Diversity and classification of rheophilic communities of macrobenthos in middle latitudes of European Russia

Based on original data (450 samples from 115 streams of European Russia middle latitudes--from Pskov to Kostroma Regions) the attempt is made to describe the overall diversity of rheophilic communities dwelling on streams bottom and in macrophytes. In total, 39 community types were identified by the Brown-Blankuet method; their taxonomical and structural characteristics are described; the associations with biotopes are outlined; and a biotopical nomenclature is proposed. All communities are subdivided into four biotopical classes: crenal (springs and springbrooks with mixed substrates), rhitral (stony and woody substrates), phythal (macrophytes), and pelal (soft ground). It is shown that all communities may be divided by their organization as R-type of M-type community. 36 out of 39 studied communities belong to R-type and are characterized mainly by prevalence of insect, unstable dominance, and rather distinct association to the biotope. In M-type communities (3 out of 39 studied communities) eurybiontic mullusk Viviparus viviparus and amphipod Dikerogammarus haemobaphes predominate; these communities are interbiotopic, with stable species structure and high total abundance. The effect of the study spatial scale on the definition of communities is discussed along with problems of the communities dynamics.     

Intercalation-mediated synthesis and replication: a new approach to the origin of life

We propose that a molecular midwife, a flat molecule approximately 10 Ax10 A with two hydrophobic faces, was essential to the origin of life. This molecule was positively charged, water soluble and did not strongly associate with itself in solution. It may have been a derivative of phthalocyanine that no longer exists on the Earth today, and might have been formed solely from hydrogen cyanide and formaldehyde. The midwife tended to intercalate between side groups (bases, similar to those in RNA) of polymers to form stacks, which incorporated bare bases. The midwife alternated in these stacks with hydrogen-bonded tetrads of bases. Under conditions of low water activity, as in a desert during the day, bare bases in the stacks were joined together by neutral and chemically heterogeneous backbones of no fixed chirality. The components of the backbones were the products of the formose reaction of formaldehyde, and were involved in the reversible formation of N -glycosides and acetals catalysed by divalent metal ions. The final product of this assemblage was a fully intercalated quadruplex of four information-containing polymer strands (four proto -RNA molecules). This process constituted replication of the original polymer that had seeded the formation of the stack. The stack structure ensured that the polymer's base sequence was replicated faithfully despite the lack of both homochirality and chemical homogeneity in the backbone. At night, water from condensing dew would suddenly come in contact with these products, quenching all chemical reactions and releasing midwife molecules and single- or double-stranded proto-RNA. Evaporation of water during the day then gave new stacks containing one or two proto-RNA strands, bare bases, and midwife molecules, which could begin a new replication cycle. Our model also allows for the generation of new stacks and the extension of existing ones, without restricting the base sequence of either, thereby providing a source of genetic information. The proto-RNA replication cycle is driven purely by concentration changes caused by the Sun and the rotation of the Earth. We propose that this system as a whole could have gradually evolved into the RNA World.     

A new approach to the minimal area of a plant community

Current methods for the determination of the minimal area of a phytocoenosis are compared. A new method is described. It is based on the increase in average quantitative similarity between plots in series of nested plots of increasing size in relation to species richness anddominance relations. A simulation model composed of coenotic molecules sensu Moravec is developed from which these relations can be deduced. Both a quantitative and a qualitative minimal area are derived in this way. The analytical minimal area is then defined in relation to the largest of the two minimal area values, because in this way both the species richness and the dominance relations will be represented.Some examples of grasslands and heathlands are presented. Some further investigations are suggested to improve the approach and to link it with pattern and dominance-diversity studies.Nomenclature of plant species follows Heukels-van Ooststroom (1977), of syntaxa Westhoff & den Held (1969) and de Smidt (1975)We thank Dr. Jaroslav Moravec, Pruhonice, for discussions, Drs. Onno van Tongeren, Nijmegen for help with calculations and Cyril Liebrand and Leo Mertens, Nijmegen for help with salt marsh analyses and discussions on dominance-diversity relations.Research was carried out when the authors were at the Division of Geobotany, University of Nijmegen.     

Family fingerprints: a global approach to structural classification

Protein domain classification is a useful tool to deduce functional properties of proteins. Many software to classify domains according to available databases have been proposed so far. This paper introduces the notion of "fingerprint" as an easy and readable digest of the similarities between a protein fragment and an entire set of sequences. This concept offers us a rationale for building an automatic SCOP classifier which assigns a query sequence to the most likely family. Fingerprint-based analysis has been implemented in a software tool and we report some experimental validations for it.     

The rithral macrobenthos community biogeography of southeastern Europe

The rithral and hypocrenal (of small rapid streams) macrobenthos faunas of northern Greece, eastern Carpathians, montane Crimea, and northwestern Caucasus are comparatively analyzed based on original material. Peculiarities of the rheophile communities and faunas of each region and of the whole studied area are described. The area is provisionally divided into biogeographic unites based on rithral fauna; this classification is essentially different from those of other authors. The main faunistic border runs meridionally between Greece-Carpathians on one side and Caucasus-Crimea on the other. The present authors believe that the biogeographic variability of macrobenthos rithral faunas results from the position of regions containing rithron communities and from spatial ties between them. Three fundamental biogeographic zones, suggested to be ranked as subregions, are recognized in the West Palearctic: the Balkan-Alpine (West European), the Scandinavian-Ural (North European), and the Caucasian. All the data available fit the suggested scheme, which shows that this approach is of universal value to biogeographic analysis and to divisions of the rithral into biogeographic zones. The local-scale variability of rheophile macrobenthos fauna in the northwestern Caucasus is discussed. Significant faunistic similarity of territories comprising the studied area is shown, internal division into biogeographic zones is conducted, and the lowest scale border of the faunistic diversity of rheophile macrobenthos is established at about 100-150 km.     

A new approach to the species classification problem in floristic analysis

A new method of species (inverse) classification of vegetation data, i.e. classification of species into groups with similar ecological tolerances, is presented which overcomes the problems of species abundance distorting the results. The algorithm TWO-STEP is based on the use of an asymmetric measure of dissimilarity: where i, j are species, h is the stand, n is the total number of stands, and x_ih is the amount of species i in stand h. The algorithm uses the rows of the asymmetric dissimilarity matrix generated as above to form a second symmetric dissimilarity matrix using the measure: where m is the number of species and k the species. Flexible sorting is applied to generate a species classification. Comparison of results after applying the TWO-STEP algorithm and a standard alternative to an artificial data set demonstrates its efficacy. TWO-STEP also shows considerable advantages over previous analyses for a Queensland rainforest data set (quantitative) and an English heath (qualitative) data set. Normalization of species data appears advantageous for quantitative data only.     

Morphological classification and sexual dimorphism of hyoid bone: new approach

Hyoid bone is a part of viscerocranium placed between the tongue root and thyroid cartilage to which it is connected by thyrohyoid membrane. Widely accepted morphological classification does not exist. Sexual dimorphism was analysed in this study and new guidelines for anatomical classification of hyoid bones based on anthropometric parameters were given. Total number of analysed bones was 70. The bones were classified into three groups: symmetrical U-type, symmetrical V-type and asymmetrical type according to the angle between greater horns and the proportion of greater horns length. In the females incidence of asymmetrical type is considerably higher than in the males, while the incidence of symmetrical V-type is lower The angle value that is on average higher in males may be the parameter indicating that in puberty hyoid bone, still not completely ossified, to some extent follows development of thyroid cartilage because of their close anatomical relation.     

Analysis of damped oscillations during reentry: a new approach to evaluate cardiac restitution

Reentry is a mechanism underlying numerous cardiac arrhythmias. During reentry, head-tail interactions of the action potential can cause cycle length (CL) oscillations and affect the stability of reentry. We developed a method based on a difference-delay equation to determine the slopes of the action potential duration and conduction velocity restitution functions, known to be major determinants of reentrant arrhythmogenesis, from the spatial period P and the decay length D of damped CL oscillations. Using this approach, we analyzed CL oscillations after the induction of reentry and the resetting of reentry with electrical stimuli in rings of cultured neonatal rat ventricular myocytes grown on microelectrode arrays and in corresponding simulations with the Luo-Rudy model. In the experiments, P was larger and D was smaller after resetting impulses compared to the induction of reentry, indicating that reentry became more stable. Both restitution slopes were smaller. Consistent with the experimental findings, resetting of simulated reentry caused oscillations with gradually increasing P, decreasing D, and decreasing restitution slopes. However, these parameters remained constant when ion concentrations were clamped, revealing that intracellular ion accumulation stabilizes reentry. Thus, the analysis of CL oscillations during reentry opens new perspectives to gain quantitative insight into action potential restitution.     

Biosensor approach to psychopathology classification

We used a multi-round, two-party exchange game in which a healthy subject played a subject diagnosed with a DSM-IV (Diagnostic and Statistics Manual-IV) disorder, and applied a Bayesian clustering approach to the behavior exhibited by the healthy subject. The goal was to characterize quantitatively the style of play elicited in the healthy subject (the proposer) by their DSM-diagnosed partner (the responder). The approach exploits the dynamics of the behavior elicited in the healthy proposer as a biosensor for cognitive features that characterize the psychopathology group at the other side of the interaction. Using a large cohort of subjects (n = 574), we found statistically significant clustering of proposers' behavior overlapping with a range of DSM-IV disorders including autism spectrum disorder, borderline personality disorder, attention deficit hyperactivity disorder, and major depressive disorder. To further validate these results, we developed a computer agent to replace the human subject in the proposer role (the biosensor) and show that it can also detect these same four DSM-defined disorders. These results suggest that the highly developed social sensitivities that humans bring to a two-party social exchange can be exploited and automated to detect important psychopathologies, using an interpersonal behavioral probe not directly related to the defining diagnostic criteria.     

Selecting appropriate forms of nitrogen fertilizer to enhance soil arsenic removal by Pteris vittata: a new approach in phytoremediation

Certain plant species have been shown to vigorously accumulate some metals from soil, and thus represent promising and effective remediation alternatives. In order to select the optimum forms of nitrogen (N) fertilizers for the arsenic (As) hyperaccumulator, Pteris vittata L., to maximize As extraction, five forms of N were added individually to different treatments to study the effect of N forms on As uptake of the plants under soil culture in a greenhouse. Although shoot As concentration tended to decrease and As translocation from root to shoot was inhibited, overall As accumulation was greater due to higher biomass when N fertilizer was added. Arsenic accumulation in plants with N fertilization was 100-300% more than in the plants without N fertilization. There were obvious differences in plant biomass and As accumulation among the N forms, i.e., NH4HCO3, (NH4)2S04, Ca(NO3)2, KNO3, urea. The total As accumulation in the plants grown in As-supplied soil, under different forms of N fertilizer, decreased as NH4HCO3>(NH4)2S04 > urea > Ca(NO3)2 >KNO3>CK. The plants treated with N and As accumulated up to 5.3-7.97 mg As/pot and removed 3.7-5.5% As from the soils, compared to approximately 2.3% of As removal in the control. NH4+ -N was apparently more effective than other N fertilizers in stimulating As removal when soil was supplied with As at initiation. No significant differences in available As were found among different forms of N fertilizer after phytoremediation. It is concluded that NH4+ -N was the preferable fertilizer for P. vittata to maximize As removal.     

Protein nanocrystallography: a new approach to structural proteomics

This article describes a new approach to structural proteomics that can produce and characterize diffracting, stable and radiation-resistant crystals of miniscule dimensions using nanotechnology. We believe that the protein microcrystals obtained by nanotechnology-based protein thin-film template crystallization, as well as groundbreaking technology, such as atomic force microscopy, nanogravimetry and synchrotron microfocus, have enabled protein nanocrystallography to be defined as a unique technology capable of forming and characterizing stable protein microcrystals down to atomic resolution. A new route from art to science and technology has, therefore, been opened in protein crystallography, and it could be used to unravel the mysteries of many systems that remain unsolved.     

In search of universal patterns in community organization: the concept of neutrality paved the way to a new approach

The recent renewal of interest in community structure was strongly stimulated by the concept of neutrality, a new view on the problem of species coexistence. In contrast to traditional approach claiming that species competing for common resources should occupy different ecological niches, the neutrality concept assumes that species can coexist if they are ecologically identical, i.e., they have similar specific (per individual) rate of population growth, probability of extinction and the rate of colonization of free space. The analysis of recent literature, full of contradictory opinions on the ideas of neutrality and niche, can be resulted in form of following questions: (1) What do we suggest when we say that species coexist? (2) How can we explain the usual pattern of species relative abundances in a community, the so-called hollow curve (the distribution of numbers of species arranged in classes of abundance)? (3) Do rare species have some advantages in comparison with abundant species? (4) Can the mechanisms implied by neutrality concept and traditional niche approach work simultaneously in the same community? Trying to answer these questions we should: (1) refuse the demand of indefinite coexistence of species although this condition was considered as necessary in classical mathematical models of competition; (2) accept that community structure depends not only on ecological processes (species dispersal, competition and others) but also on the evolutionary ones (speciation) that determine the pool of species; (3) accept that rare species have some advantages as compared with the most abundant species; (4) accept that in any real community species can coexist either occupying the different niches or approaching ecological similarity. Despite considerable progress achieved in understanding of general principles of community organization, we still don't know how to answer the question Why are there so many kinds of animals? that was posed by Hutchinson 50 years ago.     

A new approach to the detection and statistical classification of Ca2+ sparks

The availability of high-speed, two-dimensional (2-D) confocal microscopes and the expanding armamentarium of fluorescent probes presents unprecedented opportunities and new challenges for studying the spatial and temporal dynamics of cellular processes. The need to remove subjectivity from the detection process, the difficulty of the human eye to detect subtle changes in fluorescence in these 2-D images, and the large volume of data produced by these confocal microscopes call for the need to develop algorithms to automatically mark the changes in fluorescence. These fluorescence signal changes are often subtle, so the statistical estimate of the likelihood that the detected signal is not noise is an integral part of the detection algorithm. This statistical estimation is fundamental to our new approach to detection; in earlier Ca(2+) spark detectors, this statistical assessment was incidental to detection. Importantly, the use of the statistical properties of the signal local to the spark, instead of over the whole image, reduces the false positive and false negative rates. We developed an automatic spark detection algorithm based on these principles and used it to detect sparks on an inhomogeneous background of transverse tubule-labeled rat ventricular cells. Because of the large region of the cell surveyed by the confocal microscope, we can detect a large enough number of sparks to measure the dynamic changes in spark frequency in individual cells. We also found, in contrast to earlier results, that cardiac sparks are spatially symmetric. This new approach puts the detection of fluorescent signals on a firm statistical foundation.     

AI-based approach to automatic sleep classification

The primary goal of this paper is to introduce the potential of artificial intelligence (AI) methods to researchers in sleep classification. AI provides learning procedures for the construction of a sleep classifier, prescribing how to combine the observed parameters and how to derive the corresponding decision thresholds. A case study reporting a successful application of an automatic induction of decision trees and of a learning vector quantizer to this domain is presented. Received: 24 May 1993/Accepted in revised form: 8 September 1993