Janos Podani

Janos Podani
Eötvös Loránd University

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134
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Publications

Publications (134)
Article
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Background Hawthorn species ( Crataegus L.; Rosaceae tribe Maleae) form a well-defined clade comprising five subgeneric groups readily distinguished using either molecular or morphological data. While multiple subsidiary groups (taxonomic sections, series) are recognized within some subgenera, the number of and relationships among species in these...
Article
Sister groups at the root of large plant clades (with ≥1000 extant species) are described in terms of variables expressing species richness, geographical distribution, age, diversification rate and speed of molecular evolution. Standard statistical tools and principal component analysis are used to determine and visualize their relationships. In th...
Article
Thinking about the dynamics of populations of plants and animals goes back to Linnaeus. He used at least three examples to show what happens when the population of a species grows without limitations and to illustrate the potential reproductive capacity of organisms. We examined the mathematical precision of calculations Linnaeus used in presenting...
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The present article has two primary objectives. First, the article provides a historical overview of graphical tools used in the past centuries for summarizing the classification and phylogeny of plants. It is emphasized that each published diagram focuses on only a single or a few aspects of the present and past of plant life on Earth. Therefore,...
Article
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An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Nowadays, the complementary diagnostics based on the suspicious thyroid lesion specific mutational state analysis is indispensable in the clinical practice. We aimed to test and validate our novel 568-mutational hotspot panel (23 cancer-related genes) on papillary thyroid cancers (PTCs) and their tumor-free pairs to find the most powerful mutation...
Article
Introduction: Twenty-five percent of fine-needle aspiration biopsy samples of thyroid nodules produce indeterminate cytological results. Genetic testing of nodules can contribute to accurate diagnosis. Aim: Developing the first gene panel in Europe utilizing the 23 most relevant thyroid oncogenes with 568 mutations. Method: Examination of the isola...
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The Tree of Life (ToL) has been of central importance in the biological sciences, usually understood as a model or a metaphor, and portrayed in various graphical forms to summarize the history of life as a single diagram. If it is seen as a mathematical construct—a rooted graph theoretical tree or, as more recently viewed, a directed network [Netwo...
Article
Gonadal hormones including 17β-estradiol exert important protective functions in skeletal homeostasis. However, numerous details of ovarian hormone deficiency in the common bone marrow microenvironment have not yet been revealed and little information is available on the tissue-specific acts either, especially those via estrogen receptor beta (ERβ)...
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Community structure as summarized by presence–absence data is often evaluated via diversity measures by incorporating taxonomic, phylogenetic and functional information on the constituting species. Most commonly, various dissimilarity coefficients are used to express these aspects simultaneously such that the results are not comparable due to the l...
Cover Page
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Vale, David. Thank you for life well lived!
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In “The Origin of Species,” Darwin describes a hypothetical example illustrating that large, slowly reproducing mammals such as the elephant can reach very large numbers if population growth is not affected by regulating factors. The elephant example has since been cited in various forms in a wide variety of books, ranging from educational material...
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Methods that quantify multiple-site resemblance are basic toolkits of ecology for studying community variation in space and time. Although both pairwise and multiple-site coefficients have received increasing attention in the past decade, the high variety of methodologies combined with the absence of a systematic review prevents full understanding...
Article
The Elements of Metacommunity Structure (EMS) framework originally suggested by Leibold and Mikkelson (2002) in Oikos is a popular approach to identify idealized metacommunity patterns (i.e. checkerboard, nested, evenly spaced, Clementsian, Gleasonian), and hereby to infer the existence of structuring processes in metacommunities. Essentially, the...
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Although islands are model systems for investigating assembly of biological communities, long-term changes in archipelago communities are not well understood because of the lack of reliable data. By using a vast amount of floristic data we assembled a dataset of the plant species occurring on 16 islands of the Tuscan Archipelago, Italy, across two...
Article
In this paper, we examine some basic properties of the Bray-Curtis dissimilarity as compared with other distance and dissimilarity functions applied to ecological abundance data. We argue that the ability of every coefficient to measure species-level contributions is a fundamental requirement. By suggesting an additive decomposition formula for the...
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Voles are among the most common and abundant rodents in Central Europe, represented by several species of Microtus and other genera. This group is also common in Pleistocene fossil assemblages. However, the taxonomy of fossil finds, largely based on lower first molars, is fraught with problems and opinions of various authors often diverge, hamperin...
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One of the most vulnerable community types in the Mediterranean basin are the Isoetes histrix swards. The present study, based on a literature review, was aimed to define patterns of plant communities with I. histrix and to identify the key factors driving these patterns at large spatial scale. Data from 7 areas (Corsica, Crete, Italian peninsula,...
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The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylo...
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There has long been ambiguity in the use of the term tree in phylogenetic systematics, which is a continuous source of misinterpretation of evolutionary relationships. The basic problem is that while many trees with phylogenetic or evolutionary relevance, such as cladograms, are consistent with graph theory, tree-like visualization of phylogeny may...
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Although several studies have examined the functional diversity of freshwater macroinvertebrates, the variety of methodologies combined with the absence of a synthetic review make our understanding of this field incomplete. Therefore, we reviewed the current methodology for assessing functional diversity in freshwater macroinvertebrate research. Ou...
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This study is an attempt to expand a previous survey by Fisler and Lecointre (FL) for systematizing ideas on the use of the tree metaphor in classification, as expressed by various historically important figures in their writings. FL used a cladistic approach to analyze their data, as employed in biological classification. We supplement this analys...
Preprint
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This study is an attempt to expand a previous survey by Fisler and Lecointre (FL) for systematizing ideas on the use of the tree metaphor in classification, as expressed by various historically important figures in their writings. FL used a cladistic approach to analyze their data, as employed in biological classification. We supplement this analys...
Article
In Philosophia Botanica (1751), Carolus Linnaeus (1707–1778) presented a calculation of the number of plant genera that may be distinguished based on his taxonomic concepts. In order to derive that number, he relied upon the organs of fructification, which represent the flower and the fruit, by selecting over 30 elements from them, and then assumin...
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Plot-to-plot dissimilarity measures are considered a valuable tool for understanding the complex ecological mechanisms that drive community composition. Traditional presence/absence coefficients are usually based on different combinations of the matching/mismatching components of the 2 9 2 contingency table. However, more recently, dissimilarity me...
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Helichrysum italicum (Asteraceae) is a small shrub of the Mediterranean area which colonizes a wide range of habitats. In Sardinia, Italy, the species is widely dispersed in different environments ranging from sandy beaches to holm hoak forests 1250 m above sea level (a. s. l.). Recently, the species has been attributed an increasing economical val...
Article
QuestionsWhat is the relative importance of our methodological decisions concerning sampling (plot size) and data analysis (data transformation, resemblance coefficient, hierarchical clustering strategy and number of clusters) in vegetation classification? Are there differences between the conclusions when the full range or only a more practical na...
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Traits-based community analyses are receiving increasing attention. However, consistent interpretation of empirical results and ecological understanding in stream ecology are limited by ambiguous terminology. Furthermore, the measurement scales used to analyze trait data, especially ordinal-scale data, are often inappropriately applied. We identify...
Article
The increasing availability of phylogenetic information facilitates the use of evolutionary methods in community ecology to reveal the importance of evolution in the species assembly process. However, while several methods have been applied to a wide range of communities across different spatial scales with the purpose of detecting non-random phylo...
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The collection of epiphyllous bryophytes in the lowland rainforests of Phang-Nga province and in the neighbouring Phuket and Surat Thani provinces resulted in 54 liverwort and one moss species, of which 14 are new records for the bryoflora of Thailand. Epiphyllous bryophyte assemblages from nine localities are evaluated for species richness and bet...
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Objective: The aims of the present study were to examine gene and protein expression of the vitamin D-inactivating 24-hyroxylase (CYP24A1) and the activating 1-alpha-hydroxylase (CYP27B1) enzyme in human papillary thyroid cancer (PTC), furthermore, to investigate the association between CYP24A1 expression and numerous clinical, histological parame...
Article
We propose the use of a new methodological scheme for exploring and quantifying structure in bipartite ecological networks. In this, graphical visualization and numerical measurement are combined, offering a unique possibility for network analysis on a coherent conceptual basis. Dissimilarity between all species pairs in either group of constitutin...
Article
Monaghan and Soares (2014) suggested that combining traits with log-transformed abundance of taxa may cause anomalies in analyses of stream macroinvertebrate communities. While they addressed an important issue in stream ecology, here we present an opposite view. To identify the causes of these contrasting opinions, we carefully examined the exampl...
Article
AimTo propose a unified framework for quantifying taxon (Tβ), phylogenetic (Pβ) and functional (Fβ) beta diversity via pairwise comparisons of communities, which allows these types of beta diversity to be partitioned into ecologically meaningful additive components. LocationGlobal, with case studies in Europe and the Azores archipelago. Methods Usi...
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A new approach to the measurement of functional diversity based on two-state nominal traits is developed from the florula diversity concept of P. Juhasz-Nagy. For evaluating functional diversity of an assemblage, first a traits by species matrix is compiled. Various information theory functions are used to examine structural properties in this matr...
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Background: The myrtle (Myrtus communis) is a common shrub widespread in the Mediterranean Basin. Its fruit and leaves exhibit antioxidant, antibacterial and antifungal properties, and are used for their content of essential oils and for their medicinal properties, but most commonly as an ingredient in locally made liquor. The uncontrolled exploita...
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QuestionsWhich are the most effective plant communities for honeybee foraging and honey production in Mediterranean sylvo-pastoral systems? What is the relationship between flowering phenology and pollen occurring in honey sediments? LocationMediterranean sylvo-pastoral system in Gallura, Sardinia, Italy. Methods Phytosociological and phenological...
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This paper presents a graph theoretical overview of tree diagrams applied extensively in systematic biology. Simple evolutionary models involving three speciation processes (splitting, budding and anagenesis) are used for evaluating the ability of different rooted trees to demonstrate temporal and ancestor–descendant relationships within or among s...
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This paper deals with nestedness measures that are based on pairwise comparisons of sites, evaluates their performance and suggests improvements and generalizations. There are several conceptual and technical criteria to judge their ecological applicability. It is of primary concern whether the measures 1) have a clear mathematical definition, 2) a...
Article
Osteonecrosis of the jaw (ONJ) is a major complication associated with long-term use of bisphosphonates (BP). We aimed to investigate the effect of CYP2C8 rs1934951 SNP and its relationship to a number of clinical and biochemical factors in 46 Hungarian subjects with bisphosphonate-induced ONJ. Blood samples were collected from each subject and gen...
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Beta diversity, species replacement and nestedness are often examined through pairwise comparisons of sites based on presence-absence data, and the relative importance of these ecological phenomena is evaluated by operations with dissimilarity coefficients. An example is the nestedness resultant dissimilarity (NRD) procedure recently proposed by Ba...
Article
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Osteonecrosis of the femoral head (ONFH) is the result of an interruption of the local circulation and the injury of vascular supply of bone. Multiple factors have been implicated in the development of the disease. However the mechanism of ischemia and necrosis in non-traumatic ONFH is not clear. The aim of our investigation was to identify genes t...
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Network analysis examines the role of species in ecological communities. The most common approach involves measurement of centrality of species or other groups of individuals based on their topological positions in food webs, followed by establishing the rank order of importance of these groups. However, ranking may differ considerably with indices...
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The indicator value (IndVal) of a species has long been the most popular measure to express species importance in community classifications. Nevertheless, a few problems concerning the original definition of IndVal still require clarification and some modifications are also in order so as to exploit the capabilities of the method more fully. In par...
Article
Fibrous dysplasia is an isolated skeletal disorder caused by a somatic activating mutation of GNAS1 gene with abnormal unmineralized matrix overproduction and extensive undifferentiated bone cell accumulation in fibro-osseous lesions. The aim of the investigation was to identify genes that are differently expressed in fibrous vs. non-fibrous human...
Article
Antlers of deer display the fastest and most robust bone development in the animal kingdom. Deposition of the minerals in the cartilage preceding ossification is a specific feature of the developing antler. We have cloned 28 genes which are upregulated in the cartilaginous section (called mineralized cartilage) of the developing ("velvet") antler o...
Article
Fibrous dysplasia is an isolated skeletal disorder caused by a somatic activating mutation of GNAS gene with abnormal unmineralized matrix overproduction and extensive undifferentiated bone cell accumulation in the fibro-osseous lesions. The aim of our investigation was to identify genes that are differently expressed in fibrous versus non-fibrous...
Article
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The ongoing discourse on monophyly versus paraphyly shows apparent lack of mutual understanding among schools of biological taxonomy. The principal reason behind the frozen disagreement is that these terms were redefined repeatedly. Although terminological discrepancy has long been recognized, relatively few attempts have been made to clarify this....
Article
The ongoing discourse on monophyly versus paraphyly shows apparent lack of mutual understanding among schools of biological taxonomy. The principal reason behind the frozen disagreement is that these terms were redefined repeatedly. Although terminological discrepancy has long been recognized, relatively few attempts have been made to clarify this....
Article
Full-text available
With this issue, Community Ecology enters its second decade. We feel it is the right time to put the past into perspective by taking stock of the achievements on which the Journal’s future can be predicated. Community Ecology was established in 2000 by the merger of two other journals, Coenoses published by CETA in Gorizia, Italy, and Ab-stracta Bo...
Article
Isozyme, RAPD (random amplified polymorphic DNA) and microsatellite techniques were applied to determine the genetic diversity of a reed stand declining at the open water fringe for several decades and the accuracy of these methods was evaluated. Sampling was carried out along three transects parallel with and one transect at right angle to the lak...
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There is a recent proposal to apply convex hulls to the measurement of habitat filtering, trophic diversity and functional richness. Although this approach has successful applications, some conceptual difficulties with the interpretation of results should not be overlooked. The basic assumption that trait convergence and the associated deflation of...
Article
Four major taxonomical issues are commented briefly in view of evolutionary biology: classification, hierarchy, trees and nomenclature. It is argued that distinction between diachronous and synchronous classification schemes is of primary importance in taxonomy. The currently adopted classification of life is meant to be diachronous and Linnaean at...
Article
Introduction The molecular and cellular interactions between the immune system and bone tissue have been established. Sex hormone deficiency after menopause has multifunctional role by influencing growth, differentiation, and metabolism of the skeletal and the immune system. Discussion We have used nonparametric and multidimensional expression patt...
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A novel discrete mathematical approach is proposed as an additional tool for molecular systematics which does not require prior statistical assumptions concerning the evolutionary process. The method is based on algorithms generating mathematical representations directly from DNA/RNA or protein sequences, followed by the output of numerical (scalar...
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Osteoporosis attacks 10% of the population worldwide. Humans or even the model animals of the disease cannot recover from porous bone. Regeneration in skeletal elements is the unique feature of our newly investigated osteoporosis model, the red deer (Cervus elaphus) stag. Cyclic physiological osteoporosis is a consequence of the annual antler cycle...
Article
The functional interaction between the immune system and bone metabolism has been established at both molecular and cellular levels. We have used non-parametric and multidimensional expression pattern analyses to determine significantly changed mRNA profile of immune system-associated genes in postmenopausal osteoporotic (OP) vs. non-osteoporotic (...
Article
Menopausal changes influence the growth, differentiation, and metabolism of bone tissue. Hormonal deficiency at the time of menopause results in marked increases in bone resorption and formation, leading to rapid bone loss. The aim of our investigation was to determine genes characterized by significantly changed mRNA expression rates in postmenopa...
Article
This paper is a reflection on a recent study on input order sensitivity of data analysis methods commonly used in vegetation science. It is pointed out that variability of results is due to some arbitrary element in the method, either in its algorithm or in its computer program. Many methods produce unique results theoretically; this implies that t...
Article
Procedures are currently available for the evaluation of hierarchical classifications of produce tree dissimilarities or consensus dendrograms. Some tests of cluster validity operate by comparing all possible partitions from a tree with a reference partition. We propose an exhaustive search procedure to compare all partitions from one dendrogram wi...
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To identify genes that are differently expressed in osteoporotic and non-osteoporotic human bone and to describe the relationships between these genes using multivariate data analysis. Seven bone tissue samples from postmenopausal osteoporotic patients and 10 bone tissue samples from postmenopausal non-osteoporotic women were examined in our study....
Article
This communication is a response to a recent suggestion that ordinal data of the Braun-Blanquet type (BB) can be directly or, after conversion to ranks, indirectly analysed by metric methods. I show that the proposals on structure in topological spaces made by Ricotta & Avena in a recent contribution to this Forum are confounding because (1) they u...
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Link distribution is an important architectural feature of ecological networks, since it is thought to influence community dynamics. Several attempts have been made in order to characterize the typical link distribution of food webs, but the number of webs studied thus far is low and their quality is unbalanced. Comparability is a rarely asked meth...