bluuebunny/crossref_metadata_2025 huggingface dataset:
A contrastive study of proverbalization
Authors: Eriksson Olof
Published: December 2008

This article deals with a linguistic phenomenon which, in analogy with the well established term ‘pronominalization’, may be called ‘proverbalization’. In comparison with its counterpart in the nominal sphere, this phenomenon, despite its crucial importance to any language possessing the verb category, has received little attention in modern linguistic research. The article compares, synchronically and diachronically, the proverbal systems of English, French and Swedish. In order to obtain maximal analytic efficiency, by excluding factors not directly relevant to the purpose of the analysis, the article focuses on one particular case of proverbalization, namely the one in which it occurs in a comparative clause as a result of this clause having a verb identical to that of the main clause but taking an object different from that of the main clause verb: X – V1 – O1 – Comparative Connector – X/Y – V1 – O2.
On identifiability and definiteness in English and German
Authors: Breul Carsten
Published: December 2008

Despite increasingly numerous works dealing with issues of information structure from a cross-linguistic perspective, contrastive information structure analysis is not an established field of research yet. The paper aims at showing that it is worthwhile staking out and exploring such a field. Starting off from a brief reminder of what information structure is, as conceived of by Lambrecht (1994), the paper proposes guiding questions that contrastive information structure analysis should strive to answer. It then turns to the discussion of an example of contrastive analysis which involves the information structural category of identifiability. It is argued that the variable x in the English formula ‘as for x’ and the corresponding German formula was x {(an)betrifft / angeht} in sentence initial position can only be instantiated by expressions that have identifiable discourse referents. Results of a corpus-based comparison of expressions which instantiate x in these English and German formulas are presented. These results show contrasts between English and German in the lexicogrammatical expression of identifiable referents that go beyond the better-known differences in the use of the definite article. A methodological point to be made is that Lambrechtian categories of information structure (identifiability and activation of discourse referents, focus structure) may serve as tertia comparationis for the analysis of contrasts on the lexicogrammatical level.
Magnetic resonance imaging-guided renal artery stent placement in a swine model: Comparison of two tracking techniques
Authors: Frericks B. B. , Elgort D. R. , Hillenbrand C. , Duerk J. L. , Lewin J. S. , Wacker F. K.
Published: December 2008

Background: Magnetic resonance (MR)-guided interventions have evolved from a pure research application to a preclinical method over the last decade. Among the device-tracking techniques, susceptibility artifact-based tracking relies on the contrast between the surrounding blood and the device, and radiofrequency coil-based tracking relies on the local gradient field amplification in a resonating circuit attached to the interventional device.

Purpose: To evaluate the feasibility and precision of susceptibility artifact-based and microcoil-based MR guidance methods for renal artery stent placement in a swine model.

Material and Methods: MR imaging-guided renal artery stent placements were performed in six fully anesthetized pigs using a 1.5T short-bore MR scanner. Susceptibility artifact-based tracking with manual scan-plane adjustments and microcoil tracking with automatic scan-plane adjustments were used for renal artery stent placements in three pigs in each group. With both methods, near real-time steady-state free-precession (SSFP) imaging was used. Differences between the two tracking approaches on stenting time, total procedure time, and stent position were measured.

Results: The microcoil-based approach yielded a shorter mean procedure time (17 vs. 23 min). There was no relevant difference for the mean stenting time (12 vs. 13 min). The mean stent deviation from the aortic wall with the susceptibility approach was larger than with the microcoil approach (10 vs. 4.0 mm).

Conclusion: For MRI-guided renal artery stent placement, the microcoil-based technique had a shorter procedure time and a higher stent placement precision than the susceptibility artifact-based approach.
Complete ablation of a renal tumor abutting the inferior vena cava using a radiofrequency electrode as a lever: A case report
Authors: Park Byung Kwan , Kim Chan Kyo
Published: December 2008

Radiofrequency ablation is accepted as a minimally invasive treatment for renal tumors in patients who are poor candidates for surgery. However, ablation of tumors that abut large vessels is likely to be incomplete due to the heat-sink effect or may result in vascular injury. We report a case of a renal tumor abutting the inferior vena cava, which was successfully treated with radiofrequency ablation, with an emphasis on the technical aspects required to avoid both incomplete ablation and vascular injury by using a radiofrequency electrode as a lever.
Correction of displaced peritoneal dialysis catheters with an angular stiff rod
Authors: Ozyer U. , Harman A. , Aytekin C. , Boyvat F. , Ozdemir N.
Published: December 2008

Background: Fluoroscopically guided guidewire manipulations are readily available and inexpensive methods of correcting malfunctioning peritoneal dialysis catheters, with reported success rates ranging from 25% to 67%.

Purpose: To improve the success rates of guidewire manipulations with a modified technique.

Material and Methods: Using a stiff rod and a stiff wire under fluoroscopy guidance, catheters that had migrated were drawn back into the rectovesical pouch. An angular rod was used to lever the catheter downward, and the guidewire was used to push the catheter down.

Results: No complications developed, and immediate success was achieved in 13 of 14 interventions. With this technique, catheter patency in chronic ambulatory peritoneal dialysis (CAPD) patients (11/12) was higher than that of previously reported methods. Durable success was maintained in nine of 12 patients after a single intervention. All re-manipulations (2/2) were successful.

Conclusion: Although used in only 14 interventions in 12 patients, the outcome was promising. This method is a safe and favorable alternative to other guidewire manipulations, based on absence of complications and high success.
Critical review of information relevant to the correction of the effect of chemical impurities in gases used for the realization of ITS-90 fixed points
Authors: Pavese Franco
Published: December 2008

According to theGuide to the Expression of Uncertainty in Measurement(GUM) on which the expression of uncertainty in the field of metrology is based, since 1995, ‘it is assumed that the results of a measurement have been corrected for all recognised significant systematic effects’. Since the International Temperature Scale of 1990 specifies that the substances used for the realization of the ‘fixed points’ be ‘ideally pure’, to fully implement the intent of the GUM corrections should be applied for any chemical impurities that affect the value of the measurand. In general, thermometrists' opinion is that significant laboratory research and more literature search are still needed for further progress towards reliable corrections. This paper, reviewing the available literature data, shows that the situation is more favourable in the case of the substances used for the realization of the Scale reference points in the range 13.8 K to 273.16 K based on the use of hydrogen, neon, oxygen and argon. The appendix reports a similar review also for nitrogen. Then the paper discusses the other conditions, physical–chemical and thermal, of the substances inside the thermometric cells, concurring with the chemical impurity effects to the overall state of knowledge of the realized triple point temperature relevant to the solution of the problem of performing the corrections.
ECH pre-ionization and assisted startup in the fully superconducting KSTAR tokamak using second harmonic
Authors: Bae Y.S. , Jeong J.H. , Park S.I. , Joung M. , Kim J.H. , Hahn S.H. , Yoon S.W. , Yang H.L. , Kim W.C. , Oh Y.K. , England A.C. , Namkung W. , Cho M.H. , Jackson G.L. , Bak J.S.
Published: December 2008

This letter reports on the successful demonstration of the second harmonic electron cyclotron heating (ECH)-assisted startup in the first plasma experiments recently completed in the fully superconducting Korea Superconducting Tokamak Advanced Research (KSTAR) device whose major and minor radii are 1.8 m and 0.5 m, respectively. For the second harmonic ECH-assisted startup, an 84 GHz EC wave at 0.35 MW was launched before the onset of the toroidal electric field of the Ohmic system. And it was observed that this was sufficient to achieve breakdown in the ECH pre-ionization phase, allow burn-through and sustain the plasma during the current ramp with a low loop voltage of 2.0 V and a corresponding toroidal electric field of 0.24 V m−1at the innermost vacuum vessel wall (R = 1.3 m). This is a lower value than 0.3 Vm−1 which is the maximum electric field in ITER. Due to the limited volt-seconds and the loop voltage of the Ohmic power system, the extended pulse duration of the ECH power up to 180 ms allowed the plasma current to rise up to more than 100 kA with a ramp-up rate of 0.8 MA s−1.
Excitation of the beta-induced Alfvén eigenmodes by a magnetic island
Authors: Marchenko V.S. , Reznik S.N.
Published: December 2008

It is shown that a pair of counter-propagating, tearing-parity, beta-induced Alfvén eigenmodes (BAEs) with low mode numbers can be excited in the presence of a magnetic island of the same helicity. The instability mechanism consists of the reversal of ion Landau damping due to island-induced modification of the equilibrium distribution function. This instability seems to be responsible for the BAE excitation in ohmic plasmas with tearing mode activity at the FTU tokamak (Buratti P. et al
2005 Nucl. Fusion
45 1446).
Matching methods for observational microarray studies
Authors: Heller Ruth , Manduchi Elisabetta , Small Dylan S.
Published: December 2008

Motivation: We address the problem of identifying differentially expressed genes between two conditions in the scenario where the data arise from an observational study, in which confounding factors are likely to be present.

Results: We suggest to use matching methods to balance two groups of observed cases on measured covariates, and to identify differentially expressed genes using a test suited to matched data. We illustrate this approach on two microarray studies: the first study consists of data from patients with two cancer subtypes, and the second study consists of data from AMKL patients with and without Down syndrome.

Availability: R code (www.r-project.org) for implementing our approach is included as Supplementary Material.

Contact:  ruheller@whatron.upenn.edu

Supplementary information:  Supplementary data are available at Bioinformatics online.
PuMA: Bayesian analysis of

p

artitioned (and

u

npartitioned)

m

odel

a

dequacy
Authors: Brown Jeremy M. , ElDabaje Robert
Published: December 2008

Summary: The accuracy of Bayesian phylogenetic inference using molecular data depends on the use of proper models of sequence evolution. Although choosing the best model available from a pool of alternatives has become standard practice in statistical phylogenetics, assessment of the chosen model's adequacy is rare. Programs for Bayesian phylogenetic inference have recently begun to implement models of sequence evolution that account for heterogeneity across sites beyond variation in rates of evolution, yet no program exists to assess the adequacy of these models. PuMA implements a posterior predictive simulation approach to assessing the adequacy of partitioned, unpartitioned and mixture models of DNA sequence evolution in a Bayesian context. Assessment of model adequacy allows empirical phylogeneticists to have appropriate confidence in their results and guides efforts to improve models of sequence evolution.

Availability: This program is available as source code, a Java.jar application, and a native Mac OS X application. It is distributed under the terms of the GNU General Public License at http://code.google.com/p/phylo-puma.

Contact:  jembrown@mail.utexas.edu
SNPHarvester: a filtering-based approach for detecting epistatic interactions in genome-wide association studies
Authors: Yang Can , He Zengyou , Wan Xiang , Yang Qiang , Xue Hong , Yu Weichuan
Published: December 2008

Motivation: Hundreds of thousands of single nucleotide polymorphisms (SNPs) are available for genome-wide association (GWA) studies nowadays. The epistatic interactions of SNPs are believed to be very important in determining individual susceptibility to complex diseases. However, existing methods for SNP interaction discovery either suffer from high computation complexity or perform poorly when marginal effects of disease loci are weak or absent. Hence, it is desirable to develop an effective method to search epistatic interactions in genome-wide scale.

Results: We propose a new method SNPHarvester to detect SNP–SNP interactions in GWA studies. SNPHarvester creates multiple paths in which the visited SNP groups tend to be statistically associated with diseases, and then harvests those significant SNP groups which pass the statistical tests. It greatly reduces the number of SNPs. Consequently, existing tools can be directly used to detect epistatic interactions. By using a wide range of simulated data and a real genome-wide data, we demonstrate that SNPHarvester outperforms its recent competitor significantly and is promising for practical disease prognosis.

Availability:  http://bioinformatics.ust.hk/SNPHarvester.html

Contact:  eeyang@ust.hk

Supplementary information:  Supplementary data are available at Bioinformatics online.
SNPnexus: a web database for functional annotation of newly discovered and public domain single nucleotide polymorphisms
Authors: Chelala Claude , Khan Arshad , Lemoine Nicholas R
Published: December 2008

Motivation: Design a new computational tool allowing scientists to functionally annotate newly discovered and public domain single nucleotide polymorphisms in order to help in prioritizing targets in further disease studies and large-scale genotyping projects.

Summary: SNPnexus database provides functional annotation for both novel and public SNPs. Possible effects on the transcriptome and proteome levels are characterized and reported from five major annotation systems providing the most extensive information on alternative splicing. Additional information on HapMap genotype and allele frequency, overlaps with potential regulatory elements or structural variations as well as related genetic diseases can be also retrieved. The SNPnexus database has a user-friendly web interface, providing single or batch query options using SNP identifiers from dbSNP as well as genomic location on clones, contigs or chromosomes. Therefore, SNPnexus is the only database currently providing a complete set of functional annotations of SNPs in public databases and newly detected from sequencing projects. Hence, we describe SNPnexus, provide details of the query options, the annotation categories as well as biological examples of use.

Availability: The SNPnexus database is freely available at http://www.snp-nexus.org.

Contact:  claude.chelala@cancer.org.uk
SAFEGUI: resampling-based tests of categorical significance in gene expression data made easy
Authors: Gatti Daniel M. , Sypa Myroslav , Rusyn Ivan , Wright Fred A. , Barry William T.
Published: December 2008

Summary: A large number of websites and applications perform significance testing for gene categories/pathways in microarray data. Many of these packages fail to account for expression correlation between transcripts, with a resultant inflation in Type I error. Array permutation and other resampling-based approaches have been proposed as solutions to this problem. SAFEGUI provides a user-friendly graphical interface for the assessment of categorical significance in microarray studies, while properly accounting for the effects of correlations among genes. SAFEGUI incorporates both permutation and more recently proposed bootstrap algorithms that are demonstrated to be more powerful in detecting differential expression across categories of genes.

Availability:  http://cebc.unc.edu/software/

Contact:  fwright@bios.unc.edu; dmgatti@email.unc.edu
A Pollen Protein, NaPCCP, That Binds Pistil Arabinogalactan Proteins Also Binds Phosphatidylinositol 3-Phosphate and Associates with the Pollen Tube Endomembrane System
Authors: Lee Christopher B. , Kim Sunran , McClure Bruce
Published: December 2008

As pollen tubes grow toward the ovary, they are in constant contact with the pistil extracellular matrix (ECM). ECM components are taken up during growth, and some pistil molecules exert their effect inside the pollen tube. For instance, the Nicotiana alata 120-kD glycoprotein (120K) is an abundant arabinogalactan protein that is taken up from the ECM; it has been detected in association with pollen tube vacuoles, but the transport pathway between these compartments is unknown. We recently identified a pollen C2 domain-containing protein (NaPCCP) that binds to the carboxyl-terminal domain of 120K. As C2 domain proteins mediate protein-lipid interactions, NaPCCP could function in intracellular transport of 120K in pollen tubes. Here, we describe binding studies showing that the NaPCCP C2 domain is functional and that binding is specific for phosphatidylinositol 3-phosphate. Subcellular fractionation, immunolocalization, and live imaging results show that NaPCCP is associated with the plasma membrane and internal pollen tube vesicles. Colocalization between an NaPCCP∷green fluorescent protein fusion and internalized FM4-64 suggest an association with the endosomal system. NaPCCP localization is altered in pollen tubes rejected by the self-incompatibility mechanism, but our hypothesis is that it has a general function in the transport of endocytic cargo rather than a specific function in self-incompatibility. NaPCCP represents a bifunctional protein with both phosphatidylinositol 3-phosphate- and arabinogalactan protein-binding domains. Therefore, it could function in the transport of pistil ECM proteins in the pollen tube endomembrane system.
Overexpression of Flavodoxin in Bacteroids Induces Changes in Antioxidant Metabolism Leading to Delayed Senescence and Starch Accumulation in Alfalfa Root Nodules
Authors: Redondo Francisco J. , de la Peña Teodoro Coba , Morcillo César N. , Lucas M. Mercedes , Pueyo José J.
Published: December 2008

Sinorhizobium meliloti cells were engineered to overexpress Anabaena variabilis flavodoxin, a protein that is involved in the response to oxidative stress. Nodule natural senescence was characterized in alfalfa (Medicago sativa) plants nodulated by the flavodoxin-overexpressing rhizobia or the corresponding control bacteria. The decline of nitrogenase activity and the nodule structural and ultrastructural alterations that are associated with nodule senescence were significantly delayed in flavodoxin-expressing nodules. Substantial changes in nodule antioxidant metabolism, involving antioxidant enzymes and ascorbate-glutathione cycle enzymes and metabolites, were detected in flavodoxin-containing nodules. Lipid peroxidation was also significantly lower in flavodoxin-expressing nodules than in control nodules. The observed amelioration of the oxidative balance suggests that the delay in nodule senescence was most likely due to a role of the protein in reactive oxygen species detoxification. Flavodoxin overexpression also led to high starch accumulation in nodules, without reduction of the nitrogen-fixing activity.
Ectopic Expression of VvMybPA2 Promotes Proanthocyanidin Biosynthesis in Grapevine and Suggests Additional Targets in the Pathway
Authors: Terrier Nancy , Torregrosa Laurent , Ageorges Agnès , Vialet Sandrine , Verriès Clotilde , Cheynier Véronique , Romieu Charles
Published: December 2008

Grapevine (Vitis vinifera) proanthocyanidins contribute to plant defense mechanisms against biotic stress and also play a critical role in organoleptic properties of wine. In grapevine berry, these compounds are mainly accumulated in exocarps and seeds in the very early stages of development. A previous study has already identified VvMybPA1 as the first transcription factor involved in the regulation of the proanthocyanidin pathway during seed development in grapevine. A novel Myb factor, VvMybPA2, which is described in this study, is in contrast mainly expressed in the exocarp of young berries and in the leaves. This transcription factor shows very high protein sequence homology with other plant Myb factors, which regulate flavonoid biosynthesis. Ectopic expression of either VvMybPA1 or VvMybPA2 in grapevine hairy roots induced qualitative and quantitative changes of the proanthocyanidin profiles. High-throughput transcriptomic analyses of transformed grapevine organs identified a large set of putative targets of the VvMybPA1 and VvMybPA2 transcription factors. Both genes significantly activated enzymes of the flavonoid pathway, including anthocyanidin reductase and leucoanthocyanidin reductase 1, the specific terminal steps in the biosynthesis of epicatechin and catechin, respectively, but not leucoanthocyanidin reductase 2. The functional annotation of the genes whose expression was modified revealed putative new actors of the proanthocyanidin pathway, such as glucosyltransferases and transporters.
Ricinosomes Predict Programmed Cell Death Leading to Anther Dehiscence in Tomato
Authors: Senatore Adriano , Trobacher Christopher P. , Greenwood John S.
Published: December 2008

Successful development and dehiscence of the anther and release of pollen are dependent upon the programmed cell death (PCD) of the tapetum and other sporophytic tissues. Ultrastructural examination of the developing and dehiscing anther of tomato (Solanum lycopersicum) revealed that cells of the interlocular septum, the connective tissue, the middle layer/endothecium, and the epidermal cells surrounding the stomium all exhibit features consistent with progression through PCD. Ricinosomes, a subset of precursor protease vesicles that are unique to some incidents of plant PCD, were also present in all of these cell types. These novel organelles are known to harbor KDEL-tailed cysteine proteinases that act in the final stages of corpse processing following cell death. Indeed, a tomato KDEL-tailed cysteine proteinase, SlCysEP, was identified and its gene was cloned, sequenced, and characterized. SlCysEP transcript and protein were restricted to the anthers of the senescing tomato flower. Present in the interlocular septum and in the epidermal cells surrounding the stomium relatively early in development, SlCysEP accumulates later in the sporophytic tissues surrounding the locules as dehiscence ensues. At the ultrastuctural level, immunogold labeling localized SlCysEP to the ricinosomes within the cells of these tissues, but not in the tapetum. It is suggested that the accumulation of SlCysEP and the appearance of ricinosomes act as very early predictors of cell death in the tomato anther.
Multidrug and Toxic Compound Extrusion-Type Transporters Implicated in Vacuolar Sequestration of Nicotine in Tobacco Roots
Authors: Shoji Tsubasa , Inai Koji , Yazaki Yoshiaki , Sato Yasutaka , Takase Hisabumi , Shitan Nobukazu , Yazaki Kazufumi , Goto Yumi , Toyooka Kiminori , Matsuoka Ken , Hashimoto Takashi
Published: December 2008

Nicotine is a major alkaloid accumulating in the vacuole of tobacco (Nicotiana tabacum), but the transporters involved in the vacuolar sequestration are not known. We here report that tobacco genes (NtMATE1 and NtMATE2) encoding transporters of the multidrug and toxic compound extrusion (MATE) family are coordinately regulated with structural genes for nicotine biosynthesis in the root, with respect to spatial expression patterns, regulation by NIC regulatory loci, and induction by methyl jasmonate. Subcellular fractionation, immunogold electron microscopy, and expression of a green fluorescent protein fusion protein all suggested that these transporters are localized to the vacuolar membrane. Reduced expression of the transporters rendered tobacco plants more sensitive to the application of nicotine. In contrast, overexpression of NtMATE1 in cultured tobacco cells induced strong acidification of the cytoplasm after jasmonate elicitation or after the addition of nicotine under nonelicited conditions. Expression of NtMATE1 in yeast (Saccharomyces cerevisiae) cells compromised the accumulation of exogenously supplied nicotine into the yeast cells. The results imply that these MATE-type proteins transport tobacco alkaloids from the cytosol into the vacuole in exchange for protons in alkaloid-synthesizing root cells.
Characterization of Raphanus sativus Pentatricopeptide Repeat Proteins Encoded by the Fertility Restorer Locus for Ogura Cytoplasmic Male Sterility
Authors: Uyttewaal M. , Arnal N. , Quadrado M. , Martin-Canadell A. , Vrielynck N. , Hiard S. , Gherbi H. , Bendahmane A. , Budar F. , Mireau H.
Published: December 2008

Cytoplasmic male sterility is a maternally inherited trait in higher plants that prevents the production of functional pollen. Ogura cytoplasmic male sterility in radish (Raphanus sativus) is regulated by the orf138 mitochondrial locus. Male fertility can be restored when orf138 accumulation is suppressed by the nuclear Rfo locus, which consists of three genes putatively encoding highly similar pentatricopeptide repeat proteins (PPR-A, -B, and -C). We produced transgenic rapeseed (Brassica napus) plants separately expressing PPR-A and PPR-B and demonstrated that both encoded proteins accumulated preferentially in the anthers of young flower buds. Immunodetection of ORF138 showed that, unlike PPR-B, PPR-A had no effect on the synthesis of the sterility protein. Moreover, immunolocalization experiments indicated that complete elimination of ORF138 from the tapetum of anthers correlated with the restoration of fertility. Thus, the primary role of PPR-B in restoring fertility is to inhibit ORF138 synthesis in the tapetum of young anthers. In situ hybridization experiments confirmed, at the cellular level, that PPR-B has no effect on the accumulation of orf138 mRNA. Lastly, immunoprecipitation experiments demonstrated that PPR-B, but not PPR-A, is associated with the orf138 RNA in vivo, linking restoration activity with the ability to directly or indirectly interact with the orf138 RNA. Together, our data support a role for PPR-B in the translational regulation of orf138 mRNA.
Dynamic Evolution ofOryzaGenomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set
Authors: Ammiraju Jetty S.S. , Lu Fei , Sanyal Abhijit , Yu Yeisoo , Song Xiang , Jiang Ning , Pontaroli Ana Clara , Rambo Teri , Currie Jennifer , Collura Kristi , Talag Jayson , Fan Chuanzhu , Goicoechea Jose Luis , Zuccolo Andrea , Chen Jinfeng , Bennetzen Jeffrey L. , Chen Mingsheng , Jackson Scott , Wing Rod A.
Published: December 2008

Oryza (23 species; 10 genome types) contains the world's most important food crop — rice. Although the rice genome serves as an essential tool for biological research, little is known about the evolution of the other Oryza genome types. They contain a historical record of genomic changes that led to diversification of this genus around the world as well as an untapped reservoir of agriculturally important traits. To investigate the evolution of the collective Oryza genome, we sequenced and compared nine orthologous genomic regions encompassing the Adh1-Adh2 genes (from six diploid genome types) with the rice reference sequence. Our analysis revealed the architectural complexities and dynamic evolution of this region that have occurred over the past ∼15 million years. Of the 46 intact genes and four pseudogenes in the japonica genome, 38 (76%) fell into eight multigene families. Analysis of the evolutionary history of each family revealed independent and lineage-specific gain and loss of gene family members as frequent causes of synteny disruption. Transposable elements were shown to mediate massive replacement of intergenic space (>95%), gene disruption, and gene/gene fragment movement. Three cases of long-range structural variation (inversions/deletions) spanning several hundred kilobases were identified that contributed significantly to genome diversification.
Representing God's Presence
Authors: Dalferth Ingolf
Published: December 2008

The article tackles two myths: the modern myth that God has vanished from human life, and the religious myth that the apostles, patriarchs, mystics and martyrs were in a more privileged position vis‐´‐vis God than we are. Dalferth argues that God has never been more present than today, has never been less hidden than today, and develops the thessis that the importance of God being present is central to the Christian understanding of God. Christian faith is faith in a present reality, not a set of beliefs about past events. The implications of this for the task of Christian communication are clear: the prime interest of Christian communication is to help those to whom it is addressed to develop a sense of the presence of God.
Do competitive intraguild interactions affect space and habitat use by small carnivores in a forested landscape?
Authors: St‐Pierre Caroline , Ouellet Jean‐Pierre , Crête Michel
Published: December 2008

Complex interactions such as interference competition and predation, including intraguild predation, are now recognized as important components in animal community structure. At the lower end of a guild, weasels may be highly affected by other guild members due to small body size in relation to other predators. In 2000 and 2001, we radio‐collared 24 erminesMustela ermineaand 25 long‐tailed weaselsM. frenatain 2 areas that differed in abundance of guild members. We tested the hypothesis that when faced with an increased density of other guild members, weasels would modify space and habitat use to reduce the risk of predation associated with encounters involving guild members. We predicted that weasels would increase use of specific habitats (such as refuges) to reduce encounter rates in the presence of a greater number of guild members. BecauseM. ermineais smaller thanM. frenataand thus better able to take advantage of small rodent burrows as refuges from predators and as feeding grounds, we also predicted thatM. frenatawould show a stronger response to a higher abundance of guild members thanM. erminea. Results were consistent with our predictions. Faced with an increased abundance of guild members,M. frenatashowed increased habitat selectivity and reduced activity levels, which resulted in increased daily travel distances and increased home ranges.Mustela erminearesponded to an increased abundance of guild members through reduced use of preferred habitat whichM. frenataalready occupied. The contrasting pattern of habitat selection observed between the 2 mustelid species suggested cascading effects, whereby large‐predator pressure onM. frenatarelaxed pressure ofM. frenataonM. erminea. Our results draw attention to the likelihood that competitive intraguild interactions play a facilitating role inM. erminea–M. frenatacoexistence.
Moose and vole browsing patterns in experimentally assembled pure and mixed forest stands
Authors: Vehviläinen Harri , Koricheva Julia
Published: December 2008

Plants growing in diverse communities are believed to exhibit associational resistance to herbivores, but this hypothesis has seldom been tested experimentally for vertebrate herbivores in forest ecosystems. We examined browsing patterns of the two principal mammalian herbivores of Finnish boreal forests, moose and voles, in young stands where tree species diversity and composition were experimentally manipulated. The stands were composed either of monocultures or different 2–5 species mixtures of Norway spruce, Scots pine, Siberian larch, silver birch, and black alder. Voles and moose showed contrasting responses to stand diversity and species composition. In accordance with the predictions of the associational resistance hypothesis, vole damage was higher in tree monocultures than in mixed stands, although stand diversity effects were statistically significant only at one of the three study areas. Voles also damaged more trees in coniferous than in deciduous stands. In contrast, moose browsing tended to increase with the number of tree species in a stand and with the presence of the preferred tree species, birch, in a mixture. The observed differences in vole and moose responses to stand diversity and species composition are likely to be due to different feeding specialisation, foraging patterns, and movement ability of these herbivores. Voles switched to trees only when the supply of a more preferred food (grasses and forbs) was depleted and restricted their feeding choice only to the most palatable tree species regardless of the number of tree species present per stand. In contrast, tree branches and foliage represented an important part of moose diet throughout the year; moose may be able to tolerate secondary plant metabolites of different tree species better than voles and may thus benefit from diet broadening when more tree species are available. Furthermore, the home range size and foraging ability of these two very differently sized herbivores may partly explain the observed differences in utilisation of different tree species. Finally, both moose and voles showed high spatial and temporal variation in their feeding; in particular, vole damage was more influenced by tree species diversity in areas and years with high vole densities. Thus, diversification of forest stands may have very different effects on mammalian browsing depending on the herbivores present, their densities, and the tree species used in reforestation.
Conservatism of host specificity in parasites
Authors: Mouillot David , R. Krasnov Boris , I. Shenbrot Georgy , J. Gaston Kevin , Poulin Robert
Published: December 2008

As information becomes available for many groups of organisms a general pattern of phylogenetic conservatism in ecological characters or morphological traits is now widely recognized. Conversely, conservatism of external ecological attributes throughout a lineage is still a contentious theme in ecology. Moreover, the studies exploring this topic have focused on free‐living organisms, and have ignored parasites. The main external ecological attribute of parasite species is certainly their host specificity, which is a key determinant of both their range size and local abundance. We address the subject of conservatism and predictability of host specificity using 2 large databases concerning, respectively, ectoparasites and endoparasites. We found a significant positive relationship between the numbers of host species infested by flea sister species. Moreover, this result was consistent whether we used sympatric or allopatric flea species, suggesting no influence of the mode of speciation on this conservatism of specificity. Additionally, our results showed that congeneric helminth species have more similar host taxonomic diversities than expected by chance, although this conservatism is due mostly to trematodes. Whilst there is evidence of conservatism, the moderate levels preclude robust prediction of host specificity for one species based on that of closely related species.
Ecoregions as predictors of lotic assemblages of blackflies (Diptera: Simuliidae)
Authors: McCreadie John W. , Adler Peter H.
Published: December 2008

Local ecological attributes of streams are known to have strong influences on community membership for many aquatic insects. Differences in aquatic insect assemblages, therefore, should be clearly detectable across large scale ecological “units”, such as ecoregions. Many studies of aquatic invertebrates however, have suffered from a lack of species level identifications. In addition, many previous studies that examined the influence of ecoregion on aquatic assemblages have the implicit assumption that members of different taxa are responding in the same manner. Our study, therefore, was restricted to an ecologically (lotic) and functionally (mostly filter‐feeding) homogenous group, the Simuliidae. In the current study, we examine the relationship between species assemblages of preimaginal blackflies and the landscape through which their stream habitats flow. Accordingly, the larval simuliid faunas from South Carolina, USA, are compared among three ecoregions established a priori: Blue Ridge Mountains, Piedmont, and Sandhills. Using discriminant function analysis, we show that each ecoregion produces a distinct stream habitat; factors responsible for regionalization are quantified. We also show that streams can be assigned correctly to ecoregion of origin 85% of the time on the basis of the simuliid assemblage. We suggest that our results can be interpreted most readily by considering the distribution of individual species.
Structure of a plant‐pollinator network on a pahoehoe lava desert of the Galápagos Islands
Authors: Philipp Marianne , Böcher Jens , R. Siegismund Hans , R. Nielsen Lene
Published: December 2008

Plant‐pollinator interactions are important for the evolution and survival of the species involved. Plant‐pollinator networks on oceanic islands are often small in size and as a consequence the connectance is high suggesting a substantial generalisation level. Further, linkage level for insular plants is shown to be lower than on mainland. The present study investigates a plant‐pollinator network on the Galápagos Islands that is unique because of its very small size. We recorded pollinator visits to plant species as well as pollen grains on insect bodies. The combination of these data increased the observed number of interactions. The values for connectance and linkage level for plants were found to be consistent with similar values found in other network studies. There were no relation between the abundance of plant species and the number of pollinating species. The dominating pollinator species was the Galápagos carpenter bee Xylocopa darwini. Specimens of the shorthorned grasshopper Halmenus cuspidatus turned out to carry pollen from five plant species out of twelve and are probably functioning as pollinator. Bagging experiments revealed dependency on insect visits for a high seed set for most of the plant species, but only one species Plumbago scandens seemed to possess a pollen limited seed set. The network showed an asymmetric pattern of number of interactions per species with a few species having several interactions and many species a few. This pattern is supposed to result in a rather robust community, but is also fairly sensitive if the dominant species are threatened. The high connectance value found could, however, counteract this vulnerability.
Landscape partitioning and spatial inferences of competition between black and grizzly bears
Authors: Apps Clayton D. , McLellan Bruce N. , Woods John G.
Published: December 2008

Population effects of competition between large carnivore species may be evident by contrasting actual distributions of putative competitors against predictions of inherent landscape quality for each species. Such comparison can be insightful if covariation with external factors known to influence the occurrence, density, or persistence of each species over space and time can be controlled. We used systematically‐distributed DNA hair‐trap stations to sample the occurrence of black bears (Ursus americanus) and grizzly bears (U. arctos) across 5496 km2 in southeastern British Columbia, Canada. We describe interspecific landscape partitioning according to terrain, vegetation and land‐cover variables at 2 spatial scales. We developed multivariate models to predict the potential distribution of each species. At sampling site‐session combinations that detected either species, we then investigated whether the expected or actual occurrence of each influenced the likelihood of detecting the other while controlling for human influence and inherent landscape quality. Black bears were more likely than grizzly bears to occur in gentle, valley bottom terrain with lower proportions of open habitats. Each species also was detected less frequently with the other species than predicted by their respective models; however, the strength of this relationship decreased as landscapes became more characteristic of black bear habitat. As landscapes showed higher inherent potential to support grizzly bears, black bears occurred more than model prediction in areas with higher human access and proximity to major highways but less in national parks. As potential to support black bears increased, grizzly bears occurred more than model prediction only in national parks and less with increasing human access and proximity to major highways. Results suggest that competition is occurring between the species, and that the differential response of each species to human disturbance or excessive mortality may influence the outcome and hence landscape partitioning. Moreover, black bears are more likely to benefit from human encroachment into landscapes of high inherent value for grizzly bears than vice versa. Conservation implications relate to potential mediating effects of habitat and human influence on competitive interactions between the species.
Fear factor: prey habitat selection and its consequences in a predation risk landscape
Authors: L. Thomson Robert , T. Forsman Jukka , Sardà‐Palomera Francesc , Mönkkönen Mikko
Published: December 2008

Predation risk influences prey use of space. However, little is known about how predation risk influences breeding habitat selection and the fitness consequences of these decisions. The nest sites of central‐place foraging predators may spatially anchor predation risk in the landscape. We explored how the spatial dispersion of avian predator nests influenced prey territory location and fitness related measures. We placed 249 nest boxes for migrant pied flycatchersFicedula hypoleuca, at distances between 10 and 630 m, around seven different sparrowhawk nestsAccipiter nisus. After closely monitoring flycatcher nests we found that flycatcher arrival dates, nest box occupation rates and clutch size showed a unimodal relationship with distance from sparrowhawk nests. This relationship suggested an optimal territory location at intermediate distances between 330 and 430 m from sparrowhawk nests. Furthermore, pied flycatcher nestling quantity and quality increased linearly with distance from sparrowhawk nests. These fitness related measures were between 4 and 26% larger in flycatcher nestlings raised far from, relative to those raised nearby, sparrowhawk nests. Our results suggest that breeding sparrowhawk affected both flycatcher habitat selection and reproductive success. We propose that nesting predators create predictable spatial variation in predation risk for both adult prey and possibly their nests, to which prey individuals are able to adaptively respond. Recognising predictable spatial variation in perceived predation risk may be fundamental for a proper understanding of predator‐prey interactions and indeed prey species interactions.
Local versus landscape determinants of butterfly movement behaviors
Authors: Kuefler Daniel , Haddad Nick M.
Published: December 2008

Large‐scale patterns of animal distributions and abundances may be determined by mechanisms that act at local or landscape scales. We studied the movement behaviors of four species of bottomland butterflies in a natural setting to examine the determinants of movement behavior across different scales. We tested the relative importance of three landscape attributes: drainage slope, boundary type, and stream proximity, and local habitat attributes related to food plants and plants that influence habitat structure. Across species, we tested the relative importance of organism size and habitat specificity to explain response variation. In general, butterfly responses to landscape features were more universal than responses to local features. Specifically, results from this study showed that drainage slope did not influence movement behaviors but boundary type, stream proximity, and host plant abundance all influenced movement patterns. Responses to local features varied by species and often complemented landscape effects on movement. Responses to all features were not related to butterfly size, but did vary in accordance with butterfly host plant specificity. These behaviors help to explain landscape‐level variation in population distribution among species.
The role of soil pH in linking groundwater flow and plant species density in boreal forest landscapes
Authors: Zinko Ursula , Dynesius Mats , Nilsson Christer , Seibert Jan
Published: December 2008

In hilly boreal landscapes topography governs groundwater flow which strongly influences soil development, and thus vegetation composition. Soil pH is known to correlate well with plant species density and composition, but in boreal forests this relationship has been little studied. Previously, we successfully used a topography‐based hydrological index, the topographical wetness index (TWI), as an approximation of the variation in groundwater flow to predict local plant species density in a boreal forest landscape. Data on species indicator values demonstrated that soil pH can be an important soil variable linking groundwater flow and plant species density. In the present paper we explore this link by relating measured soil pH to species numbers of vascular plants and TWI in 200‐m2 plots within two boreal forest landscapes, differing in average soil pH. The two landscapes showed almost identical relationships between plant species number and soil pH, implying that this relationship is robust. The landscapes also had similar relationships between soil pH and TWI as well as between plant species number and TWI except at high TWI values, which indicate groundwater discharge areas. In these areas soil pH and plant species numbers were higher in the high‐pH landscape at any given TWI value. We conclude that for predictive mapping of the species density of vascular plants in boreal forests, soil pH is a major factor. However, TWI as a measure of groundwater flow is a practical alternative predictor.
Combining richness and abundance into a single diversity index using matrix analogues of Shannon's and Simpson's indices
Authors: Gorelick Root
Published: December 2008

Shannon's and Simpson's indices have been the most widely accepted measures of ecological diversity for the past fifty years, even though neither statistic accounts for species abundances across geographic locales (“patches”). An abundant species that is endemic to a single patch can be as much of a conservation concern as a rare cosmopolitan species. I extend Shannon's and Simpson's indices to simultaneously account for species richness and relative abundances – i.e. extend them to multispecies metacommunities – by making the inputs to each index a matrix, rather than a vector. The Shannon's index analogue of diversity is mutual entropy of species and patches divided by marginal entropy of the individual geographic patches. The Simpson's index analogue of diversity is a modification of mutual entropy, with the logarithm moved to the outside of the summation, divided by Simpson's index of the patches. Both indices are normalized for number of patches, with the result being inversely proportional to biodiversity. These methods can be extended to account for time‐series of such matrices and average age‐classes of each species within each patch, as well as provide a measure of spatial coherence of communities.