MPI code encapsulating using parallel CORBA object

This paper describes a technique that allows an MPI code to be encapsulated into a component. Our technique is based on an extension to the Common Object Request Broker Architecture (CORBA) from the OMG (Object Management Group). The proposed extensions do not modify the CORBA core infrastructure (the Object Request Broker) so that it can fully coexist with existing CORBA applications. An MPI code is seen as a new kind of CORBA object that hides most of the cumbersome problems when dealing with parallelism. Such a technique can be used to connect MPI codes to existing CORBA software infrastructures which are now being developed in the framework of several research and development projects such as JACO3^*, JULIUS^** or TENT^*** from DLR. To illustrate the concept of parallel CORBA object, we present a virtual reality application that is made of the coupling of a light simulation application (radiosity) and a visualisation tool using VRML and Java.     

CHROMOSOMES IN TWENTY-FIVE SPECIES OF CHINESE MEM-BRACIDS (HOMOPTERA: MEMBRACIDAE)*

Abstract Chromosomes in 25 species of Membracidae are recorded. Numbers, size and behaviors of the chromosomes during meiosis and mitosis are used as specific or generic features for the taxonomy of this group. Chromosome numbers vary from n=5 to 12, and sex mechanism are of XO type except two species with neo-XY system. The histogram indicates that 2n=11 with XO sex mechanism is the modal chromosome number, and another type n=10 is also commonly found in this family.     

Groups Partitioning Over CORBA for Cooperative Work

Many examples illustrate the usefulness of group partitioning in distributed systems. The process group abstraction is a powerful tool for the development of fault-tolerant distributed applications. This solution is also particularly relevant to group entities sharing similar properties or stakes when applied to the field of cooperative work. When dealing with distributed applications, communication standards have evolved from socket-based interfaces to Remote Procedure Calls and nowadays, towards distributed object platforms like CORBA. This standard from the Object Management Group masks distribution and heterogeneity and provides a good basis for distributed application development. This paper presents a review of group mechanisms found in the literature then focuses on the implementation of groups over CORBA. An implementation of such a service over CORBA illustrates the impact of group auto-organization. Performance we obtain show that our service is efficient and provides good mechanisms to manage operations in a group.     

Motion-based prediction explains the role of tracking in motion extrapolation

During normal viewing, the continuous stream of visual input is regularly interrupted, for instance by blinks of the eye. Despite these frequents blanks (that is the transient absence of a raw sensory source), the visual system is most often able to maintain a continuous representation of motion. For instance, it maintains the movement of the eye such as to stabilize the image of an object. This ability suggests the existence of a generic neural mechanism of motion extrapolation to deal with fragmented inputs. In this paper, we have modeled how the visual system may extrapolate the trajectory of an object during a blank using motion-based prediction. This implies that using a prior on the coherency of motion, the system may integrate previous motion information even in the absence of a stimulus. In order to compare with experimental results, we simulated tracking velocity responses. We found that the response of the motion integration process to a blanked trajectory pauses at the onset of the blank, but that it quickly recovers the information on the trajectory after reappearance. This is compatible with behavioral and neural observations on motion extrapolation. To understand these mechanisms, we have recorded the response of the model to a noisy stimulus. Crucially, we found that motion-based prediction acted at the global level as a gain control mechanism and that we could switch from a smooth regime to a binary tracking behavior where the dot is tracked or lost. Our results imply that a local prior implementing motion-based prediction is sufficient to explain a large range of neural and behavioral results at a more global level. We show that the tracking behavior deteriorates for sensory noise levels higher than a certain value, where motion coherency and predictability fail to hold longer. In particular, we found that motion-based prediction leads to the emergence of a tracking behavior only when enough information from the trajectory has been accumulated. Then, during tracking, trajectory estimation is robust to blanks even in the presence of relatively high levels of noise. Moreover, we found that tracking is necessary for motion extrapolation, this calls for further experimental work exploring the role of noise in motion extrapolation.     

Phylogenetic reassessment and biogeography of the Ectateus generic group (Coleoptera: Tenebrionidae: Platynotina)

Owing to the reinterpretation of its morphological synapomorphies, the taxonomic composition of the Ectateus generic group had been ambiguous. The present study scrutinized all existing taxonomic concepts of the group based on a cladistic analysis of the adult morphology of all of the Afrotropical platynotoid Platynotina genera. The phylogenetic relationships were reconstructed using parsimony and Bayesian inference. The results show that all previous taxonomic concepts of the Ectateus generic group concerned paraphyletic entities. The cladistic analysis revealed the following synapomorphies for the taxon: (1) presence of basal indentations of the pronotal disc, (2) ratio of prothorax width to its maximal height > 6.0, and (3) ratio of maximal height of the prothorax to total height < 0.3. Moreover, phylogenetic studies revealed the existence of the Upembarus generic group, a sister‐taxon group to the Ectateus generic group, within the Afrotropical platynotoid Platynotina. Autapomorphic and synapomorphic character mapping show that several taxonomic and nomenclatural changes are needed to consider the particular generic‐level entities traditionally assigned to Afrotropical platynotoid Platynotina as monophyletic lineages. The following taxonomic and nomenclatural adjustments are made in this paper: P teroselinus gen. nov. is erected to accommodate a single species that was previously assigned to Zidalus: Pteroselinus insularis comb. nov. Additionally, the following synonymies are proposed: Anchophthalmops (= Platykochius syn. nov. ), Angolositus (= Aberlencus syn. nov. , = Platymedvedevia syn. nov. ), Glyptopteryx (= Microselinus syn. nov. , = Quadrideres syn. nov. , = Synquadrideres syn. nov. ). In addition, Kochogaster is lowered in rank and is treated as one of the subgenera of Anchophthalmus. Moreover, Pseudoselinus is treated as a subgenus of Upembarus. An identification key to all Afrotropical platynotoid Platynotina genera and subgenera is presented. Zoogeographical analyses revealed the following dispersal barriers for the Ectateus generic group: (1) the Sahara (northern barrier); (2) the dry ecosystems of Botswana, Namibia, and South Africa (southern barrier); and (3) the Congolian rainforests (internal distributional gap). The ancestor of the taxon probably originated in East African ecoregions that predominantly contained wattletrees (acacias) and Commiphora Jacq. Moreover, past climate changes seem to have had a great impact on the observed generic distribution. © 2015 The Linnean Society of London     

Characterization of <Emphasis Type="Italic">Bradyrhizobium</Emphasis> Strains Isolated from Different Varieties of Soybean with 16SrDNA RFLP from Agricultural Land of Madhya Pradesh,India

Madhya Pradesh is the major soybean contributor in India. The taxonomy of nitrogen fixing bacteria forming symbiotic associations with leguminous plants has been deeply changed in recent years. The use of very sensitive and accurate molecular methods has enabled the detection of large rhizobial diversity. Molecular biotyping and characterization the Bradyrhizobium, isolates from eleven varieties of soybean from agricultural field of Sehore district of Madhya Pradesh is done using 16S rDNA typing. Bradyrhizobia were identified genetically by determining the %Guanine plus Cytosine content of the whole genome, followed by 16S rDNA-RFLP analysis % Guanine plus Cytosine content of all the Bradyrhizobium isolates reflects similarity at generic level among all Bradyrhizobial isolates. Restriction Fragment Length Polymorphism (RFLP) further showed a considerable level of genetic diversity among the Bradyrhizobial isolates. PCR-RFLP of 16S rDNA supported existence of two divergent groups among indigenous Bradyrhizobial isolates, at similarity level of 66, and 75 and 74% of similarity within the group. The technique used was helpful in characterizing Bradyrhizobium isolates to be used as inoculants for improving productivity of agricultural land of Madhya Pradesh (India).     

EUGLOSSINE BEE POLLINATION OF THE ORCHID,COCHLEANTHES LIPSCOMBIAE: A FOOD SOURCE MIMIC

Cochleanthes lipscombiae is pollinated by large male and female euglossine bees. The flowers lack pollinator rewards, but attract bees searching for nectar. The euglossines extend their long tongues and crawl into the gullet-flower. The bees probe the back-swept lateral sepals for nectar. Pollination occurs as a pollinarium laden bee backs out, deposits pollinia on the stigma, and obtains a new pollinarium load by dislodging the anther. Some related orchid species have similar morphological characteristics as those essential to the pollination mechanism of C. lipscombiae. These features may have taxonomic significance at the generic level. Cochleanthes lipscombiae may be a floral mimic of a sympatric legume, but may also receive exploratory visits by bees searching for food resources. The latter may be young, recently emerged naive bees, or individuals seeking new nectar hosts during a period of rapid host species turnover.     

In vivo baseline measurements of hip joint range of motion in suspensory and nonsuspensory anthropoids

Hominoids and atelines are known to use suspensory behaviors and are assumed to possess greater hip joint mobility than nonsuspensory monkeys, particularly for range of abduction. This assumption has greatly influenced how extant and fossil primate hip joint morphology has been interpreted, despite the fact that there are no data available on hip mobility in hominoids or Ateles. This study uses in vivo measurements to test the hypothesis that suspensory anthropoids have significantly greater ranges of hip joint mobility than nonsuspensory anthropoids. Passive hip joint mobility was measured on a large sample of anesthetized captive anthropoids (nonhuman hominids = 43, hylobatids = 6, cercopithecids = 43, Ateles = 6, and Cebus = 6). Angular and linear data were collected using goniometers and tape measures. Range of motion (ROM) data were analyzed for significant differences by locomotor group using ANOVA and phylogenetic regression. The data demonstrate that suspensory anthropoids are capable of significantly greater hip abduction and external rotation. Degree of flexion and internal rotation were not larger in the suspensory primates, indicating that suspension is not associated with a global increase in hip mobility. Future work should consider the role of external rotation in abduction ability, how the physical position of the distal limb segments are influenced by differences in ROM proximally, as well as focus on bony and soft tissue differences that enable or restrict abduction and external rotation at the anthropoid hip joint. Am J Phys Anthropol 153:417–434, 2014. © 2013 Wiley Periodicals, Inc.     

A molecular phylogeny of the checkered beetles and a description of Epiclininae a new subfamily (Coleoptera: Cleroidea: Cleridae)

We provide the first molecular phylogeny of the clerid lineage (Coleoptera: Cleridae, Thanerocleridae) within the superfamily Cleroidea to examine the two most recently proposed hypotheses of higher level classification. Phylogenetic relationships of checkered beetles were inferred from approximately ～5000 nt of both nuclear and mitochondrial rDNA (28S, 16S and 12S) and the mitochondrial protein‐coding gene COI. A worldwide sample of ～70 genera representing almost a quarter of generic diversity of the clerid lineage was included and phylogenies were reconstructed using Bayesian and Maximum Likelihood approaches. Results support the monophyly of many proposed subfamilies but were not entirely congruent with either current classification system. The subfamilial relationships within the Cleridae are resolved with support for three main lineages. Tillinae are supported as the sister group to all other subfamilies within the Cleridae, whereas Thaneroclerinae, Korynetinae and a new subfamily formally described here, Epiclininae subf.n ., form a sister group to Clerinae + Hydnocerinae.     

Molecules,morphology and minute hooded beetles: a phylogenetic study with implications for the evolution and classification of Corylophidae (Coleoptera: Cucujoidea)

Eight genes (nuclear: 18S, 28S, H3, CAD; mitochondrial: 12S, 16S, COI, COII) and morphology were used to infer the evolutionary history of Corylophidae, some of the smallest free‐living insects. The study included 36 corylophid exemplars, representing approximately 60% of the known generic diversity of the family and 16 cucujoid outgroup taxa. Multiple partitioning strategies, molecular datasets, combined datasets and different taxon sampling regimes using maximum likelihood and mixed‐model Bayesian inference were utilized to analyse these data. Most results were highly concordant across analyses. There was strong agreement across (i) partitioning strategies, (ii) maximum likelihood and Bayesian inference analyses of the molecular data, and (iii) Bayesian inference of the molecular data alone and Bayesian inference of the combined morphological and molecular data when all terminal taxa were included. When a strict taxon sampling protocol was employed so that only single generic exemplars were included, deep relationships were affected in the resulting phylogenetic hypotheses. Under such narrow sampling strategies, deep phylogenetic relationships were also sensitive to the choice of generic exemplars. Although it is often challenging to obtain single representatives for many taxa in higher‐level phylogenetic analyses, these results indicate the importance of using denser taxon sampling approaches even at the specific level for genera included in such studies. Molecular data alone support Anamorphinae (Endomychidae) strongly as the sister group of Corylophidae. In combined data analyses, Coccinellidae is recovered as the sister group to Corylophidae. In all analyses, Corylophidae and the subfamily Corylophinae are recovered as monophyletic. The monophyly of Periptyctinae was untested, as only a single species was included. All included corylophine tribes were recovered as monophyletic with the exception of Aenigmaticini; Aenigmaticum Matthews forms the sister group to Orthoperus Stephens and Stanus?lipiński et al. is recovered as the sister group of Sericoderus Stephens. Stanus tasmanicus?lipiński et al. is transferred to a new genus, Pseudostanus Robertson, ?lipiński & McHugh gen.n. incertae sedis. We propose a new tribe, Stanini Robertson, ?lipiński & McHugh trib.n. for Stanus bowesteadi?lipiński et al. and a new concept of Aenigmaticini sensu.n. to include only the nominate genus. Anatomical transitions associated with corylophid miniaturization are highlighted. Key phenotypic modifications and elevated rates of substitution in nuclear rRNA genes are evident in a subgroup of Corylophinae that includes the most diminutive species. Other taxonomic and evolutionary implications are discussed in light of the results.     

Cyclamen: time, sea and speciation biogeography using a temporally calibrated phylogeny

Aim The Mediterranean region is a species‐rich area with a complex geographical history. Geographical barriers have been removed and restored due to sea level changes and local climatic change. Such barriers have been proposed as a plausible mechanism driving the high levels of speciation and endemism in the Mediterranean basin. This raises the fundamental question: is allopatric isolation the mechanism by which speciation occurs? This study explores the potential driving influence of palaeo‐geographical events on the speciation of Cyclamen (Myrsinaceae), a group with most species endemic to the Mediterranean region. Cyclamen species have been shown experimentally to have few genetic barriers to hybridization. Location The Mediterranean region, including northern Africa, extending eastwards to the Black Sea coast. Methods A generic level molecular phylogeny of Myrsinaceae and Primulaceae is constructed, using Bayesian approximation, to produce a secondary age estimate for the stem lineage of Cyclamen. This estimate is used to calibrate temporally an infrageneric phylogeny of Cyclamen, built with nrDNA ITS, cpDNA trnL‐F and cpDNA rps16 sequences. A biogeographical analysis of Cyclamen is performed using dispersal–vicariance analysis. Results The emergence of the Cyclamen stem lineage is estimated at 30.1–29.2 Ma, and the crown divergence at 12.9–12.2 Ma. The average age of Cyclamen species is 3.7 Myr. Every pair of sister species have mutually exclusive, allopatric distributions relative to each other. This pattern appears typical of divergence events throughout the evolutionary history of the genus. Main conclusions Geographical barriers, such as the varying levels of the Mediterranean Sea, are the most plausible explanation for speciation events throughout the phylogenetic history of Cyclamen. The genus demonstrates distributional patterns congruent with the temporally reticulate palaeogeography of the Mediterranean region.     

Phylogeny, character evolution, and classification of Sapotaceae (Ericales)

We present the first cladistic study of the largely tropical family Sapotaceae based on both morphological and molecular data. The data were analyzed with standard parsimony and parsimony jackknife algorithms using equally and successive weighted characters. Sapotaceae are confirmed to constitute two main evolutionary lineages corresponding to the tribes Isonandreae‐Mimusopeae‐Sideroxyleae and Chrysophylleae‐Omphalocarpeae. The Sideroxyleae are monophyletic, Isonandreae are polyphyletic as presently circumscribed, and as suggested by the analyses, the subtribe Mimusopeae‐Mimusopinae has evolved within the Mimusopeae‐Manilkarinae, which hence is also paraphyletic. Generic limits must be altered within Sideroxyleae with the current members Argania, Nesoluma and Sideroxylon. Argania cannot be maintained at a generic level unless a narrower generic concept is adopted for Sideroxylon. Nesoluma cannot be upheld in a narrow or broad generic concept of Sideroxylon. The large tribe Chrysophylleae circumscribes genera such as Chrysophyllum, Pouteria, Synsepalum, and Xantolis, but the tribe is monophyletic only if the taxa from Omphalocarpeae are also included. Neither Chrysophyllum nor Pouteria are monophyletic in their current definitions. The results indicate that the African taxa of Pouteria are monophyletic and distinguishable from the South American taxa. Resurrection of Planchonella, corresponding to Pouteria section Oligotheca, is proposed. The African genera Synsepalum and Englerophytum form a monophyletic group, but their generic limits are uncertain. Classification of the Asian genus Xantolis is particularly interesting. Morphology alone is indecisive regarding Xantolis relationships, the combined unweighted data of molecules and morphology indicates a sister position to Isonandreae‐Mimusopeae‐Sideroxyleae, whereas molecular data alone, as well as successive weighted combined data point to a sister position to Chrysophylleae‐Omphalocarpeae. An amended subfamily classification is proposed corresponding to the monophyletic groups: Sarcospermatoideae (Sarcosperma), Sapotoideae (Isonandreae‐Mimusopeae‐Sideroxyleae) and Chrysophylloideae (Chrysophylleae‐Omphalocarpeae), where Sapotoideae circumscribes the tribes Sapoteae and Sideroxyleae as well as two or three as yet unnamed lineages. Morphological characters are often highly homoplasious and unambiguous synapomorphies cannot be identified for subfamilies or tribes, which we believe are the reason for the variations seen between different classifications of Sapotaceae. © The Willi Hennig Society 2005.     

Developing and evaluating abstractions for distributed supercomputing

To fully realize its potential, distributed supercomputing requires abstractions and environments facilitating development of efficient applications. In this paper we present PARDIS, a system which addresses this demand by providing support for interoperability of PARallel DIStributed applications. The design of PARDIS is based on the Common Object Request Broker Architecture (CORBA). Like CORBA, it provides interoperability between heterogeneous components by specifying their interfaces in a meta-language, the CORBA IDL, which can be translated into the language of interacting components. However, PARDIS extends the CORBA object model by introducing SPMD objects representing data-parallel computations. This extension allows us to build interactions involving data-parallel components, which exchange distributed data structures whose definitions are captured by distributed sequences. We present microbenchmark results which evaluate the performance potential of SPMD objects for data structures of diverse complexity and different network configurations. Based on these results, we conclude that while encapsulating the existence of multiple interactions SPMD objects also allow their efficient utilization, and therefore constitute a useful abstraction. This revised version was published online in July 2006 with corrections to the Cover Date.     

Phylogenetic relationships among the phyllotini (rodentia: Sigmodontinae) using morphological characters

Thirty-three species representing all 14 genera of the South American rodent tribe Phyllotini and 5 problematic genera are surveyed for 96 multistate and binary dental, cranial, skeletal, external, and male reproductive tract characters. Wagner parsimony analysis confirmsCalomys as the most basal phyllotine genus, and as currently constituted it is likely paraphyletic. The results are consistent with the exclusion ofPseudoryzomys from the phyllotines and the separation ofReithrodon andNeotomys fromHolochilus at the tribal level. Several highly differentiated generic groups that include a radiation of altiplano endemics centered onAuliscomys and the largely southern Andean/PatagonianReithrodon group appear to form a clade. AGraomys generic group that includesAndalgalomys andEligmodontia is also apparent, but its relationships to other phyllotines are obscured by poorly resolved internal nodes in the more species-rich and probably paraphyletic genusPhyllotis. The significance and consequences of more intensive taxonomic sampling are discussed. The taxonomic consequences of the phylogeny are presented.     

The phylogenetic relationships of the Andean swamp rat genus <Emphasis Type="Italic">Neotomys</Emphasis> (Rodentia,Cricetidae, Sigmodontinae) based on mitochondrial and nuclear markers

The aim of this study was to assess the phylogenetic position of the South American cricetid genus Neotomys using two molecular markers: one nuclear (Irbp) and one mitochondrial (mt-cyb). This genus is currently considered as incertae sedis in the Sigmodontinae radiation. The phylogenetic relationships were estimated using three approaches: Bayesian inference, maximum likelihood and parsimony. We found the genus Neotomys closely related to the genera Euneomys and Irenomys, which are also considered incertae sedis. Our results suggest a common origin for this group of genera; this fact should be reflected in the taxonomy as a supra generic group with a tribal level. However, further and deeper analysis of both molecular and morphological data are needed to diagnose and formalize the proposed tribe. The relationships of this clade to the other members of Sigmodontinae were not clear as assessed by these data sets. The three genera are distributed around the Central and Southern Andes in South America evidencing that the Andes have played an important role in the diversification of several tribes of sigmodontine rodents.     

A catalogue of the nominal species of the monogenean genus Dactylogyrus Diesing, 1850 and their host genera

Dactylogyrus is the largest helminth genus, with more than 900 nominal species, and is consequently in a state of considerable confusion. In an attempt to consolidate our knowledge of this large taxon, this work surveys the nominal species and catalogues them and their hosts (to the generic level) in the form of a species list which is cross-referenced to host-parasite list. A reference list to the authorities for the taxa is included.     

An ontology driven architecture for derived representations of macromolecular structure

SUMMARY: An object metamodel based on a standard scientific ontology has been developed and used to generate a CORBA interface, an SQL schema and an XML representation for macromolecular structure (MMS) data. In addition to the interface and schema definitions, the metamodel was also used to generate the core elements of a CORBA reference server and a JDBC database loader. The Java source code which implements this metamodel, the CORBA server, database loader and XML converter along with detailed documentation and code examples are available as part of the OpenMMS toolkit. AVAILABILITY: http://openmms.sdsc.edu CONTACT: dsg@sdsc.edu     

The range of action of the mother and the avoidance of big novel objects in long-tailed macaques

Most surrogate-reared long-tailed macaques persistently avoid a big novel object, whereas most mother-reared subjects approach it. A striking difference between these attachment figures is that the mothers moved about with their infants, whereas the surrogates were fixed to the wall In this experiment, we aimed to find out whether mobility of the attachment figure plays a part in the development of an infant’s responses to big novel objects. We studied the effects of mobility of the attachment figure by restraining mothers in their range of action. We confined mothers of the experimental group in a small part of the home cage. Their infants could leave the cage in which their mothers were restrained. Infants that were growing up with unrestrained mothers made up the control group. At two different ages all infants encountered a big novel object. We used two different objects. We found that the range of action of the mother did not significantly affect the responses of infants to big novel objects. As in the previous studies, most of the mother-reared monkeys approached the objects. The age at which an infant was first exposed to an object did not significantly affect its behavior toward it. Further, the two different objects evoked the same reactions.