633 research outputs found
Microbial co-occurrence network reveals climate and geographic patterns for soil diversity on the planet
No full text<p>The Earth Microbiome Project has produced a variety of microbiome datasets that equally reflect various settings (EMPO level 3) and investigations conducted. These datasets are based on sequence data from the EMP database that have been corrected for errors and trimmed using Deblur in Qiime1. The complete workflow for soil collection, metadata curation, DNA extraction, sequencing, and sequence preparation, as well as the various subsets, can be retrieved from the EMP website (or FTP site). The complete quality filtered 90-bp BIOM table of release1 samples was used for the purposes of this study. Additionally, only samples that fit the EMPO3 ontology "Soil (non-saline)" were selected for analysis due to their simplicity. These samples were classified and labelled with climatic zones in line with the Köppen-Geiger climate classification system, based on the geographic coordinates of each location.</p>
Nikolaos Politis: Study on the life of modern Greeks
No full textTitle: Μελέτη ἐπί τοῦ βίου τῶν νεοτέρων Ἑλλήνων (Study on the life of modern Greeks) Originally published: in Τόμος Α’ (vol. I), ‘Νεοελληνική Μυθολογία’ of the four-volume Μελέτη ἐπί τοῦ βίου τῶν νεοτέρων Ἑλλήνων (Athens: τύποις Σαραντάκος Οἰκονόμου, 1871). Language: Greek The excerpts used are from the original, Preface, pp. α’- γ.’ About the author Nikolaos Politis [1852, Kalamata..
The Early Byzantine Domed Basilicas of West Asia Minor, An essay in Graphic Reconstruction
No full textThis paper investigates the methodology employed in the recent survey and reconstruction of the major Early Byzantine domed churches of west Asia Minor. This involved both the documentation of construction details as well as their interpretation by reference to coeval monuments elsewhere. Focusing on this methodology, the author explores techniques of graphic recording and the theoretical framework within which parallels with other buildings can inform the work of reconstruction. The detailed examination of two case studies illustrates the way in which seemingly random scraps of testimony were interpreted to provide evidence for the missing superstructure of the churches. These case studies also serve to explore the adaptation of the methodology to sites with different characteristics and help to assess the credibility of the resulting graphic reconstructions
Author self-citation in orthodontics is associated with author origin and gender.
No full textBACKGROUND
The aims of this bibliometric study were to determine author self-citation trends in high-impact orthodontic literature and to investigate possible association between self-citation and publication characteristics.
METHODS
Six orthodontic journals with the highest impact factor as ranked by 2017 Journal Citation Reports were screened for a full publication year (2018) for original research articles, reviews, and case reports. Eligible articles were scrutinized for article and author characteristics and citation metrics. Univariable and multivariable negative binomial regression was used to examine associations between self-citation incidence and publication characteristics.
RESULTS
Medians for author self-citation rate of the most self-citing authors and self-citations were 3.03% (range 0-50) and 1 (range 0-19), respectively. In the univariable analysis, there was no association between self-citation counts and study type (P = 0.41), article topic (P = 0.61), number of authors (P = 0.62), and rank of authors (P = 0.56). Author origin (P = 0.001), gender (P = 0.001) and journal (P = 0.05) were associated with self-citation counts and in the multivariable analysis only origin and gender remained strong self-citation predictors. Asian authors and females self-cited significantly less often than all other regions and male authors.
CONCLUSIONS
Authors in orthodontics do not self-cite at a frequency that suggests potential citation manipulation. Author origin and gender were the only variables associated with citations counts. More bibliometric research is necessary to draw solid conclusions about author self-citation trends in orthodontic literature
Information theory methods in communication complexity
No full textThis dissertation is concerned with the application of notions and methods from the field of information theory to the field of communication complexity. It consists of two main parts. In the first part of the dissertation, we prove lower bounds on the randomized two-party communication complexity of functions that arise from read-once boolean formulae. A read-once boolean formula is a formula in propositional logic with the property that every variable appears exactly once. Such a formula can be represented by a tree, where the leaves correspond to variables, and the internal nodes are labeled by binary connectives. Under certain assumptions, this representation is unique. Thus, one can define the depth of a formula as the depth of the tree that represents it. The complexity of the evaluation of general read-once formulae has attracted interest mainly in the decision tree model. In the communication complexity model many interesting results deal with specific read-once formulae, such as disjointness and tribes. In this dissertation we use information theory methods to prove lower bounds that hold for any read-once formula. Our lower bounds are of the form n(f )/c^d(f ) , where n(f ) is the number of variables and d(f ) is the depth of the formula, and they are optimal up to the constant in the base of the denominator. In the second part of the dissertation, we explore the applicability of the information-theoretic method in the number-on-the-forehead model. The work of Bar-Yossef, Jayram, Kumar & Sivakumar [BYJKS04] revealed a beautiful connection between Hellinger distance and two-party randomized communication protocols. Inspired by their work and motivated by the open questions in the number-on-the-forehead model, we introduce the notion of Hellinger volume. We show that it lower bounds the information cost of multi-party protocols. We provide a small toolbox that allows one to manipulate several Hellinger volume terms and also to lower bound a Hellinger volume when the distributions involved satisfy certain conditions. In doing so, we prove a new upper bound on the difference between the arithmetic mean and the geometric mean in terms of relative entropy. Finally, we show how to apply the new tools to obtain a lower bound on the informational complexity of the ANDk function.Ph. D.Includes bibliographical referencesby Nikolaos Leonardo
Nikolaos Mesarites, Description of the Church of the Holy Apostles at Constantinople. New critical perspectives.
No full textThis study offers a reappraisal of Nikolaos Mesarites’ Description of the church of the Holy Apostles at Constantinople, by providing new insights into its genre and the context of its composition. By concentrating on the text’s encomiastic features, the first part of the study retraces its carefully carved rhetorical construction. The second part analyses the so far neglected concluding section of the Description, in which the author, by hinting at the current historical juncture – the very years preceding the fourth Crusade – would seem to disclose a specific purpose for its composition. Finally, an hypothesis for dating the Description is also suggested, with the intention of defining it further in a forthcoming dedicated article.
Training Data for "Binning of metagenomic sequencing data" tutorial
No full textMetagenomics is the study of genetic material recovered directly from environmental samples, such as soil, water, or gut contents, without the need for isolation or cultivation of individual organisms. Metagenomics binning is a process used to classify DNA sequences obtained from metagenomic sequencing into discrete groups, or bins, based on their similarity to each other. The goal of metagenomics binning is to assign the DNA sequences to the organisms or taxonomic groups that they originate from, allowing for a better understanding of the diversity and functions of the microbial communities present in the sample. This is typically achieved through computational methods that use sequence similarity, composition, and other features to group the sequences into bins.
There are two main types of metagenomics binning: reference-based and de novo.
reference-based binning involves aligning the sequences to a database of known genomes or reference sequences
de novo binning involves clustering the sequences based on similarity without prior knowledge of the organisms or reference sequences present in the sample.
Both methods have their strengths and limitations, and researchers often use a combination of approaches to improve the accuracy of their binning results. Metagenomics binning is an important tool for understanding the functional potential of microbial communities in various environments and has applications in fields such as biotechnology, environmental science, and human health.
In this tutorial, we will learn how to run metagenomic binning tools and evaluate the quality of the results. In order to do that, we will use data from the study: Temporal shotgun metagenomic dissection of the coffee fermentation ecosystem and MetaBAT2 algorithm. For an in-depth analysis of the structure and functions of the coffee microbiome, a temporal shotgun metagenomic study (six time points) was performed. The six samples have been sequenced with Illumina MiSeq utilizing whole genome sequencing.
Based on the 6 original dataset of the coffee fermentation system, we generated mock datasets for this tutorial
Correction: Operative management of acute abdomen after bariatric surgery in the emergency setting: the OBA guidelines (World Journal of Emergency Surgery, (2022), 17, 1, (51), 10.1186/s13017-022-00452-w)
No full textFollowing publication of the original article [1], the co-author “Nikolaos Pararas” has misspelled wrongly as “Nikolaos Parasas”. The original article has been corrected. © The Author(s) 2022
Καινοτόμες μέθοδοι ανάλυσης βιολογικών δεδομένων μεγάλου όγκου στη βιοπληροφορική
No full textMicrobial ecology examines microbial communities to uncover trends and variables that affect their distribution, interactions, and population structure. Various environmental factors, such as distance, salinity, temperature, oxygen concentration, nutrition availability, pH, and interspecies interactions, all influence the development of these communities. A comprehensive study of microbial diversity is essential, since it significantly impacts human health, ecosystem functionality, organic matter decomposition, and soil health maintenance. Notwithstanding the advancements achieved, the predominant focus of the study has been on specific geographical areas or sample types, hence limiting the ability to generalize the results. Standardized methodologies are essential to unify various research efforts, enabling comparisons and fostering the advancement of comprehensive insights into the distribution of microorganisms and their role within ecological systems. The synthesis and interpretation of the growing volume of data are getting progressively challenging due to rapid advancements in research. Although this strategy sometimes employs divergent and fragmented information, meta-analyses indicate that integrating datasets is crucial for identifying universal trends among diverse microorganisms. This underscores the imperative for tools that are both robust and intuitive to effectively assess vast quantities of biological data. This dissertation aims to present innovative bioinformatics methodologies for analyzing vast biological datasets, focusing specifically on the complex relationships between geoclimatic factors and microbial biodiversity. Microorganisms significantly contribute to nutrient cycling, carbon sequestration, soil fertility, and disease prevention. To address global challenges in sustainable agriculture, climate resilience, and environmental conservation, it is crucial to comprehend the interactions between environmental factors and diverse microorganisms. This research examines the diversity of microorganisms across climatic zones as described by the Köppen-Geiger classification, utilizing the comprehensive data from the Earth Microbiome Project. A key focus is the integration of diverse datasets to address differences in data collection methods, resolutions, and platforms. An advanced analytical pipeline was created to handle, integrate, and analyze microbiome-related data. This pipeline guaranteed the reliability and consistency of cross-dataset comparisons. The pipeline aims to facilitate the accessibility and use of results for research follow-up and information dissemination. The current examination primarily focuses on the microbiomes of global soil, utilizing data derived from the sequencing of the 16S rRNA gene as the foundation for the research. Ecological trends and microbial interactions are examined using computational frameworks. Specifically, microbial co-occurrence networks are the focus of inquiry. Employing advanced statistical techniques, notable taxa may be discerned, community structures can be shown, and ecological linkages can be emphasized, particularly for keystone species and hub classifications. This study has yielded significant findings:1. What are the effects of geography and climate on microbial diversity? The "distance-decay" phenomenon, characterized by significant differences in microbial communities across various regions, may be corroborated by the negative correlation between Bray-Curtis similarity and geographic distance. Non-metric multidimensional scaling data indicate that climatic zones significantly influence the overall makeup of microorganisms. 2. Diversity and network dynamics: Diversity indices vary by habitat, with arid, polar, and tropical regions displaying less diversity yet more concentrated co-occurrence networks. Both cold and temperate zones possess networks that are more modular and exhibit a greater degree of diversity. The SpiecEasi approach was employed to create climate-specific microbial networks that exhibit scale-free topologies. These topologies suggest the presence of a limited number of tightly interconnected hub taxa. Environments characterized by a reduced number of edges per node signify constrained networks, whereas those with higher ratios denote more interconnected systems. 3.The analysis of network characteristics in various climates indicates that climatic zones, particularly polar regions, display high-density networks with low modularity, reflecting the close interrelation among microbial communities. Hot deserts, cold deserts, and Mediterranean zones exhibit greater modular architecture, indicating the existence of significant taxa or clusters. 4.Distribution and community composition of ESV: The analysis of Exact Sequence Variants (ESVs) reveals distribution patterns specific to the environment. Certain species are disproportionately represented in specific zones, illustrating the substantial impact of climate on the distribution of microorganisms. 5. Significant taxa in climate-specific networks: Various climatic zones are predominantly characterized by hub taxa, including Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria, and Actinobacteria. The current analysis has enhanced our understanding of microbial community structure, their ecological functions, and their responses to environmental changes. The findings of this study enhance the field of microbial biogeography by identifying keystone microbial communities and differences in network structure across climate gradients. Our results provide insights into how these communities adapt to various environments by emphasizing the intricate network of microbial interactions. This research has practical implications for agriculture, water management, conservation, and climate adaptation strategies.Η μικροβιακή οικολογία εξετάζει τις μικροβιακές κοινότητες για να αποκαλύψει πρότυπα και μεταβλητές που επηρεάζουν την κατανομή, τις αλληλεπιδράσεις και τη δομή των πληθυσμών τους. Διάφοροι περιβαλλοντικοί παράγοντες, όπως η απόσταση, η αλατότητα, η θερμοκρασία, η συγκέντρωση οξυγόνου, η διαθεσιμότητα θρεπτικών συστατικών, το pH και οι αλληλεπιδράσεις μεταξύ των ειδών, επηρεάζουν την ανάπτυξη αυτών των κοινοτήτων. Η ολοκληρωμένη μελέτη της μικροβιακής ποικιλομορφίας είναι απαραίτητη, καθώς έχει σημαντικό αντίκτυπο στην ανθρώπινη υγεία, τη λειτουργικότητα των οικοσυστημάτων, την αποικοδόμηση της οργανικής ύλης και τη διατήρηση της υγείας του εδάφους. Παρά την πρόοδο που έχει σημειωθεί, η έρευνα επικεντρώνεται κυρίως σε συγκεκριμένες γεωγραφικές περιοχές ή τύπους δειγμάτων, περιορίζοντας έτσι τη δυνατότητα γενίκευσης των αποτελεσμάτων. Η χρήση τυποποιημένων μεθοδολογιών είναι ζωτικής σημασίας για την ενοποίηση διαφορετικών ερευνητικών προσπαθειών, επιτρέποντας συγκρίσεις και προωθώντας την εις βάθος κατανόηση της κατανομής των μικροοργανισμών και του ρόλου τους στα οικολογικά συστήματα. Η συνεχώς αυξανόμενη ποσότητα δεδομένων καθιστά τη σύνθεση και την ερμηνεία τους ολοένα και πιο απαιτητική λόγω των ραγδαίων εξελίξεων στην έρευνα. Αν και αυτή η προσέγγιση χρησιμοποιεί συχνά ετερογενείς και αποσπασματικές πληροφορίες, οι μετα-αναλύσεις δείχνουν ότι η ενοποίηση των δεδομένων είναι καθοριστικής σημασίας για την αναγνώριση γενικών προτύπων μεταξύ διαφορετικών μικροοργανισμών. Αυτό αναδεικνύει την ανάγκη για ισχυρά και φιλικά προς τον χρήστη εργαλεία που επιτρέπουν την αποτελεσματική ανάλυση μεγάλων βιολογικών δεδομένων. Η παρούσα διατριβή στοχεύει στην παρουσίαση καινοτόμων βιοπληροφορικών μεθοδολογιών για την ανάλυση μεγάλων βιολογικών συνόλων δεδομένων, με έμφαση στις περίπλοκες σχέσεις μεταξύ γεωκλιματικών παραγόντων και μικροβιακής βιοποικιλότητας. Οι μικροοργανισμοί συμβάλλουν σημαντικά στην ανακύκλωση των θρεπτικών συστατικών, τη δέσμευση του άνθρακα, τη γονιμότητα του εδάφους και την πρόληψη ασθενειών. Η κατανόηση των αλληλεπιδράσεων μεταξύ περιβαλλοντικών παραγόντων και μικροβιακής ποικιλομορφίας είναι απαραίτητη για την αντιμετώπιση παγκόσμιων προκλήσεων που σχετίζονται με τη βιώσιμη γεωργία, την ανθεκτικότητα στο κλίμα και τη διατήρηση του περιβάλλοντος. Η έρευνα εξετάζει τη μικροβιακή ποικιλομορφία σε διαφορετικές κλιματικές ζώνες, όπως αυτές περιγράφονται από την ταξινόμηση Köppen-Geiger, αξιοποιώντας τα εκτενή δεδομένα του Earth Microbiome Project. Ιδιαίτερη έμφαση δίνεται στην ενοποίηση ετερογενών δεδομένων, λαμβάνοντας υπόψη τις διαφορές στις μεθόδους συλλογής, τις αναλύσεις διαφορετικής ανάλυσης και τις πλατφόρμες παραγωγής δεδομένων. Για την αντιμετώπιση αυτών των προκλήσεων, αναπτύχθηκε μια προηγμένη αναλυτική υποδομή, η οποία επιτρέπει την αξιόπιστη και συνεπή σύγκριση δεδομένων μικροβιώματος. Αυτή η υποδομή διασφαλίζει τη διαθεσιμότητα και την αξιοποίηση των αποτελεσμάτων τόσο για περαιτέρω έρευνα όσο και για τη διάδοση πληροφοριών. Η ανάλυση επικεντρώνεται κυρίως στα μικροβιώματα των εδαφών παγκοσμίως, χρησιμοποιώντας δεδομένα αλληλούχησης του γονιδίου 16S rRNA ως βάση της έρευνας. Οι οικολογικές δυναμικές και οι μικροβιακές αλληλεπιδράσεις διερευνώνται μέσω υπολογιστικών προσεγγίσεων, με έμφαση στα δίκτυα συνεμφάνισης μικροοργανισμών. Χρησιμοποιώντας προηγμένες στατιστικές τεχνικές, μπορούν να εντοπιστούν σημαντικά ταξινομικά σύνολα, να περιγραφεί η δομή των κοινοτήτων και να αναδειχθούν οικολογικές συνδέσεις, ειδικά για είδη-κλειδιά και κεντρικούς κόμβους του δικτύου. Βασικά ευρήματα της έρευνας: 1. Επίδραση γεωγραφίας και κλίματος στη μικροβιακή ποικιλομορφία: Το φαινόμενο της «εξασθένησης με την απόσταση» (distance-decay), το οποίο περιγράφει τις σημαντικές διαφορές μεταξύ μικροβιακών κοινοτήτων σε διαφορετικές γεωγραφικές περιοχές, μπορεί να επιβεβαιωθεί μέσω της αρνητικής συσχέτισης μεταξύ της ομοιότητας Bray-Curtis και της γεωγραφικής απόστασης. Τα δεδομένα πολυδιάστατης μη μετρικής κλιμάκωσης υποδεικνύουν ότι οι κλιματικές ζώνες επηρεάζουν σημαντικά τη σύνθεση των μικροοργανισμών. 2. Δυναμική ποικιλότητας και δικτύων: Οι δείκτες ποικιλομορφίας διαφέρουν ανάλογα με το περιβάλλον. Οι ξηρές, πολικές και τροπικές περιοχές παρουσιάζουν χαμηλότερη ποικιλομορφία, αλλά πιο συγκεντρωμένα δίκτυα συνεμφάνισης. Αντίθετα, οι εύκρατες και ψυχρές ζώνες εμφανίζουν πιο αρθρωτά και πλούσια δίκτυα. Η ανάλυση με τη μέθοδο SpiecEasi έδειξε ότι τα μικροβιακά δίκτυα σε διαφορετικά κλίματα εμφανίζουν τοπολογίες τύπου scale-free, όπου λίγα ταξινομικά σύνολα διαδραματίζουν κεντρικό ρόλο. 3. Χαρακτηριστικά δικτύων ανά κλιματική ζώνη: Τα πολικά περιβάλλοντα εμφανίζουν δίκτυα υψηλής πυκνότητας με χαμηλή αρθρωτότητα, γεγονός που αντικατοπτρίζει τη στενή διασύνδεση των μικροβιακών κοινοτήτων. Οι θερμές και ψυχρές ερήμοι, καθώς και οι μεσογειακές ζώνες, εμφανίζουν πιο έντονα αρθρωτή αρχιτεκτονική, υποδεικνύοντας την ύπαρξη σημαντικών ταξινομικών ομάδων. 4. Κατανομή και σύνθεση κοινοτήτων ESV: Η ανάλυση των Exact Sequence Variants (ESVs) δείχνει συγκεκριμένα πρότυπα κατανομής ανάλογα με το περιβάλλον. Ορισμένα είδη είναι δυσανάλογα εκπροσωπημένα σε συγκεκριμένες ζώνες, γεγονός που καταδεικνύει την επίδραση του κλίματος στην κατανομή των μικροοργανισμών. 5. Σημαντικά ταξινομικά σύνολα στα κλιματικά δίκτυα: Οι κλιματικές ζώνες χαρακτηρίζονται κυρίως από ταξινομικά σύνολα-κλειδιά, όπως οι Alphaproteobacteria, Betaproteobacteria, Gammaproteobacteria, Deltaproteobacteria και Actinobacteria. Η ανάλυση αυτή συμβάλλει στην καλύτερη κατανόηση της δομής των μικροβιακών κοινοτήτων, των οικολογικών τους λειτουργιών και της απόκρισής τους στις περιβαλλοντικές μεταβολές. Τα ευρήματα αυτής της μελέτης προάγουν τον τομέα της μικροβιακής βιογεωγραφίας, εντοπίζοντας βασικές μικροβιακές κοινότητες και διαφορές στη δομή των δικτύων κατά μήκος κλιματικών κλιμάκων. Τα αποτελέσματα έχουν πρακτικές εφαρμογές στη γεωργία, τη διαχείριση υδάτων, τη διατήρηση του περιβάλλοντος και τις στρατηγικές προσαρμογής στην κλιματική αλλαγή
Correction: Operative management of acute abdomen after bariatric surgery in the emergency setting: the OBA guidelines (World Journal of Emergency Surgery, (2022), 17, 1, (51), 10.1186/s13017-022-00452-w)
No full textFollowing publication of the original article [1], the co-author “Nikolaos Pararas” has misspelled wrongly as “Nikolaos Parasas”. The original article has been corrected
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