) από το γαλλικό ιστορικό περιοδικό Annales d'histoire économique et sociale (εφεξής Annales). Αφενός η πανθομολογούμενη σημασία της Οκτωβριανής επανάστασης και της Σ.Ε. στην διαμόρφωση της νεώτερης και σύγχρονης ιστορίας, αφετέρου η καθοριστική για την γαλλική και τουλάχιστον σημαντική για την παγκόσμια ιστοριογραφία επιρροή του Annales υπαγορεύουν την ερευνητική συσχέτιση των δύο αυτών όρων. Αποδελτιώθηκαν τα παντός είδους κείμενα (δοκιμιακά άρθρα, κριτικές σημειώσεις, σύντομα άρθρα σχολιασμού, βιβλιοπαρουσιάσεις και βιβλιοκριτικές), που σχετίζονται με την τελευταία περίοδο της Τσαρικής Αυτοκρατορίας, την Οκτωβριανή επανάσταση και την Σ.Ε. και είχαν δημοσιευτεί στο Annales από την αρχή της έκδοσής τους, το 1929, μέχρι και την έναρξη του Β’ Π.Π. Η έρευνά μας εντάσσεται στο πεδίο της ιστορίας της ιστοριογραφίας και ευρύτερα της ιστορίας των ιδεών. Επιχειρεί να αναδείξει την πολυεπίπεδη σχέση των ανωτέρω κειμένων με την ιστορική συγκυρία του λεγόμενου “ευρωπαϊκού εμφυλίου πολέμου” (Enzo Traverso) και ειδικότερα με την υπό-περίοδο του Μεσοπολέμου. Πιο συγκεκριμένα, λαμβάνονται υπόψιν οι καθοριστικές όψεις της υπό-περιόδου, δηλαδή η γενίκευση της καπιταλιστικής κρίσης μετά τον κραχ του 1929, η εξάπλωση των δικτατορικών και φασιστικών μορφών διακυβέρνησης, η ενδυνάμωση παγκοσμίως της κομμουνιστικής ιδεολογίας και της αίγλης της Σ.Ε και οι πολιτικές και οικονομικές εξελίξεις στο εσωτερικό της τελευταίας. Συνεκτιμούνται η πολιτική και κοινωνική κατάσταση στην Γαλλία, όπου εδράζεται το περιοδικό. Τέλος, αξιοποιείται ως πρίσμα ανάλυσης η κοινωνική και πολιτική κατηγορία του διανοούμενου. Πριν την παρουσίαση, ιστορική τοποθέτηση και κριτική ανάλυση των εξεταζόμενων κειμένων, προηγείται η ανασκόπηση της εξέλιξης της γαλλικής ιστοριογραφίας έως την εμφάνιση του Annales, ώστε να αναδειχθούν οι νέες μεθοδολογικές προσεγγίσεις που κομίζει και πως αποτυπώνονται στα υπό εξέταση κείμενα. Τα συμπεράσματα κωδικοποιούνται ως εξής: Πρώτον, διαπιστώνεται η καθοριστική συμβολή του G. Méquet, καθώς αποτελεί τον συγγραφέα της μεγάλης πλειοψηφίας των εξεταζόμενων άρθρων. Όντας ερευνητής του Διεθνούς Γραφείου Εργασίας της I.L.O., η συμμετοχή του αποτελεί τον καρπό της πολιτικής των Annales για συνεργασία με « ανθρώπους της δράσης ». Δεύτερον, τα εξεταζόμενα κείμενα επιβεβαιώνουν και εντάσσονται εντός του γενικότερου μεθοδολογικού προσανατολισμού του Annales. Τρίτον, διαπιστώνεται μία θετικά διακείμενη παρουσίαση της Σ.Ε. και μία σχεδόν ολοκληρωτική απουσία δυσμενούς ανάδειξης όψεών της, εντάσσοντάς έτσι το Annales στο “Μέτωπο της Άρνησης” (Marc Ferro). Τέταρτον, παρατηρείται μία αντικειμενική σύμπλευση των αναλύσεων του Annales με την προπαγάνδα της Σ.Ε., σύμπλευση που εντοπίζεται μεταξύ άλλων στην ευμενή σκιαγράφηση των νέων πρότυπων κοινωνικών φιγούρων (Σταχανοβίτη εργάτη, αγρότη μέλους των Κολχόζ), στην ανάδειξη του πρωταγωνιστικού ρόλου του Κ.Κ.Σ.Ε και των ηγετών του, στην ανάδειξη του Πενταετούς Πλάνου της Σ.Ε. ως καινοτόμου συμβολής στην οικονομική σκέψη και πρακτική και τέλος στην ελαφρώς περιφρονητική παρουσίαση των εσωκομματικών αντιπάλων της σοβιετικής ηγεσίας. Πέμπτον, διαπιστώνεται η κυριαρχία της ανάγνωσής της Σ.Ε. ως συνέχειας της Τσαρικής Αυτοκρατορίας και ως ρωσικού κράτους, με συχνή αναπαραγωγή στερεότυπων δυτικοευρωπαϊκών αντιλήψεων σχετικά με το ρώσικο λαό και έθνος. Έκτον, διαπιστώνεται η θεώρηση της Σ.Ε. ως συστατικού μέρους της Ευρώπης και κυρίως του ευρωπαϊκού πολιτισμού. Τέλος, παρά την ευμενή παρουσίαση της Σ.Ε και την σαφή επιρροή μαρξιστικών ιδεών, τεκμαίρεται η απουσία μίας ανάλυσης, υποστήριξης και στράτευσης κομμουνιστικού τύπου στα εξεταζόμενα κείμενα και ευρύτερα στο Annales. Βεβαιώνεται η οργανική σχέση τους με το λαϊκό-μετωπικό διανοητικό κλίμα στην Γαλλία και με τις πολιτικές συντεταγμένες που αυτό έθετε (υπεράσπιση της κοινοβουλευτικής αστικής δημοκρατίας, υπεράσπιση του ελεύθερου εμπορίου).This thesis explores the perception of the October Revolution of 1917 in the Tsarist Empire and that of the Soviet Union (henceforth S.U.) by the French history journal Annales d'histoire économique et sociale (henceforth Annales). On one hand, the universally acknowledged importance of the October Revolution and that of the S.U. in the shaping of modern and contemporary history and, on the other hand, the decisive influence of Annales on French historiography and its important -at the very the least- influence on global historiography, suggest an exploratory correlation of these two terms. All types of texts related to the last period of the Tsarist Empire, the October Revolution and the S.U that had been published in the Annales from the start of its publication, in 1929, until the beginning of World War II have been indexed (essay articles, critical notes, short commentary articles, book presentations and book reviews). Our research belongs to the field of the history of historiography and, in a wider sense, in that of the history of ideas. It attempts to give prominence to the multilevel relation of the aforementioned texts with the historical juncture of the so-called “European Civil War” (Enzo Traverso), namely of the sub-period of Interwar. More specifically, the decisive aspects of the sub-period have also been taken into account, that is the generalization of the capitalist crisis after the Crash of 1929, the expansion of dictatorial and fascist forms of government, the worldwide empowerment of the communist ideology and of the prestige of the S.U., and the political and economic developments within the latter. The political and social situation in France, where the journal is based, has also been taken into account. Finally, the social and political class of the intellectual is employed as an analysis aspect. Before the presentation, the historical contextualization and critical analysis of the examined texts, comes the review of the development of French historiography until the appearance of Annales, so that the new methodological approaches it brings and their depiction upon the examined texts are accentuated. The conclusions are codified as follows: At first, the decisive contribution of G. Méquet is ascertained, as he is the writer of the vast majority of the examined articles. Being a researcher of the International Bureau of Labor of I.L.O., his participation is the fruit of the policy of the Annales for co-operation with “men of action”. Secondly, the examined texts confirm and belong to the wider methodological orientation of Annales. Thirdly, a favorably disposed presentation of the S.U. is ascertained and an almost total absence of its negative aspects, thus integrating Annales within the “Front of Refusal” (Marc Ferro). Fourthly, an objective concurrence of the analysis of Annales with the S.U. propaganda is observed, a convergence that is detected amongst others in the favorable portrayal of the new role model social figure (the Stakhanovite worker, farmer member of the Kolkhoz), in the accentuation of the leading role of the CPSU and its leaders, the accentuation of the Five-Year Plan of the S.U. as an innovative contribution to economic thought and practice and, finally, the slightly disdainful presentation of the intraparty enemies of the soviet leadership. Fifthly, the recognition of the S.U. as the continuance of the Tsarist Empire and the Russian state, with a frequent reproduction of stereotypical west-European beliefs concerning the Russian state and nation is ascertained. Sixthly, the consideration of the S.U. as a component of Europe and, mainly, of European culture is ascertained. Finally, despite of the favorable depiction of the S.U. and the obvious influence of Marxist ideas, the absence of an analysis, support and communist-type affiliation in the examined texts and, in general, in the Annales is proved. Its organic relation to the popular-front intellectual climate in France and the political coordinates it established (defense of bourgeois parliamentary democracy and of the regulated capitalist economy)

Modeling of Durum Wheat Yield Based on Sentinel-2 Imagery

In this study, a modelling approach for the estimation/prediction of wheat yield based on Sentinel-2 data is presented. Model development was accomplished through a two-step process: firstly, the capacity of Sentinel-2 vegetation indices (VIs) to follow plant ecophysiological parameters was established through measurements in a pilot field and secondly, the results of the first step were extended/evaluated in 31 fields, during two growing periods, to increase the applicability range and robustness of the models. Modelling results were examined against yield data collected by a combine harvester equipped with a yield-monitoring system. Normalized Difference Vegetation Index (NDVI) and Enhanced Vegetation Index (EVI) were examined as plant signals and combined with Normalized Difference Water Index (NDWI) and/or Normalized Multiband Drought Index (NMDI) during the growth period or before sowing, as water and soil signals, respectively. The best performing model involved the EVI integral for the 20 April–31 May period as a plant signal and NMDI on 29 April and before sowing as water and soil signals, respectively (R2 = 0.629, RMSE = 538). However, model versions with a single date and maximum seasonal VIs values as a plant signal, performed almost equally well. Since the maximum seasonal VIs values occurred during the last ten days of April, these model versions are suitable for yield prediction

Effective organisation and operation characteristics of Internal Audit Departments (IAD) in Greek hotel units (HUs): an empirical perspective

Summarization: The Internal Audit Department (IAD) provides management with sufficient information to determine whether operations are functioning efficiently, effectively and according to management's goals. The paper attempts to investigate how a well organised IAD in the Greek hotel industry results in lower operating costs and higher quality of services offered. To this context, the research is based on qualitative data derived through questionnaires addressed towards 28 large luxury hotel units (HUs) in Greece. According to up-to-date theoretical and empirical literature, the results point out that the internal control is a crucial function in the firm and especially in the hotel industry, contributing to both the good reputation and the effectiveness of an HU. The findings suggest that there is a significant relationship between HUs size and efficiency and size of the audit department. Large hotels with well organised IADs are found to face lower risks in terms of false information and non-compliance with existing rules and legislation than HUs of smaller size.Presented on: International Journal of Business Performance Managemen

Integrating a novel smart control system for outdoor lighting infrastructures in ports

Summarization: Lighting is amongst the most energy-demanding ports’ operations due to the strict legislative illuminance limits ensuring the safety and the visual comfort of ports' end-users. Lighting exceeds 70% of a port's energy demand in most cases. In parallel, they should be harmonised during the energy transition. This research proposes a novel replicable typology of smart-controlling the outdoor lighting infrastructures in three stages: the reallocation and replacement of the obsolete luminaires, the integration of the daylight harvesting techniques, and the implementation of the occupational-based dimming strategy based on the actual data. A typical Mediterranean port was used as a testbed, the port of Rethymno. The innovative aspect of the proposed typology is that it improves two existing smart lighting control techniques and combines them to a complete typology that responds fast and accurately to any possible lighting conditions' alteration in each space distinctively. The system incorporates high replicability and applicability to a great variety of needs, technologies, and spaces. The energy wastes are diminished while the end-used visual comfort is significantly enhanced. The system's energy savings potential and impacts on the port's infrastructures are quantified, discussed and evaluated. The suggested tool leads to a 56.8% decrease in the port's lighting operations' annual energy demand, which may reach up to 90% in some months. The port’s environmental footprint is also reduced to half than the baseline levels. In conclusion, the investment is viable and feasible, leading to an investment paid back in less than ten years in some instances.Presented on: Energy Conversion and Managemen

HVAC optimization genetic algorithm for industrial near-zero-energy building demand response

Summarization: Demand response offers the possibility of altering the profile of power consumption of individual buildings or building districts, i.e., microgrids, for economic return. There is significant potential of demand response in enabling flexibility via advanced grid management options, allowing higher renewable energy penetration and efficient exploitation of resources. Demand response and distributed energy resource dynamic management are gradually gaining importance as valuable assets for managing peak loads, grid balance, renewable energy source intermittency, and energy losses. In this paper, the potential for operational optimization of a heating, ventilation, and air conditioning (HVAC) system in a smart near-zero-energy industrial building is investigated with the aid of a genetic algorithm. The analysis involves a validated building energy model, a model of energy cost, and an optimization model for establishing HVAC optimum temperature set points. Optimization aims at establishing the trade-off between the minimum daily cost of energy and thermal comfort. Predicted mean vote is integrated in the objective function to ensure thermal comfort requirements are met.Παρουσιάστηκε στο: Energie