A multidisciplinary critical review of ecosystem services studies in Greece: approaches, shortcomings and the pathway to implementation

During the last two decades, ecosystem services (ES) research is used to inform the various steps of decision- and policy- making process, regarding environmental management, spatial planning and natural capital accounting. In the EU, this vast and rapid publication boom was triggered by the enactment of Action 5 of the EU Biodiversity Strategy to 2020, urging Member States to implement Mapping and Assessment of Ecosystem and their Services (MAES); few countries pioneered, while others are still lagging behind. In Greece, the implementation of MAES started in 2014 and since then an impressive progress has been made, with Greece now being among the countries with the most rapid progress. However, there are still major knowledge and data gaps on ecosystem services in Greece; know-how on specific methods, tools and practices is still to be developed. This poses obstacles in integrative efforts to identify and/or interpret the various co-variates affecting ecosystems and their services in space and time and hinders the incorporation of the ES generated information into the decision-making process. Making the first steps towards overcoming these hurdles, the present study aims to (i) synthesize the ecosystem services literature relevant to the ES implementation in Greece, (ii) validate and classify each literature source to the relevant ecosystem services categories, (iii) identify shortcomings in terms of ES assessed and data available, and (iv) critically review the variety of approaches to ES assessments that are followed. The outcomes of this study will facilitate the efficient implementation of ecosystem services assessments in Greece

A Modified Method for Whole Exome Resequencing from Minimal Amounts of Starting DNA

Next generation DNA sequencing (NGS) technologies have revolutionized the pace at which whole genome and exome sequences can be generated. However, despite these advances, many of the methods for targeted resequencing, such as the generation of high-depth exome sequences, are somewhat limited by the relatively large amounts of starting DNA that are normally required. In the case of tumour analysis this is particularly pertinent as many tumour biopsies often return submicrogram quantities of DNA, especially when tumours are microdissected prior to analysis. Here, we present a method for exome capture and resequencing using as little as 50 ng of starting DNA. The sequencing libraries generated by this minimal starting amount (MSA-Cap) method generate datasets that are comparable to standard amount (SA) whole exome libraries that use three micrograms of starting DNA. This method, which can be performed in most laboratories using commonly available reagents, has the potential to enhance large scale profiling efforts such as the resequencing of tumour exomes

Proposing a Governance model for environmental crises

During August 2021, a wildfire outbreak in Evia, Greece's second largest island, resulted in a major environmental and economic crisis. Apart from biodiversity and habitat loss, the disaster triggered a financial crisis because it wiped out wood-productive forests and outdoor areas that attract visitors. This crisis highlighted the need for a new governance model in order to respond to environmental crises more effectively. The aim of this study was to investigate the acceptance and attitudes of relevant stakeholders towards establishing a Hub a proposed governance model responsible for monitoring and restoring the natural capital and biodiversity after environmental crises. Results based on quantitative data collected via questionnaires showed that most respondents were positive to the Hub and perceived that its main functions should be to recommend measures after environmental crises and to facilitate cooperation among involved stakeholders. Moreover, results pointed to preferred funding sources, stakeholder groups that should participate in the Hub and key performance indicators (KPIs) for monitoring Hub's performance. The applied methodology could guide the establishment of governance models both in the study area and other countries facing environmental crises

High-throughput RNA interference screening using pooled shRNA libraries and next generation sequencing

RNA interference (RNAi) screening is a state-of-the-art technology that enables the dissection of biological processes and disease-related phenotypes. The commercial availability of genome-wide, short hairpin RNA (shRNA) libraries has fueled interest in this area but the generation and analysis of these complex data remain a challenge. Here, we describe complete experimental protocols and novel open source computational methodologies, shALIGN and shRNAseq, that allow RNAi screens to be rapidly deconvoluted using next generation sequencing. Our computational pipeline offers efficient screen analysis and the flexibility and scalability to quickly incorporate future developments in shRNA library technology

Does combined training of biofeedback and neurofeedback affect smoking status, behavior, and longitudinal brain plasticity?

Introduction: Investigations of biofeedback (BF) and neurofeedback (NF) training for nicotine addiction have been long documented to lead to positive gains in smoking status, behavior and to changes in brain activity. We aimed to: (a) evaluate a multi-visit combined BF/NF intervention as an alternative smoking cessation approach, (b) validate training-induced feedback learning, and (c) document effects on resting-state functional connectivity networks (rsFCN); considering gender and degree of nicotine dependence in a longitudinal design.Methods: We analyzed clinical, behavioral, and electrophysiological data from 17 smokers who completed five BF and 20 NF sessions and three evaluation stages. Possible neuroplastic effects were explored comparing whole-brain rsFCN by phase-lag index (PLI) for different brain rhythms. PLI connections with significant change across time were investigated according to different resting-state networks (RSNs).Results: Improvements in smoking status were observed as exhaled carbon monoxide levels, Total Oxidative Stress, and Fageström scores decreased while Vitamin E levels increased across time. BF/NF promoted gains in anxiety, self-esteem, and several aspects of cognitive performance. BF learning in temperature enhancement was observed within sessions. NF learning in theta/alpha ratio increase was achieved across baselines and within sessions. PLI network connections significantly changed across time mainly between or within visual, default mode and frontoparietal networks in theta and alpha rhythms, while beta band RSNs mostly changed significantly after BF sessions.Discussion: Combined BF/NF training positively affects the clinical and behavioral status of smokers, displays benefit in smoking harm reduction, plays a neuroprotective role, leads to learning effects and to positive reorganization of RSNs across time.Clinical Trial Registration:https://clinicaltrials.gov/ct2/show/NCT02991781

Comprehensive Genomic Analysis of a BRCA2 Deficient Human Pancreatic Cancer

Capan-1 is a well-characterised BRCA2-deficient human cell line isolated from a liver metastasis of a pancreatic adenocarcinoma. Here we report a genome-wide assessment of structural variations and high-depth exome characterization of single nucleotide variants and small insertion/deletions in Capan-1. To identify potential somatic and tumour-associated variations in the absence of a matched-normal cell line, we devised a novel method based on the analysis of HapMap samples. We demonstrate that Capan-1 has one of the most rearranged genomes sequenced to date. Furthermore, small insertions and deletions are detected more frequently in the context of short sequence repeats than in other genomes. We also identify a number of novel mutations that may represent genetic changes that have contributed to tumour progression. These data provide insight into the genomic effects of loss of BRCA2 function

Plasticity in dendroclimatic response across the distribution range of Aleppo pine (Pinus halepensis)

We investigated the variability of the climate-growth relationship of Aleppo pine across its distribution range in the Mediterranean Basin. We constructed a network of tree-ring index chronologies from 63 sites across the region. Correlation function analysis identified the relationships of tree-ring index to climate factors for each site. We also estimated the dominant climatic gradients of the region using principal component analysis of monthly, seasonal, and annual mean temperature and total precipitation from 1,068 climatic gridpoints. Variation in ring width index was primarily related to precipitation and secondarily to temperature. However, we found that the dendroclimatic relationship depended on the position of the site along the climatic gradient. In the southern part of the distribution range, where temperature was generally higher and precipitation lower than the regional average, reduced growth was also associated with warm and dry conditions. In the northern part, where the average temperature was lower and the precipitation more abundant than the regional average, reduced growth was associated with cool conditions. Thus, our study highlights the substantial plasticity of Aleppo pine in response to different climatic conditions. These results do not resolve the source of response variability as being due to either genetic variation in provenance, to phenotypic plasticity, or a combination of factors. However, as current growth responses to inter-annual climate variability vary spatially across existing climate gradients, future climate-growth relationships will also likely be determined by differential adaptation and/or acclimation responses to spatial climatic variation. The contribution of local adaptation and/or phenotypic plasticity across populations to the persistence of species under global warming could be decisive for prediction of climate change impacts across populations. In this sense, a more complex forest dynamics modeling approach that includes the contribution of genetic variation and phenotypic plasticity can improve the reliability of the ecological inferences derived from the climate-growth relationships.This work was partially supported by Spanish Ministry of Education and Science co-funded by FEDER program (CGL2012-31668), the European Union and the National Ministry of Education and Religion of Greece (EPEAEK- Environment – Archimedes), the Slovenian Research Agency (program P4-0015), and the USDA Forest Service. The cooperation among international partners was supported by the COST Action FP1106, STREeSS

Crown fire analysis and management in allepo pine forests

The objective of this study was to investigate the pyric environment that influences the crown fire initiation and spread in Aleppo pine forests in Greece. Regression equations that predict the canopy fuel load by diameter class were developed for Aleppo pine in northern Evia, Greece. The log/log transformation of the allometric model y=axb gave the best fit for all crown fuel components except the branches with diameter >7.5 cm. The R2 values were between 0.82 and 0.88 and SEE were small. Forty Aleppo pine trees were classified into groups according to their expected available canopy fuel load, by applying multivariate statistical methods (Hierarchical Cluster Analysis and Canonical Discriminant Analysis) on the values of their most significant dendrometric characteristics (diameter at breast height, total height, live crown length, crown width). Inventory of the critical canopy fuel characteristics that influence the initiation and spread of crown fires was conducted in representative Aleppo pine stands in the Kassandra peninsula, Greece. Vertical profiles of available canopy fuel load, canopy base height and canopy bulk density are presented. Aleppo pine crown fuel complexes are characterized by low canopy base height, while available canopy fuel load and canopy bulk density values are similar with other conifer fuel types worldwide. Crown fire behavior (probability of crown fire initiation, fire type, crown fire rate of spread, fireline intensity and flame length) in Aleppo pine stands with various surface fuel types and under various meteorological conditions, was simulated with modern and field-tested models of crown fire prediction. The simulation results indicated that crown fires in Aleppo pines forests cover a wide range of expected fire behavior. The probability of crown fire initiation was found high and passive crown fires and high intensity active crown fires were observed in uneven aged and even aged stands, respectively. Assessment of potential crown fire behavior is required in regional fire management planning and suppression tactics. Nomographs for the calculation of the pyric parameters (probability of crown fire initiation, active crown fire rate of spread, fireline intensity and flame length) of crown fires burning in the Aleppo pines stands in Greece were created. Fuel complexes typical of Aleppo pine forests were comprised and used as inputs to recent models of crown fire prediction, in order to calculate the pyric parameters under a wide range of environmental conditions. The results are considered as realistic, based on common experience of crown fire behavior in conifer forests, worldwide. Such nomographs are presented for the first time in Greece and are expected to offer substantial help to fire management practice. Fuel treatments that affect crown fire behavior in Aleppo pine stands were simulated under extreme and normal fuel moisture conditions. Treatments were simulated by adjusting surface fuels (total load, load-by-size class, depth) and canopy fuels (available canopy fuel load, canopy base height, canopy bulk density). Under typical conditions, stand thinning followed by prescribed burning and/or controlled grazing with slash removal avert crown fire initiation in most cases. Restoration of Aleppo pines ecosystems must include an analysis of how proposed treatments affect fuel structures. Fuel treatments must be incorporated in the forest management plan of Aleppo pine forests in Greece.Σκοπός της εργασίας είναι να αναλυθούν οι πυρικές παράμετροι που συνεπιδρούν στο φαινόμενο των πυρκαγιών κόμης σε δάση χαλεπίου πεύκης στην Ελλάδα. Δημιουργήθηκαν μοντέλα παλινδρόμησης με ανεξάρτητη μεταβλητή τη στηθιαία διάμετρο για την εκτίμηση του φορτίου της εναέριας καύσιμης ύλης ανά κατηγορία διαμέτρου, σε άτομα χαλεπίου πεύκης στη Βόρεια Εύβοια. Το αλλομετρικό μοντέλο, y=axb, που χρησιμοποιείται ευρέως σε σπουδές βιομάζας, έδωσε την καλύτερη προσαρμογή για όλες τις κατηγορίες διαμέτρου εκτός από την κατηγορία >7.5 cm. Οι τιμές του R2adj κυμάνθηκαν από 0.82 έως 0.88 και τα τυπικά σφάλματα εκτίμησης ήταν στατιστικά αμελητέα. Τα μοντέλα αυτά μπορούν να χρησιμοποιηθούν για την εκτίμηση του διαθέσιμου φορτίου της εναέριας καύσιμης ύλης σε συστάδες χαλεπίου πεύκης στην Ελλάδα. Σαράντα άτομα χαλεπίου πεύκης ομαδοποιήθηκαν σε τρεις ομάδες σύμφωνα με το διαθέσιμο φορτίο εναέριας καύσιμης ύλης, εφαρμόζοντας πολυμεταβλητές στατιστικές μεθόδους (ανάλυση σε συστάδες, διαχωριστική ανάλυση) σε σχέση με κοινά δενδρομετρικά χαρακτηριστικά (στηθιαία διάμετρος, ύψος δένδρου, μήκος κόμης, πλάτος κόμης). Πλήρης απογραφή των παραμέτρων των συστάδων και των χαρακτηριστικών της εναέριας καύσιμης ύλης που επηρεάζουν την έναρξη και τη διάδοση πυρκαγιών κόμης, διενεργήθηκε σε αντιπροσωπευτικές συστάδες χαλεπίου πεύκης στη Κασσάνδρα Χαλκιδικής. Εκτιμήθηκε η κάθετη κατανομή του φορτίου της διαθέσιμης εναέριας καύσιμης ύλης καθώς και το ύψος έναρξης και το πορώδες της εναέριας καύσιμης ύλης απεικονίζονται γραφικά. Τα δάση χαλεπίου πεύκης χαρακτηρίζονται από χαμηλό ύψος έναρξης της εναέριας καύσιμης ύλης, ενώ το διαθέσιμο φορτίο και το πορώδες κυμαίνεται σε τιμές παρόμοιες με άλλα κωνοφόρα είδη. Τα παραπάνω χαρακτηριστικά της εναέριας καύσιμης ύλης μπορούν να χρησιμεύσουν ως εισαγωγικά στοιχεία σε μοντέλα προσομοίωσης πυρκαγιών κόμης. Έγινε προσομοίωση της συμπεριφοράς των πυρκαγιών κόμης (πιθανότητα έναρξης πυρκαγιών κόμης, τύπος πυρκαγιάς, ταχύτητα διάδοσης πυρκαγιάς κόμης, θερμική ένταση και μήκος φλόγας πυρκαγιάς κόμης) σε δάση χαλεπίου πεύκης με διαφορετικούς τύπους υπορόφου βλάστησης και κάτω από διαφορετικές μετεωρολογικές συνθήκες, με τα πλέον πρόσφατα και δοκιμασμένα παγκοσμίως μοντέλα πρόβλεψης πυρκαγιών κόμης. Παρατηρήθηκε μεγάλο εύρος συμπεριφοράς πυρκαγιών κόμης. Η μετάδοση από την επιφάνεια του εδάφους στην κόμη είναι συχνό φαινόμενο, ενώ παθητικές και ενεργητικές πυρκαγιές κόμης παρατηρούνται συχνά σε ανομήλικες και ομήλικες συστάδες, αντίστοιχα. Η πρόγνωση των πυρικών παραμέτρων των πυρκαγιών κόμης σε δάση χαλεπίου πεύκης βοηθάει στη λήψη ορθολογικών μέτρων τόσο για την επιτυχή πρόληψη όσο και την αποτελεσματική καταστολή των πυρκαγιών κατά τη διάρκεια του αντιπυρικού αγώνα

Μελέτη του προφίλ ζωοτεχνικής διαχείρισης αγελαδοτροφικών εκμεταλλεύσεων της Κ. Μακεδονίας σε συνάρτηση με την παραγωγή, την ποιότητα γάλακτος και το περιβάλλον

[…] The aim of the PhD thesis was the recording of the major characteristics of the structure and the animal production management of the dairy farms as far as the housing, nutrition, reproduction, milking and manure management as well as the study of the applied management practices and the development of the farm profile within the geographical area where the research has been conducted. The data collection was made on a random sample of 123 dairy farms within the geographical area of the research using questionnaires. The methodology of analysis includes: frequency analysis, categorical analysis in principal components of the factors concerning every one of the five issues under study, the two step analysis of clusters, which can be used to develop alternative animal management profiles, and the investigation of the characteristics of the farms and the farmers of every management profile using logit polynomials as reference models. The results highlight the management deficiencies in some farms which are affecting production level and the economic output, and in some cases, the quality of the milk produced. […][…] Στόχος της παρούσης διδακτορικής διατριβής ήταν η καταγραφή των κύριων χαρακτηριστικών της δομής και της ζωοτεχνικής διαχείρισης των αγελαδοτροφικών εκμεταλλεύσεων που αφορά τις μεθόδους σταβλισμού, διατροφής, αναπαραγωγής, άμελξης και διαχείρισης των αποβλήτων, η μελέτη των εφαρμοζόμενων διαχειριστικών πρακτικών και η διαμόρφωση της φυσιογνωμίας των εκτροφών στην περιοχή της έρευνας. Η συλλογή των δεδομένων έγινε σε τυχαίο δείγμα 123 εκμεταλλεύσεων της περιοχής μελέτης, με τη συμπλήρωση ερωτηματολογίου. Το μεθοδολογικό πλαίσιο της ανάλυσης περιλαμβάνει την ανάλυση συχνοτήτων, την Κατηγορική Ανάλυση σε Κύριες Συνιστώσες των μεταβλητών που αφορούν κάθε ένα από τα πέντε εξεταζόμενα ζητήματα, τη Διβηματική Ανάλυση κατά Συστάδες, βάσει της οποίας διαμορφώνονται εναλλακτικά προφίλ ζωοτεχνικής διαχείρισης των εκτροφών και τη διερεύνηση των χαρακτηριστικών των εκτροφών και των ιδιοκτητών κάθε διαχειριστικού προφίλ με πολυωνυμικά logit υποδείγματα. Τα αποτελέσματα αναδεικνύουν διαχειριστικές ανεπάρκειες σε ορισμένες από τις εκμεταλλεύσεις, οι οποίες επηρεάζουν τις αποδόσεις και τα οικονομικά αποτελέσματά τους, καθώς και σε ορισμένες περιπτώσεις, την ποιότητα του παραγόμενου γάλακτος […

A review and classification of heuristic algorithms for the inventory routing problem

The inventory routing problem (IRP) is an integration of vehicle routing and inventory management problems. In the recent years, it has increasingly drawn the attention of the researchers because of its potentially significant practical value. The IRP is classified as NP-hard problem since it subsumes the vehicle routing problem (VRP). This fact led to the development of many heuristic or metaheuristic approaches, although a small number of exact methods have been introduced recently. Heuristic methods offer the advantage of shorter time scales, i.e., greater computational efficiency, on the expense of course of the accuracy of the results. The immediate trigger for this study is our concern about results validation, which has been debatable in early papers, and only recently a systematic effort to create a set of optimally solved benchmark instances has been made. This article presents the heuristic methods for solving the basic variants of IRP found in the literature, stressing the computational results and the solution verification approach, rather than the methodology of the algorithms. The paper concludes with a discussion on the quality of the performance assessment of the proposed algorithms