bluuebunny/crossref_metadata_2025_split huggingface dataset:
Microbial nitrate-dependent cyclohexane degradation coupled with anaerobic ammonium oxidation
Authors: Musat Florin , Wilkes Heinz , Behrends Astrid , Woebken Dagmar , Widdel Friedrich 
Published: April 2010

Abstract
An anaerobic nitrate-reducing enrichment culture was established with a cyclic saturated petroleum hydrocarbon, cyclohexane, the fate of which in anoxic environments has been scarcely investigated. GC–MS showed cyclohexylsuccinate as a metabolite, in accordance with an anaerobic enzymatic activation of cyclohexane by carbon–carbon addition to fumarate. Furthermore, long-chain cyclohexyl-substituted cell fatty acids apparently derived from cyclohexane were detected. Nitrate reduction was not only associated with cyclohexane utilization but also with striking depletion of added ammonium ions. Significantly more ammonium was consumed than could be accounted for by assimilation. This indicated the occurrence of anaerobic ammonium oxidation (anammox) with nitrite from cyclohexane-dependent nitrate reduction. Indeed, nitrite depletion was stimulated upon further addition of ammonium. Analysis of 16S rRNA genes and subsequent cell hybridization with specific probes showed that approximately 75% of the bacterial cells affiliated with the Geobacteraceae and approximately 18% with Candidatus ‘Brocadia anammoxidans’ (member of the Planctomycetales), an anaerobic ammonium oxidizer. These results and additional quantitative growth experiments indicated that the member of the Geobacteraceae reduced nitrate with cyclohexane to nitrite and some ammonium; the latter two and ammonium added to the medium were scavenged by anammox bacteria to yield dinitrogen. A model was established to quantify the partition of each microorganism in the overall process. Such hydrocarbon oxidation by an alleged ‘denitrification’ (‘pseudo-denitrification’), which in reality is a dissimilatory loop through anammox, can in principle also occur in other microbial systems with nitrate-dependent hydrocarbon attenuation.
Special issue containing papers presented at the 4th IAEA Technical Meeting on the Theory of
Plasma Instabilities
Authors: K. Itoh  , H. R. Wilson  
Published: April 2010

The 4th IAEA technical meeting (TM) on the Theory of Plasma Instabilities
was held in Kyoto, May 18th--20th 2009, following the first (Seeon), second
(Trieste) and third (York) meetings in this series. This IAEA-TM was motivated
by the recent advances in theoretical methodology, the rapid progress in
observations of laboratory and astrophysical plasmas and the evolution of
fusion research as we approach the ITER era. The international advisory
committee (IAC) and local organizing committee (LOC), the members of which are
listed below, collaborated to define the scope and the content of the scientific
programme.
Young scientists were actively encouraged to participate in this TM
to help stimulate their future research careers and raise their international
profiles. Through these young scientists, the IAEA-TM planned to identify the
future directions of research. About 90 researchers, from 13 countries and the IAEA,
participated in this IAEA-TM, with 72 scientific presentations. The talks and
posters generated enthusiastic discussions, contributing to the vibrancy of the
meeting.
This special issue of Nuclear Fusion consists of a cluster of papers, reporting
some of the main contributions to the IAEA-TM. The articles in this cluster are
representative of the scientific width of presentations at the meeting, spanning
topics from micro-turbulence to large-scale MHD dynamics and from transport to
detailed analysis of diagnostics. They demonstrate the quality and depth of the
research presented at the conference.
List of IAC (alphabetical order):
B. Breizman (USA), S. Guenter (Germany), T. S. Hahm (USA), K. Itoh (Japan, Chair of 2009), Ya. I. Kolesnichenko (Ukraine), A. G. Peeters (UK), H. Wilson (UK)
List of LOC (alphabetical order):
A. Fukuyama, R. Horiuchi, S.-I. Itoh, N. Kasuya, Y. Kishimoto (co-chair), K. Kusano, J. Li, K. Mima, S. Murakami, H. Naitou, N. Nakajima, Y. Nakamura, H. Ohtani, S. Okamura, T. Ozeki, S. Sudo (co-chair), H. Sugama, Y. Todo, S. Tokuda, S. Usami, M. Yagi, Z. Yoshida
Meta-analysis for pathway enrichment analysis when combining multiple genomic studies
Authors: Shen Kui , Tseng George C. 
Published: April 2010

Abstract
Motivation: Many pathway analysis (or gene set enrichment analysis) methods have been developed to identify enriched pathways under different biological states within a genomic study. As more and more microarray datasets accumulate, meta-analysis methods have also been developed to integrate information among multiple studies. Currently, most meta-analysis methods for combining genomic studies focus on biomarker detection and meta-analysis for pathway analysis has not been systematically pursued.
Results: We investigated two approaches of meta-analysis for pathway enrichment (MAPE) by combining statistical significance across studies at the gene level (MAPE_G) or at the pathway level (MAPE_P). Simulation results showed increased statistical power of meta-analysis approaches compared to a single study analysis and showed complementary advantages of MAPE_G and MAPE_P under different scenarios. We also developed an integrated method (MAPE_I) that incorporates advantages of both approaches. Comprehensive simulations and applications to real data on drug response of breast cancer cell lines and lung cancer tissues were evaluated to compare the performance of three MAPE variations. MAPE_P has the advantage of not requiring gene matching across studies. When MAPE_G and MAPE_P show complementary advantages, the hybrid version of MAPE_I is generally recommended.
Availability: http://www.biostat.pitt.edu/bioinfo/
Contact: ctseng@pitt.edu
Supplementary information: Supplementary data are available at Bioinformatics online.
NetRaVE: constructing dependency networks using sparse linear regression
Authors: Phatak A. , Kiiveri H. , Clemmensen L.H. , Wilson W.J. 
Published: April 2010

Abstract
Summary: NetRaVE is a small suite of R functions for generating dependency networks using sparse regression methods. Such networks provide an alternative to interpreting ‘top n lists’ of genes arising out of an analysis of microarray data, and they provide a means of organizing and visualizing the resulting information in a manner that may suggest relationships between genes.
Availability: NetRaVE is freely available for academic use and has been tested in R 2.10.1 under Windows XP, Linux and Mac OS X.
Contact: harri.kiiveri@csiro.au
Supplementary information: Supplementary data are available at Bioinformatics online.
Host defence in a developmental context
Authors: WHALEN MAUREEN C. 
Published: April 2010

SUMMARYDisease resistance takes place within the context of the host developmental programme. The cellular and molecular basis of the developmental control of resistance is virtually unknown. It is clear from mutant studies that developmental processes are impacted when defence factors are altered and it is equally clear that alteration of developmental factors impacts defence functions. A review of current knowledge regarding the interplay of resistance and development is presented. Stage‐specific limitations on defence represent an important target for crop improvement.
Optimization of pathogenicity assays to study the Arabidopsis thaliana–Xanthomonas campestris pv. campestris pathosystem
Authors: MEYER DAMIEN , LAUBER EMMANUELLE , ROBY DOMINIQUE , ARLAT MATTHIEU , KROJ THOMAS 
Published: April 2010

SUMMARYThe cruciferous weed Arabidopsis thaliana and the causal agent of black rot disease of Crucifers Xanthomonas campestris pv. campestris (Xcc) are both model organisms in plant pathology. Their interaction has been studied successfully in the past, but these investigations suffered from high variability. In the present study, we describe an improved Arabidopsis–Xcc pathosystem that is based on a wound inoculation procedure. We show that after wound inoculation, Xcc colonizes the vascular system of Arabidopsis leaves and causes typical black rot symptoms in a compatible interaction, while in an incompatible interaction bacterial multiplication is inhibited. The highly synchronous and reproducible symptom expression allowed the development of a disease scoring scheme that enabled us to analyse the effects of mutations in individual genes on plant resistance or on bacterial virulence in a simple and precise manner. This optimized Arabidopsis–Xcc pathosystem will be a robust tool for further genetic and post‐genomic investigation of fundamental questions in plant pathology.
Loss of function of the HSFA9 seed longevity program
Authors: TEJEDOR‐CANO JAVIER , PRIETO‐DAPENA PILAR , ALMOGUERA CONCEPCIÓN , CARRANCO RAÚL , HIRATSU KEIICHIRO , OHME‐TAKAGI MASARU , JORDANO JUAN 
Published: April 2010

ABSTRACTGain of function approaches that have been published by our laboratory determined that HSFA9 (Heat Shock Factor A9) activates a genetic program contributing to seed longevity and to desiccation tolerance in plant embryos. We now evaluate the role(s) of HSFA9 by loss of function using different modified forms of HaHSFA9 (sunflower HSFA9), which were specifically overexpressed in seeds of transgenic tobacco. We used two inactive forms (M1, M2) with deletion or mutation of the transcription activation domain of HaHSFA9, and a third form (M3) with HaHSFA9 converted to a potent active repressor by fusion of the SRDX motif. The three forms showed similar protein accumulation in transgenic seeds; however, only HaHSFA9‐SRDX showed a highly significant reduction of seed longevity, as determined by controlled deterioration tests, a rapid seed ageing procedure. HaHSFA9‐SRDX impaired the genetic program controlled by the tobacco HSFA9, with a drastic reduction in the accumulation of seed heat shock proteins (HSPs) including seed‐specific small HSP (sHSP) belonging to cytosolic (CI, CII) classes. Despite such effects, the HaHSFA9‐SRDX seeds could survive developmental desiccation during embryogenesis and their subsequent germination was not reduced. We infer that the HSFA9 genetic program contributes only partially to seed‐desiccation tolerance and longevity.
THE CENTRAL NERVOUS SYSTEM OF CHAMELEON VULGARIS
Authors: SHANKLIN WILLIAM MATHIAS 
Published: April 2010

ABSTRACTAn analysis of the brain of Chameleon has given evidence of a number of modifications in the general plan of the reptilian nervous system. The telencephalon shows a reduced olfactory mechanism and suggests the presence of the true motor cortex. The ventral peduncle of the lateral forebrain bundle is unusually large with the majority of its fibres terminating in two new nuclear masses in the hypothalamus, the nucleus entopeduncularis, and a few in the nucleus ruber. A high degree of effective response to optic stimuli is indicated by the extensive correlation between the optic tectum and the nuclear masses of the midbrain and the diencephalon. The wide range of eye movements is probably correlated with the development of the basal optic root ganglion and its numerous secondary connections and the elaborate relationship of the geniculate complex. The usually highly developed tecto‐bulbar system is partly replaced by a large tegmento‐bulbar system that relays the tectal impulses caudally. An interesting mesencephalic nucleus is a large nucleus profundus mesencephali that receives a great variety of impulses and appears to be an important correlation center. Ascending visceral mechanisms were described bringing the hypothalamus into relationship with the lower centers. The great excursion of the tongue is associated with a highly differentiated hypoglossal nucleus. Components of the medial lemniscus from the spinal cord and the medulla to the vicinity of the thalamus were demonstrated.
Distribution des néoblastes le long du corps de la planaire Dugesia tigrina et pouvoir de développement de différents morceaux isolés de celui‐ci
Authors: Kritchinskaya E. B. , Lenicque P. M. 
Published: April 2010

Résumé et conclusionNous avons étudié les variations de la densité en néoblastes dans la région du corps antérieure au pharynx, dans la zone de division et dans la queue chez Dugesia tigrina, au cours du cycle de reproduction asexuée. La densité est beaucoup plus grande dans la queue que dans la zone de division et elle diminue encore dans la région anté‐pharyngienne.Dans la région post‐pharyngienne, la densité diminue de 36 heures après la division jusqu'à la fin de la première semaine. Elle augmente légèrement du 7e au 10e jour, c'est‐à‐dire peu de temps avant la division suivante.Dans la région anté‐pharyngienne, la densité reste à peu près constante pendant toute la durée du cycle de reproduction.Les variations du pouvoir de régénération en fonction de l'origine des morceaux du corps et du temps écoulé après la division ont été suivies.Aucune relation nette n'a été constatée entre le nombre des néoblastes et ce pouvoir. Par contre il semble être dépendant du degré de grandeur et de l'âge des néoblastes.Quelle est l'origine et quels sont les facteurs présidant au développement des néoblastes restent les problèmes essentiels et non résolus.
Hagfish Eye: Ultrastructure of Retinal Cells
Authors: Holmberg Kaj 
Published: April 2010

AbstractThe retinal cells of the hagfish, Myxine glutinosa, possess at the ultra‐structural level features which occur in the eyes of higher vertebrates. The “receptor” cells contain outer segment, ciliary structure and synaptic region. Other structures in the diminutive eye strongly suggest a functional state.
The Development of the Osteocranium of the Egyptian Cobra
Authors: Kamal A. M. , Hammonda H. G. , Mokhtar F. M. 
Published: April 2010

AbstractIn the present article, the median dorsal bones, bones of the upper jaw, circumorbital series and occipital ring of the skull of the adult Egyptian cobra, Naja haje have been described in detail, and compared with those of the other snakes studied by the previous authors. The median dorsal bones of the cranium are the nasals, frontals, parietals, but not the premaxillae. The paired nasals are exceptionally elongated anteriorly to the extent that the premaxillae and their processus nasalis are completely hidden in a dorsal view. The paired frontals send lateral downgrowths through their whole length which unite together in the mid‐ventral line just dorsal to the parasphenoid. The fused parietals also send lateral downgrowths which articulate ventrally with the posterior part of the parasphenoid and the anterior part of the basisphenoid.The upper jaw is composed only of the premaxilla, maxilla and quadrate on either side. The fused premaxillae possess a processus nasalis, and ventrally they send backwards a palatal process. The maxilla carries two poisonous fangs and two solid small teeth. It is quite separate from the premaxilla, but connected with the palatine (through its palatal process), prefrontal and ectopterygoid. The length of the maxilla is reduced in comparison with that of the boids and colubrids.The incomplete bony orbital ring is formed only of the prefrontal, frontal and postfrontal. Thus the jugal, lacrymal and postorbital are completely lacking, and the parietal is excluded from the circumorbital series by the presence of the postfrontal. The prefrontal extends from the cranial roof to the upper jaw. It is firmly fixed dorsally with the antero‐lateral border of the frontal. Its ventral edge is firmly fixed to the dorsal surface of the maxilla and its palatal process. The antero‐dorsal edge of the postfrontal is connected with the postero‐lateral edge of the frontal, while its medial edge is in sutural contact with the parietal and its lateral downgrowth.The occipital ring consists of the four occipital bones; the basioccipital ventrally, the two exoccipitals laterally and dorsally, and the supra‐occipital dorsally. The sutures separating these bones from one another are distinct. The two exoccipitals articulate with each other dorsally above the foramen magnum, thus excluding the supraoccipital from this foramen. The occipital condyle is tripartite formed out of the basioccipital and the two exoccipitals. The exoccipital is completely fused, without any line of demarcation, with the opisthotic to form a compound bone which is called the otoccipital.
Nervus tenuis, a Hitherto Unknown Cranial Nerve of the Fourth Metamere
Authors: Bjerring Hans C. 
Published: April 2010

AbstractIn hynobiid urodele embryos there are three serially arranged muscles associated with the otic and occipital regions of the endocranium. These muscles are continuous posteriorly with the succession of trunk myomeres and most likely represent myotomic derivatives attributable to the third, fourth, and fifth metameres of the body. From front to back these muscles are designated: anterior basiotic, posterior basiotic, and occipital. A hitherto unknown cranial nerve is directed towards the posterior basiotic muscle in embryos of Hynobius retardatus. For this new somatic motor nerve the term nervus tenuis is proposed. Together with the glossopharyngeal nerve it constitutes the fourth cranionerval segment.
The Nerve Supply to the Second Metamere Basicranial Muscle in Osteolepiform Vertebrates, with Some Remarks on the Basic Composition of the Endocranium
Authors: Bjerring Hans C. 
Published: April 2010

AbstractThe endocranium of Devonian osteolepiforms includes four minor structures, called zygals, which probably represent cephalic vertebral elements belonging to the second, third, and fourth metameres. Also, the endocranium exhibits a partial segmentation in the form of vestiges of intrametameric articulations attributable to the anterior five metameres. Finally, the basicranial muscle of osteolepiforms, extending across the lower part of the endocranial articulation within the second metamere, is possibly supplied by a separate cranial nerve, for which the term nervus rarus is proposed. This hypothetical cranial nerve, which in osteolepiforms possibly emerges from the endocranium through a canal in the fourth metamere, is suggested to constitute, together with the trochlear nerve, the somatic motor component of the second cranionerval segment.
Distributional Pattern of Neuromasts in Goby, Gobius striatus Day (Gobiidae)
Authors: Srivastava C. B. L. 
Published: April 2010

AbstractDistributional pattern of the neuromasts has been described for Gobius striatus Day. The neuromasts are arranged in several lines. Canal formation, like many gobiids, is suppressed to varying extent. The supraorbital line presents interesting variations. The supraorbital lines of the two sides are separate from each other even in the so‐called common ‘interorbital chamber’. An outstanding feature of the neuromast system of the fish is the great development of the supramaxillary line which is perhaps best developed in this case.
Hypothalamo‐neurohypophysical C omplex of the Teleost Macrognathus aculeatus (BL.)
Authors: Haider Shamim , Sathyanesan A. G. 
Published: April 2010

AbstractThe hypothalamo‐neurohypophysial (HN) complex of Macrognathus aculeatus is described with the help of in situ staining technique and tissue sections. Bulk stained preparations provide a three‐dimentional view of the entire HN complex. The nucleus preopticus (NPO) which is oval in the ventral view appears boat‐shaped in the cross sectional view of the in toto stained brain. But it is in the form of an inverted L in median parasagittal section. Both pars magnocellularis and parvocellularis contribute fine fibers towards the formation of the right and the left main tracts which are composed of groups of loosely set bundles of axons. Unlike the earlier reported cases the main tract in this species runs lateral to the pituitary axis and independently enters it at the level of the proximal pars distalis without forming a common neurosecretory tract which is a feature not yet well known. In situ demonstration of the neurosecretory system in M. aculeatus has clearly revealed certain complex features which are difficult or impossible to understand through reconstruction studies of tissue sections. Extension of such in situ staining techniques to other species of teleosts may provide a wide variety of variations in the distributional patterns of their neurosecretory tracts which might throw additional light on the function and evolution of this system.
Prolactin‐producing Cells in Clupea harengus membras, Polypterus palmas and Calamoichthys calabaricus Studied by Immuno‐histochemical Methods
Authors: Aler Gudrun M. 
Published: April 2010

AbstractThe prolactin‐producing cells in Clupea harengus membras, Polypterus palmas and Calamoichthys calabaricus have been localized by fluores‐ceinlabelled antibodies to ovine prolactin.Pituitary sections were cut in a cryostat and both direct and indirect protein tracing methods have been used. As an additional method the paraffin embedding technique was carried out with Polypterus palmas. The prolactin‐producing cells in Clupea harengus membras were localized to the follicle epithelium in the rostral pars distalis. In Polypterus palmas and Calamoichthys calabaricus the prolactin producing cells were scattered all over the pars distalis.A possible relationship between the erythrosinophilic prolactin cells and the epithelium cells in the buccohypophyseal canal is discussed.
The Photoreceptor Outer Segments of the River Lamprey (Lampreta fluviatilis). An Electron‐, Fluorescence‐ and Light Microscopic Study
Authors: Öhman Peter 
Published: April 2010

AbstractThe outer segment of long and short photoreceptors in the retina of the river lamprey,Lampetra fluviatilis, were studied by light‐ and fluorescence microscopy together with some different electron microscopic methods. The outer segments show characteristics of both rods and cones and are suggested to represent intermediate kinds of photoreceptors.
The Ultrastructure of a Chemoreceptor Organ in the Head of Copepod Crustaceans
Authors: Elofsson Rolf 
Published: April 2010

AbstractThe ultrastructure of the paired nerves, previously called frontal organ or X‐organ, in copepod crustaceans was investigated. These nerves, running from the anterior margin of the brain to the frontal edge of the animals, are found to contain the dendrites of three types of morphologically different sensory neurons. The first unit consists of two dendrites (distinguished by their myelinization) leading to two small hairs on the front. Their detailed structure was not investigated. The second unit consists of a few large dendrites ending in branching cilia. The latter are surrounded by a specialized glial cell. The ciliary branches are regularly sized and arranged. The third unit consists of c. 17 dendrites ending with cilia at the cuticle. The cilia are split into irregular branches which are buried in modified epidermal cells which, in the case of Calanus, are connected with cuticular pores.By analogy with other presumed chemosensory organs in the Arthropoda, the second and the third unit are considered, on a morphological basis, to be chemoreceptors. The second unit receives internal stimuli. Because it resembles other X‐organs in the Crustacea, all X‐organs could have the same function. The third unit is thought of as receiving external stimuli.