Towards Understanding Reasoning Complexity in Practice

Although the computational complexity of the logic underlying the standard OWL 2 for the Web Ontology Language (OWL) appears discouraging for real applications, several contributions have shown that reasoning with OWL ontologies is feasible in practice. It turns out that reasoning in practice is often far less complex than is suggested by the established theoretical complexity bound, which reflects the worstcase scenario. State-of-the reasoners like FACT++, HERMIT, PELLET and RACER have demonstrated that, even with fairly expressive fragments of OWL 2, acceptable performances can be achieved. However, it is still not well understood why reasoning is feasible in practice and it is rather unclear how to study this problem. In this paper, we suggest first steps that in our opinion could lead to a better understanding of practical complexity. We also provide and discuss some initial empirical results with HERMIT on prominent ontologies

Analyzing energy-efficient configurations in hexapod robots for demining applications

Purpose – Reducing energy consumption in walking robots is an issue of great importance in field applications such as humanitarian demining so as to increase mission time for a given power supply. The purpose of this paper is to address the problem of improving energy efficiency in statically stable walking machines by comparing two leg, insect and mammal, configurations on the hexapod robotic platform SILO6. Design/methodology/approach – Dynamic simulation of this hexapod is used to develop a set of rules that optimize energy expenditure in both configurations. Later, through a theoretical analysis of energy consumption and experimental measurements in the real platform SILO6, a configuration is chosen. Findings – It is widely accepted that the mammal configuration in statically stable walking machines is better for supporting high loads, while the insect configuration is considered to be better for improving mobility. However, taking into account the leg dynamics and not only the body weight, different results are obtained. In a mammal configuration, supporting body weight accounts for 5 per cent of power consumption while leg dynamics accounts for 31 per cent. Originality/value – As this paper demonstrates, the energy expended when the robot walks along a straight and horizontal line is the same for both insect and mammal configurations, while power consumption during crab walking in an insect configuration exceeds power consumption in the mammal configuration.

La habitación subterránea en la Península Ibérica : investigación geológica

La habitación rupestre en la Península Ibérica conforma un amplio conjunto de manifestaciones cuyos orígenes son difíciles de dilucidar. Existen conjuntos primitivos, posiblemente horadados durante la Antigüedad Clásica y Tardía, y otros que probablemente se originaron y excavaron en la Alta Edad Media, en los que se mezclan grupos de origen religioso y otros de probable uso defensivo. El conjunto peninsular es sin duda el más variado de Europa Occidental, pues recibió influencias árabes y usos de la cristiandad antigua, importados de Oriente Próximo, que por tanto relacionan estas manifestaciones con otras del arco mediterráneo. La supervivencia del uso de las cuevas a lo largo de la Baja Edad Media -una vez afianzada la Reconquista- es una incógnita, pero los usos rupestres volvieron a generalizarse en ciertos sectores de la Península durante la Edad Moderna, toda vez que el hábitat cuevero manifestó una eclosión relacionada con la peripecia de los moriscos, primero desterrados de sus habitaciones en el Sur y Este peninsular y luego expulsados en los albores del siglo XVII. Los que quedaron, nominalmente conversos, debieron habitar de nuevo cuevas en sus lugares de origen. Esos núcleos son los más abundantes, particularmente en la provincia de Granada y aledañas. Este substrato fue seguramente el punto de apoyo para la proliferación de las cuevas de habitación a partir del siglo XIX, en el cual un creciente proletariado agrícola y urbano necesitó de alojamientos baratos y no hizo sino imitar usos preexistentes, que se pueden rastrear en muchos de los núcleos rupestres que sobrevivieron mayoritariamente hasta bien entrado el siglo XX, y que se abandonaron gradualmente a partir de los años 60 de esa centuria. Para entonces, existían barrios de cuevas extensos en muchas provincias, destacando, aparte de las andaluzas, ciertas zonas de la Cuenca del Ebro (aragonesa, navarra y riojana), del arco periurbano de Valencia, del Sur de Madrid, de la Mancha toledana, o de las provincias de Albacete, Guadalajara, Murcia e incluso de Palencia. Los núcleos antiguos se excavaron -en razón de su origen dedicado a defensa y refugio- en lugares poco accesibles, que mayoritariamente se dan en relieves anfractuosos, en las orlas marginales detríticas y carbonatadas de las cuencas terciarias y en terrenos más antiguos de la geológicamente denominada Cuenca Vasco Cantábrica, en las cuales florecieron centros de eremitismo del primitivo condado de Castilla. También son lugares inaccesibles los riscos asomados a cantiles fluviales, cuya regularización morfológica natural ha sido causa de la ruina de múltiples hipogeos que se labraron con las mismas intenciones de refugio, defensa o retiro espiritual. Los núcleos modernos se han excavado ya en terrenos más propicios (los que componen las cuencas terciarias o "España arcillosa", mayoritariamente), y por ello observamos cómo abundan las litologías sedimentarias, que son aquellas en las que se horadaron casi todas las "colmenas" de habitación moderna en la Península. En unos casos y otros, existen rasgos comunes en lo relativo a la litología y comportamiento de los materiales excavados, y también en lo relativo a su evolución, meteorización y conservación. Se han estudiado por ello estas pautas comunes -como un posible avance para el establecimiento futuro de estudios de geoconservación del patrimonio rupestre habitado-, que se traducen en la determinación de los procesos de meteorización más característicos en los antros de la Península Ibérica -sean modernos o antiguos- y en la determinación de las relaciones más habituales entre geomorfología y tipología de las cuevas de habitación. También se exponen algunas conclusiones relativas a la resistencia de los tipos pétreos en relación a la antigüedad de los emplazamientos. Esta relación se explica bien si tenemos en cuenta que las cuevas antiguas trataban de ser lugares apartados en los que dominan rocas más resistentes -como se ha explicado- y que en las modernas se ha buscado la habitación permanente, en los materiales más blandos ocupan las depresiones terciarias del Centro, Este y Sur de la Península, colonizados no ya como refugios sino de modo seguro, y ya en arrabales "extramuros" de las ciudades. Geomorfológicamente, esta razón histórica tiene consecuencias sobre la posición de las cuevas, sobre su organización, y sobre su conservación. La extensión del dominio estudiado obliga prácticamente a bosquejar algunas de estas conclusiones geológicas, pero permite a su vez proporcionar una visión global acerca del patrimonio troglodítico desde una perspectiva geológica, y en ello radica la principal novedad de la investigación. Cave dwelling in the Iberian Peninsula comprises a great deal of examples whose origins are sometimes difficult to elucidate. There are primitive groups of caves, probably belonging to Classical and Late Antiquity, and other settlements that appear to have been created and excavated in the Early Middle Ages. Some of them are due to religious reasons and some others may probably have served for defensive uses. The Peninsular group is very likely the most diverse in Western Europe, for it was not only influenced by Arabs, but it also assimilated uses from the Antique Christendom, imported from the Middle East. In this sense, Iberian cave dwellings connect with those of the Mediterranean area. There is not total certainty about the survival of caves serving for dwelling throughout the Late Middle Ages, once the Reconquista was a fact. However, underground excavations for human habitation were once again dispread in certain zones of the Peninsula during the Early Modern period. This growth of underground habitats appears in connexion with Morisco’s vicissitudes; first of all, their removal from their settlements in South and Eastern Peninsula, and finally their expulsion from Spanish territory at the very beginning of XVII th century. Those of them who rested in Spain –and that were nominally “converts”- seem to have returned to cave dwelling in their places of origin, particularly in the province of Granada and its neighbouring zones. This substrate may have been the toehold for a new spreading of cave dwellings since XIX th century, when the increasing rural and urban proletariat returned to the pre-existent uses of caves in order to solve the necessity of affordable housing. This fact can still be detected in many of the rock settlements that have survived during a great part of the XX th century and which were gradually abandoned from the 60´s onwards. There were important cave dwelling districts in many Spanish territories by that time, and not only in Andalusia. We also find them in certain areas of the Ebro basin (those of Aragon, Navarra and La Rioja), in the peri-urban arc of Valencia, in the South of Madrid province and also in the provinces of Toledo (the so called “Mancha toledana”), Albacete, Guadalajara, Murcia or even Palencia as well. Due to their defensive and refuge uses, primitive underground habitats were dug in hardly accessible places. The majority of them are located in mountainous and rough areas, when not in the marginal borders of Tertiary basins, where coarse detritic and carbonate formations outcrop. Cave dwellings can also be found in more ancient rock masses, such as those of the Basque Cantabrian Mesozoic Basin, which is the area where hermit centres of the primitive County of Castile first flourished. Cliffs surrounding fluvial valleys are as well inaccessible places, but here we find that geological evolution has caused the destruction of many rock sanctuaries and cliff dwellings that were originally dug with the same purposes of defence, refuge and spiritual retreat. Later modern cave settlements were dug in quite more favourable terrains, mainly in the soils that compose the Tertiary basins, generally known as “España arcillosa” or “Clayey Spain”. Therefore, we find abundant sedimentary fine and medium grained lithologies, which are the ones that have hosted the majority of Modern Era warren cave dwellings in the Iberian Peninsula. Actually, both types of cave dwelling share some standards regarding the lithology of the excavated materials, and they share as well certain patterns that affect to their evolution, weathering and preservation. These common patterns have been studied here in order to determine the most characteristic weathering processes that affect the majority of the Iberian caves, both Antique and Modern. And also with a view to establish the most habitual relationships between geomorphology and typology of cave dwellings. The study may as well provide a first basis for future studies on geo-preservation of cave dwellings heritage. We also reach some conclusions about the strength of different rocks concerning the antiquity of the sites. As we have already pointed out, this relation comes from the fact that ancient caves were placed in remote or isolated locations, where harder rocks outcrop, while more modern ones result from people´s search of permanent dwelling. In this sense, the softer rocks of the Tertiary Basins of Middle, East and South Peninsula provided a secure colonization to this second and modern group. And moreover, considering geomorphological features, this historical reason has had an effect not only on the position and location of the caves, but also on their organisation/structure/distribution and preservation. The huge extension of our domain of interest almost forces to sketch out some of these geological conclusions. But at the same time it gives a global panorama of Spanish troglodyte heritage, seen from a geological perspective. And here is the main novelty of this research.

Phylogenetic assessment of length variation at a microsatellite locus

Sixty-six haplotypes at a locus containing a simple dinucleotide (CA)n microsatellite repeat were isolated by PCR–single-strand conformational polymorphism from populations of the horseshoe crab Limulus polyphemus. These haplotypes were sequenced to assess nucleotide variation directly. Thirty-four distinct sequences (alleles) were identified in a region 570 bp long that included the microsatellite motif. In the repeat region itself, CA-number varied in integer values from 5 to 11 across alleles, except that a (CA)8 class was not observed. Differences among alleles were due also to polymorphisms at 22 sites in regions immediately flanking the microsatellite repeats. Nucleotide substitutions in these regions were used to estimate phylogenetic relationships among alleles, and the gene phylogeny was used to trace the evolution of length variation and CA repeat numbers. A low correlation between size variation and genealogical relationships among alleles suggests that absolute fragment size (as normally scored in microsatellite assays) is an unreliable indicator of historical affinities among alleles. This finding on the molecular fine structure of microsatellite variation suggests the need for caution in the use of repeat counts at microsatellite loci as secure indicators of allelic relationships.

Deciphering a neural code for vision

Deciphering the information that eyes, ears, and other sensory organs transmit to the brain is important for understanding the neural basis of behavior. Recordings from single sensory nerve cells have yielded useful insights, but single neurons generally do not mediate behavior; networks of neurons do. Monitoring the activity of all cells in a neural network of a behaving animal, however, is not yet possible. Taking an alternative approach, we used a realistic cell-based model to compute the ensemble of neural activity generated by one sensory organ, the lateral eye of the horseshoe crab, Limulus polyphemus. We studied how the neural network of this eye encodes natural scenes by presenting to the model movies recorded with a video camera mounted above the eye of an animal that was exploring its underwater habitat. Model predictions were confirmed by simultaneously recording responses from single optic nerve fibers of the same animal. We report here that the eye transmits to the brain robust “neural images” of objects having the size, contrast, and motion of potential mates. The neural code for such objects is not found in ambiguous messages of individual optic nerve fibers but rather in patterns of coherent activity that extend over small ensembles of nerve fibers and are bound together by stimulus motion. Integrative properties of neurons in the first synaptic layer of the brain appear well suited to detecting the patterns of coherent activity. Neural coding by this relatively simple eye helps explain how horseshoe crabs find mates and may lead to a better understanding of how more complex sensory organs process information.

Cryptocyanin, a crustacean molting protein: Evolutionary link with arthropod hemocyanins and insect hexamerins

Cryptocyanin, a copper-free hexameric protein in crab (Cancer magister) hemolymph, has been characterized and the amino acid sequence has been deduced from its cDNA. It is markedly similar in sequence, size, and structure to hemocyanin, the copper-containing oxygen-transport protein found in many arthropods. Cryptocyanin does not bind oxygen, however, and lacks three of the six highly conserved copper-binding histidine residues of hemocyanin. Cryptocyanin has no phenoloxidase activity, although a phenoloxidase is present in the hemolymph. The concentration of cryptocyanin in the hemolymph is closely coordinated with the molt cycle and reaches levels higher than hemocyanin during premolt. Cryptocyanin resembles insect hexamerins in the lack of copper, molt cycle patterns of biosynthesis, and potential contributions to the new exoskeleton. Phylogenetic analysis of sequence similarities between cryptocyanin and other members of the hemocyanin gene family shows that cryptocyanin is closely associated with crustacean hemocyanins and suggests that cryptocyanin arose as a result of a hemocyanin gene duplication. The presence of both hemocyanin and cryptocyanin in one animal provides an example of how insect hexamerins might have evolved from hemocyanin. Our results suggest that multiple members of the hemocyanin gene family—hemocyanin, cryptocyanin, phenoloxidase, and hexamerins—may participate in two vital functions of molting animals, oxygen binding and molting. Cryptocyanin may provide important molecular data to further investigate evolutionary relationships among all molting animals.

Heterothermal acclimation: An experimental paradigm for studying the control of thermal acclimation in crabs

A method for the study of the control of the attainment of thermal acclimation has been applied to the crabs, Cancer pagurus and Carcinus maenas. Crabs were heterothermally acclimated by using an anterior–posterior partition between two compartments, one at 8°C and the other at 22°C. One compartment held a three-quarter section of the crab including the central nervous system (CNS), eye stalks, and ipsilateral legs; the other held a quarter section including the contralateral legs. Criteria used to assess the acclimation responses were comparisons of muscle plasma membrane fatty acid composition and “fluidity.” In both species, the major fatty acids of phosphatidylcholine were 16:0, 18:1, 20:5, and 22:6, whereas phosphatidylethanolamine contained significantly less 16:0 but more 18:0; these fatty acids comprised 80% of the total. Differences in fatty acid composition were demonstrated between fractions obtained from the ipsilateral and contralateral legs from the same heterothermally acclimated individual. In all acclimation states (except 22CNS, phosphatidylcholine fraction), membrane lipid saturation was significantly increased with acclimation at 22° as compared with 8°C. Membrane fluidity was determined by using 1,3-diphenyl-1,3,5 hexatriene (DPH) fluorescence polarization. In both species, membranes from legs held at 8° were more fluid than from legs held at 22°C irrespective of the acclimation temperature of the CNS. Heterothermal acclimation demonstrated that leg muscle membrane composition and fluidity respond primarily to local temperature and were not predominately under central direction. The responses between 8°C- and 22°C-acclimated legs were more pronounced when the CNS was cold-acclimated, so a central influence cannot be excluded.

Molecular cloning of the first metazoan beta-1,3 glucanase from eggs of the sea urchin Strongylocentrotus purpuratus.

We report the molecular cloning of the first beta-1,3 glucanase from animal tissue. Three peptide sequences were obtained from beta-1,3 glucanase that had been purified from eggs of the sea urchin Strongylocentrotus purpuratus and the gene was cloned by PCR using oligonucleotides deduced from the peptide sequences. The full-length cDNA shows a predicted enzyme structure of 499 aa with a hydrophobic signal sequence. A 3.2-kb message is present in eggs, during early embryogenesis, and in adult gut tissue. A polyclonal antibody to the native 68-kDa enzyme recognizes a single band during early embryogenesis that reappears in the adult gut, and recognizes a 57-kDa fusion protein made from a full-length cDNA clone for beta-1,3 glucanase. The identity of this molecule as beta-1,3 glucanase is confirmed by sequence homology, by the presence of all three peptide sequences in the deduced amino acid sequence, and by the recognition of the bacterial fusion protein by the antibody directed against the native enzyme. Data base searches show significant homology at the amino acid level to beta-1,3 glucanases from two species of bacteria and a clotting factor from the horseshoe crab. The homology with the bacteria is centered in a 304-aa region in which there are seven scattered regions of high homology between the four divergent species. These four species were also found to have two homologous regions in common with more distantly related plant, fungal, and bacterial proteins. A global phylogeny based on these regions strongly suggests that the glucanases are a very ancient family of genes. In particular, there is an especially deep split within genes taken from the bacterial genus Bacillus.

Nucleotide sequence of the cDNA encoding the proenzyme of phenol oxidase A1 of Drosophila melanogaster.

Clones encoding pro-phenol oxidase [pro-PO; zymogen of phenol oxidase (monophenol, L-dopa:oxygen oxidoreductase, EC 1.14.18.1)] A1 were isolated from a lambda gt10 library that originated from Drosophila melanogaster strain Oregon-R male adults. The 2294 bp of the cDNA included a 13-bp 5'-noncoding region, a 2070-bp encoding open reading frame of 690 amino acids, and a 211-bp 3'-noncoding region. A hydrophobic NH2-terminal sequence for a signal peptide is absent in the protein. Furthermore, there are six potential N-glycosylation sites in the sequence, but no amino sugar was detected in the purified protein by amino acid analysis, indicating the lack of an N-linked sugar chain. The potential copper-binding sites, amino acids 200-248 and 359-414, are highly homologous to the corresponding sites of hemocyanin of the tarantula Eurypelma californicum, the horseshoe crab Limulus polyphemus, and the spiny lobster Panulirus interruptus. On the basis of the phylogenetic tree constructed by the neighbor-joining method, vertebrate tyrosinases and molluscan hemocyanins constitute one family, whereas pro-POs and arthropod hemocyanins group with another family. It seems, therefore, likely that pro-PO originates from a common ancestor with arthropod hemocyanins, independently to the vertebrate and microbial tyrosinases.

Revisão taxonômica e filogenia do gênero Megalobrachium Stimpson, 1858 (Crustacea: Decapoda: Anomura: Porcellanidae)

O presente trabalho trata do gênero de porcelanídeos Megalolobrachium Stimpson, 1858 e está organizado em três partes: (1) uma revisão taxonômica das espécies atualmente atribuídas a Megalobrachium Stimpson, 1858; (2) uma revisão da diversidade morfológica do gênero em um contexto maior dentro de Porcellanidae; e (3) uma análise cladística a partir de dados morfológicos com o intuito de testar o monofiletismo de Megalobrachium e propor a primeira hipótese filogenética para o gênero. A revisão taxonômica se baseou no estudo de material abundante de diferentes localidades do Pacífico oriental e Atlântico ocidental. Uma nova espécie de Megalobrachium é descrita com base no material das costas pacíficas do Panamá e Colômbia, totalizando 13 espécies em Megalobrachium. Para a análise filogenética, foram obtidos 151 caracteres; o grupo-externo foi composto por quatro espécies de três gêneros: Pachycheles Stimpson, 1858, Pisidia Leach, 1820, e Porcellana Lamarck, 1801. Uma única árvore (314 passos; IC: 64; IR: 80) foi obtida, com dois clados. O primeiro clado inclui espécies com lobos da fronte marcadamente flexionados, flagelo da antena curto, com artículos longos, patas ambulatórias curtas e robustas, abdome subtriangular em machos, pleópodo feminino iv com três segmentos, e urópodos curtos. O segundo clado contém espécies com lobos da fronte não flexionados, flagelo da antena longo, com artículos curtos, patas ambulatórias longas e delgadas, abdome sub-retangular, pleópodo feminino iv com dois segmentos, urópodos longos. O primeiro clado corresponde a Porcellanopsis Rathbun, 1910 (espécie-tipo P. festae (Nobili, 1901)), previamente tratado como sinônimo de Megalobrachium. Contudo, a combinação de diferenças morfológicas entre Megalobrachium e Porcellanopsis justifica a revalidação de Porcellanopsis. Três espécies foram erroneamente registradas no Pacífico oriental (M. mortenseni Haig, 1962, P. rosea (Rathbun, 1900) e P. soriata (Say, 1818)); essas espécies são exclusivamente distribuídas no Atlântico ocidental.

Nutrient Load Reduction: Challenges facing the Chesapeake 2000 Agreement

The Chesapeake Bay is the largest estuary in the United States supporting a complex ecosystem that sustains many habitats and the organisms that depend on them. The bay also supports economic, recreational, and cultural activities to over 16 million people residing in the watershed. Changes within the watershed have caused excessive levels of nutrients, mainly nitrogen and phosphorous, to pollute the bay. The Chesapeake Bay Program, guided by a complex agreement, was created to address these and other issues and oversee the restoration of the bay. The most recent version of this agreement, the Chesapeake 2000, declares its continued commitment to restore the bay with over 100 goals to be met by the year 2010. Reports show that although intensive efforts have been made to promote nutrient reduction, very little reduction has actually resulted. This project described these efforts. The final results reveal obstacles affecting progress, shortcomings to current approaches and possible solutions for future implementation.

Spatial Distribution of Marine Epibenthic Communities in the Hola Trough (Vesterålen, Northern Norway)

The Lofoten-Vesterålen marine shelf is one of the most geologically diverse coast and offshore margin areas in Norway. This leads to huge heterogeneity in marine environments, and often high biodiversity. However, little is known yet about the benthic communities in this region. Within the ARCTOS LoVe MarineEco project the epibenthic communities of the Hola trough (Vesterålen) are analysed to give a first description of their spatial distribution. In this trough both a complex hydrodynamic system and varied topographic submarine elements occur. Trawling samples were collected for two different approaches: one in a meso-scale and another in a small-scale. For the broad scale a transect consisting in three stations was developed, while for the fine scale a small area on a sand wave field, consisting in five stations called HolaBox, was sampled. All organisms were intended to be identified to species level and colonial fauna was discarded for the analysis. Different diversity indexes were assessed (Shannon index (H’) and Pielou’s eveness (J’)). Clustering and nMDS analyses identified four statistically significant groups in terms of abundance (ind./100m2). A total amount of 211 different taxa were found within all stations. The more outer part of the transect (close to the shelf edge) presented a huge abundance of organisms and was dominated by the hemi sessile tube-builder polychaetes Nothria conchylega and Eunice dubitata and the sea urchin Gacilechinus acutus, while the more inner parts presented less abundance of individuals. Probably some upwelling produced by the Norwegian Atlantic Current (NWAC) is influencing the shelf edge increasing the primary production and, therefore, enriching the seafloor in this region. The sand wave field presented two different groups with few amount of individuals. Small-scale variability could be produced by the high heterogeneity within the different types of sand waves, while the scarce abundance of animals can be produced by the permanent changing environment that movable sand waves produce. Here more active and mobile fauna was found such as brittle stars and hermit crabs (among others). Finally, a fourth group was found in the most inner station of the transect, laying on a ridge in the central part of the trough. This station, with coarse substrate, was mainly dominated again by brittle stars and sea urchins. We can conclude that this is a really heterogeneous trough in environments and therefore in communities (even in a local scale). More detailed studies that focus in the local environmental drivers have to be carried out to get an integrated understanding of the structure of benthic communities in this system.