bluuebunny/crossref_metadata_2025 huggingface dataset:
Reconsidering complete search algorithms for protein backbone NMR assignment
Authors: Vitek Olga , Bailey-Kellogg Chris , Craig Bruce , Kuliniewicz Paul , Vitek Jan
Published: October 2005

Motivation: Nuclear magnetic resonance (NMR) spectroscopy is widely used to determine and analyze protein structures. An essential step in NMR studies is determining the backbone resonance assignment, which maps individual atoms to experimentally measured resonance frequencies. Performing assignment is challenging owing to the noise and ambiguity in NMR spectra. Although automated procedures have been investigated, by-and-large they are still struggling to gain acceptance because of inherent limits in scalability and/or unacceptable levels of assignment error. To have confidence in the results, an algorithm should be complete, i.e. able to identify all solutions consistent with the data, including all arbitrary configurations of extra and missing peaks. The ensuing combinatorial explosion in the space of possible assignments has led to the perception that complete search is hopelessly inefficient and cannot scale to realistic datasets.

Results: This paper presents a complete branch-contract-and-bound search algorithm for backbone resonance assignment. The algorithm controls the search space by hierarchically agglomerating partial assignments and employing statistically sound pruning criteria. It considers all solutions consistent with the data, and uniformly treats all combinations of extra and missing data. We demonstrate our approach on experimental data from five proteins ranging in size from 70 to 154 residues. The algorithm assigns >95% of the positions with >98% accuracy. We also present results on simulated data from 259 proteins from the RefDB database, ranging in size from 25 to 257 residues. The median computation time for these cases is 1 min, and the assignment accuracy is >99%. These results demonstrate that complete search not only has the advantage of guaranteeing fair treatment of all feasible solutions, but is efficient enough to be employed effectively inpractice.

Availability: The MBA2 software package is made available under an open-source software license. The datasets featured in the Results section can also be obtained from the contact author.

Contact:  ovitek@stat.purdue.edu
Fast maximum-likelihood refinement of electron microscopy images
Authors: Scheres Sjors H.W. , Valle Mikel , Carazo José-María
Published: October 2005

Motivation: Maximum-likelihood (ML) image refinement is a promising candidate to improve attainable resolution limits in 3D-EM. However, its large CPU requirements may prohibit application to 3D-structure optimization.

Results: We speeded up ML image refinement by reducing its search space over the alignment parameters. Application of this reduced-search approach to a cryo-EM dataset yielded practically identical results as the original approach, but in approximately one day instead of one week of CPU.

Availability: This work has been implemented in the public domain package Xmipp. Documentation and download instructions may be found at: http://www.cnb.uam.es/~bioinfo

Contact:  carazo@cnb.uam.es
Web servicing the biological office
Authors: Szugat Martin , Güttler Daniel , Fundel Katrin , Sohler Florian , Zimmer Ralf
Published: October 2005

Summary: Biologists routinely use Microsoft Office applications for standard analysis tasks. Despite ubiquitous internet resources, information needed for everyday work is often not directly and seamlessly available. Here we describe a very simple and easily extendable mechanism using Web Services to enrich standard MS Office applications with internet resources. We demonstrate its capabilities by providing a Web-based thesaurus for biological objects, which maps names to database identifiers and vice versa via an appropriate synonym list. The client application ProTag makes these features available in MS Office applications using Smart Tags and Add-Ins.

Availability:  http://services.bio.ifi.lmu.de/prothesaurus/

Contact:  prothesaurus@bio.ifi.lmu.de
Membrane organization and tumorigenesis—the NF2 tumor suppressor, Merlin
Authors: McClatchey Andrea I. , Giovannini Marco
Published: October 2005

The NF2 tumor-suppressor gene was cloned more than a decade ago, but the function of its encoded protein, Merlin, remains elusive. Merlin, like the closely related ERM proteins, appears to provide regulated linkage between membrane-associated proteins and the actin cytoskeleton and is therefore poised to function in receiving and interpreting signals from the extracellular milieu. Recent studies suggest that Merlin may coordinate the processes of growth-factor receptor signaling and cell adhesion. Varying use of this organizing activity by different types of cells could provide an explanation for the unique spectrum of tumors associated with NF2 deficiency in mammals.
Cdc7–Drf1 is a developmentally regulated protein kinase required for the initiation of vertebrate DNA replication
Authors: Takahashi Tatsuro S. , Walter Johannes C.
Published: October 2005

Cdc7, a protein kinase required for the initiation of eukaryotic DNA replication, is activated by a regulatory subunit, Dbf4. A second activator of Cdc7 called Drf1 exists in vertebrates, but its function is unknown. Here, we report that in Xenopus egg extracts, Cdc7-Drf1 is far more abundant than Cdc7-Dbf4, and removal of Drf1 but not Dbf4 severely inhibits phosphorylation of Mcm4 and DNA replication. After gastrulation, when the cell cycle acquires somatic characteristics, Drf1 levels decline sharply and Cdc7-Dbf4 becomes the more abundant kinase. These results identify Drf1 as a developmentally regulated, essential activator of Cdc7 in Xenopus.
Reduced U snRNP assembly causes motor axon degeneration in an animal model for spinal muscular atrophy
Authors: Winkler Christoph , Eggert Christian , Gradl Dietmar , Meister Gunter , Giegerich Marieke , Wedlich Doris , Laggerbauer Bernhard , Fischer Utz
Published: October 2005

Spinal muscular atrophy (SMA) is a motoneuron disease caused by reduced levels of survival motoneuron (SMN) protein. Previous studies have assigned SMN to uridine-rich small nuclear ribonucleoprotein particle (U snRNP) assembly, splicing, transcription, and RNA localization. Here, we have used gene silencing to assess the effect of SMN protein deficiency on U snRNP metabolism in living cells and organisms. In HeLa cells, we show that reduction of SMN to levels found in SMA patients impairs U snRNP assembly. In line with this, induced silencing of SMN expression in Xenopus laevis or zebrafish arrested embryonic development. Under less severe knock-down conditions, zebrafish embryos proceeded through development yet exhibited dramatic SMA-like motor axon degeneration. The same was observed after silencing two other essential factors in the U snRNP assembly pathway, Gemin2 and pICln. Importantly, the injection of purified U snRNPs into either SMN- or Gemin2-deficient embryos of Xenopus and zebrafish prevented developmental arrest and motoneuron degeneration, respectively. These findings suggest that motoneuron degeneration in SMA patients is a direct consequence of impaired production of U snRNPs.
RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing
Authors: Djupedal Ingela , Portoso Manuela , Spåhr Henrik , Bonilla Carolina , Gustafsson Claes M. , Allshire Robin C. , Ekwall Karl
Published: October 2005

Fission yeast centromeric repeats are transcribed into small interfering RNA (siRNA) precursors (pre-siRNAs), which are processed by Dicer to direct heterochromatin formation. Recently, Rpb1 and Rpb2 subunits of RNA polymerase II (RNA Pol II) were shown to mediate RNA interference (RNAi)-directed chromatin modification but did not affect pre-siRNA levels. Here we show that another Pol II subunit, Rpb7 has a specific role in pre-siRNA transcription. We define a centromeric pre-siRNA promoter from which initiation is exquisitely sensitive to the rpb7-G150D mutation. In contrast to other Pol II subunits, Rpb7 promotes pre-siRNA transcription required for RNAi-directed chromatin silencing.
Evolutionary constraints in conserved nongenic sequences of mammals
Authors: Keightley Peter D. , Kryukov Gregory V. , Sunyaev Shamil , Halligan Daniel L. , Gaffney Daniel J.
Published: October 2005

Mammalian genomes contain many highly conserved nongenic sequences (CNGs) whose functional significance is poorly understood. Sets of CNGs have previously been identified by selecting the most conserved elements from a chromosome or genome, but in these highly selected samples, conservation may be unrelated to purifying selection. Furthermore, conservation of CNGs may be caused by mutation rate variation rather than selective constraints. To account for the effect of selective sampling, we have examined conservation of CNGs in taxa whose evolution is largely independent of the taxa from which the CNGs were initially identified, and we have controlled for mutation rate variation in the genome. We show that selective constraints in CNGs and their flanks are about one-half as strong in hominids as in murids, implying that hominids have accumulated many slightly deleterious mutations in functionally important nongenic regions. This is likely to be a consequence of the low effective population size of hominids leading to a reduced effectiveness of selection. We estimate that there are one and two times as many conserved nucleotides in CNGs as in known protein-coding genes of hominids and murids, respectively. Polymorphism frequencies in CNGs indicate that purifying selection operates in these sequences. During hominid evolution, we estimate that a total of about three deleterious mutations in CNGs and protein-coding genes have been selectively eliminated per diploid genome each generation, implying that deleterious mutations are eliminated from populations non-independently and that sex is necessary for long-term population persistence.
Kindling-induced changes in plasticity of the rat amygdala and hippocampus
Authors: Schubert Manja , Siegmund Herbert , Pape Hans-Christian , Albrecht Doris
Published: October 2005

Temporal lobe epilepsy (TLE) is often accompanied by interictal behavioral abnormalities, such as fear and memory impairment. To identify possible underlying substrates, we analyzed long-term synaptic plasticity in two relevant brain regions, the lateral amygdala (LA) and the CA1 region of the hippocampus, in the kindling model of epilepsy. Wistar rats were kindled through daily administration of brief electrical stimulations to the left basolateral nucleus of the amygdala. Field potential recordings were performed in slices obtained from kindled rats 48 h after the last induced seizure, and in slices from sham-implanted and nonimplanted controls. Kindling resulted in a significant impairment of long-term potentiation (LTP) in both the LA and the CA1, the magnitude of which was dependent on the number of prior stage V seizures. Saturation of CA1-LTP, assessed through repeated spaced delivery of high-frequency stimulation, occurred at lower levels in kindled compared to sham-implanted animals, consistent with the hypothesis of reduced capacity of further synaptic strengthening. Furthermore, theta pulse stimulation elicited long-term depression in the amygdala in nonimplanted and sham-implanted controls, whereas the same stimulation protocol stimulation caused LTP in kindled rats. In conclusion, kindling differentially affects the magnitude, saturation, and polarity of LTP in the CA1 and LA, respectively, most likely indicating an activity-dependent mechanism in the context of synaptic metaplasticity.
Context pre-exposure obscures amygdala modulation of contextual-fear conditioning
Authors: Huff Nicole C. , Wright-Hardesty Karli J. , Higgins Emily A. , Matus-Amat Patricia , Rudy Jerry W.
Published: October 2005

We report that post-training inactivation of basolateral amygdala region
(BLA) with muscimol impaired memory for contextual-fear conditioning (as
measured by freezing) and intra-BLA norepinephrine enhanced this memory.
However, pre-exposure to the context eliminated both of these effects. These
findings provide a likely explanation of why an earler study failed to observe
that the BLA modulates contextual fear conditioning—they pre-exposed
their rats to the context. These results also suggest that the amygdala
modulates the storage of the context fear memory and may do so by influencing
the storage of the representation of the context in which the shock
occurred.
Memory enhancement induced by post-training intrabasolateral amygdala infusions of β-adrenergic or muscarinic agonists requires activation of dopamine receptors: Involvement of right, but not left, basolateral amygdala
Authors: LaLumiere Ryan T. , McGaugh James L.
Published: October 2005

Previous findings indicate that the noradrenergic, dopaminergic, and
cholinergic innervations of the basolateral amygdala (BLA) modulate memory
consolidation. The current study investigated whether memory enhancement
induced by post-training intra-BLA infusions of a β-adrenergic or
muscarinic cholinergic agonist requires concurrent activation of dopamine (DA)
receptors in the BLA. Rats with implanted BLA cannulae were trained on an
inhibitory avoidance (IA) task and, 48 h later, tested for retention.
Infusions of the β-adrenergic agonist clenbuterol into the right BLA, but
not the left, enhanced retention, and concurrent infusions of the nonspecific
DA receptor antagonist cis-Flupenthixol (Flu) blocked the
enhancement. Post-training infusions of the muscarinic agonist oxotremorine
into the right BLA also enhanced retention, and concurrent infusions of Flu
blocked this effect. Additional experiments investigated whether memory
modulation was lateralized to the right BLA. Post-training DA infusions into
the right BLA, but not the left, enhanced retention. Post-training infusions
of lidocaine or muscimol, which impair retention when infused bilaterally, had
no effect when infused unilaterally into either the right or left BLA. These
findings, together with earlier work, suggest that the dopaminergic system in
the BLA is critically involved in memory modulation induced by noradrenergic
and cholinergic influences. Additionally, these findings indicate that the
enhancement, but not impairment, of memory consolidation is lateralized to the
right BLA.
Lack of the metabotropic glutamate receptor subtype 7 selectively modulates Theta rhythm and working memory
Authors: Hölscher Christian , Schmid Susanne , Pilz Peter K.D. , Sansig Gilles , van der Putten Herman , Plappert Claudia F.
Published: October 2005

Metabotropic glutamate receptors (mGluRs) are known to play a role in
synaptic plasticity and learning. We have previously shown that mGluR7
deletion in mice produces a selective working memory (WM) impairment, while
other types of memory such as reference memory remain unaffected. Since WM has
been associated with Theta activity (6-12 Hz) in EEGs, and since EEG
abnormalities have been observed in these mice before, we studied the effect
of mGluR7 gene ablation on EEG activity in the hippocampus, in particular in
the Theta range, during performance of a WM task. In an eight-arm maze with
four arms baited, mGluR7 knock-out (KO) and wild-type mice committed the same
number of reference memory errors, whereas KOs committed more WM errors. While
performing the task, KO mice showed substantially higher Theta amplitudes, and
the ratio of Theta to overall EEG power was much increased. No change was seen
in the Delta (0-5 Hz), or Gamma (30-40 Hz) EEG bands compared with controls.
When recording EEGs during periods of rest in the home cages, no difference
was seen between groups. These findings suggest that mGluR7 is important for
modulation and control of Theta activity. Since only WM was affected, and only
the Theta range of EEG activity was altered, these results show a correlation
between Theta rhythm and WM performance, and therefore support the concept
that Theta activity in the hippocampus is involved in WM storage.
Does intermediate care minimize relocation stress for patients leaving the ICU?
Authors: Beard Helen
Published: October 2005

Relocation stress is a phenomenon in which physical and psychological disturbances are experienced following transfer from one environment to another [Carpenito LJ. (2000). Nursing Diagnosis. Application to Clinical Practice, 8th edn]. The purpose of this review was to identify whether a period of intermediate care minimizes the problems associated with relocation stress after discharge from the intensive care unit (ICU) and before transfer to the ward. Methods of retrieving the literature involved identifying key terms, utilizing a range of databases and applying specific criteria in order to delineate the boundaries of the search. Using electronic and manual search methods, 11 studies were selected, both primary and secondary research. Following tabulation and critiquing of the studies, the findings of the review suggest that the factors which contribute towards relocation stress are the loss of one‐to‐one nursing, a reduction of visible monitoring equipment, lack of continuity of care and inadequate preparation of the patient for the transfer. The evidence also indicates that in order to minimize these factors, early planning and preparation of the patient for transfer are required, incorporating strategies of gradual reduction in nursing attention and monitoring equipment and the provision of information. Although the benefits of intermediate care are established as being advanced monitoring, appropriate nurse‐to‐patient ratio, heightened demonstration of expert knowledge and skill, there is no sufficient evidence to indicate a period of intermediate care that can ease the transition from the ICU to the ward.
Preliminary evaluation of the status of olive‐infecting viruses in Syria
Authors: Al Abdullah A. , El Beaino T. , Saponari M. , Hallak H. , Digiaro M.
Published: October 2005

Field surveys of 80 commercial groves were made in autumn 2003 in six major Syrian olive‐growing regions. A total of 300 olive samples, representative of the main cultivars grown in the country, were collected. As ascertained by dsRNA analysis, 54 out of 125 samples (about 43%) showed visible bands in polyacrylamide gel electrophoresis. All samples were tested by RT‐PCR for the presence of the following viruses: Arabis mosaic virus (ArMV), Cherry leaf roll virus (CLRV), Cucumber mosaic virus (CMV), Olive latent ringspot virus (OLRSV), Olive latent virus 1 (OLV‐1), Olive latent virus 2 (OLV‐2), Olive leaf yellowing‐associated virus (OLYaV) and Strawberry latent ringspot virus (SLRSV). All these viruses, singly or in mixed infection, were detected in about 51% of the samples. CMV was the most prevalent (22.7%), followed by CLRV (15%), OLYaV (14.3%) and OLRSV (11.5%). Less represented were the remaining four viruses. Infection rates ranged from 44% in Dara’a region to 67% in Latakia and Hama.
Détection des races 0, 1 et 2 de Fusarium oxysporum f. sp. niveum et leur distribution dans les régions de production de la pastèque en Tunisie
Authors: Boughalleb et N. , El Mahjoub M.
Published: October 2005

La détermination des races physiologiques de Fusarium oxysporum f. sp. niveum dans les régions de production de la pastèque en Tunisie a révélé la présence des 3 races 0, 1 et 2. A partir des 90 isolats obtenus à partir des plantes flétries de pastèque, 13%, 42% et 45% ont été identifiés respectivement comme étant de la race 0, de la race 1 et de la race 2. La race 0 a été trouvé dans 17% des parcelles prospectées, alors que les races 1 et 2 ont été signalées dans 70% des parcelles. La race 2 a été présente en association avec une ou les deux races au sein de la même parcelle. Notons également la dominance de la race 2 au sein de certaines régions du Sud (Gafsa et Métouia) et du Nord (Testour). Les races 1 et 2 ont été aussi détectées à partir du sol et des graines de pastèque.
Changes in stoichiometric constraints on epilithon and benthic macroinvertebrates in response to slight nutrient enrichment of mountain rivers
Authors: BOWMAN MICHELLE F. , CHAMBERS PATRICIA A. , SCHINDLER DAVID W.
Published: October 2005

1. To assess changes in stoichiometric constraints on stream benthos, we measured elemental composition of epilithon and benthic macroinvertebrates in intrinsically P‐limited mountain rivers, upstream and downstream of low‐level anthropogenic nutrient enrichment by effluents of municipal wastewater treatment plants.

2. While there was a broad range in the elemental composition of epilithon (C : P ratios of 200–16 500, C : N ratios of 8–280, N : P ratios of 8–535) and heptageniid mayfly scrapers (C : P ratios of 125–300, C : N ratios of 5.1–7.2, N : P ratios of 20–60), the average C : P ratio of epilithon was 10‐fold lower and the average C : N ratio twofold lower at more nutrient‐rich downstream sites. Nutrient ratios in benthic macroinvertebrates were lower than in epilithon and varied little between relatively nutrient‐poor and nutrient‐rich sites.

3. We modified the existing definition of producer‐consumer elemental imbalance to allow for variation in consumer nutrient content. We defined this ‘non‐homeostatic’ imbalance as the perpendicular distance between the producer and consumer C : P, C : N, or N : P ratios, and the 1 : 1 line.

4. At P‐limited sites, the estimated mayfly N : P recycling ratio was higher than the N : P ratio in epilithon, suggesting nutrient recycling by consumers could accentuate P‐limitation of epilithon.

5. Measuring the degree of producer–consumer nutrient imbalance may be important in predicting the magnitude of effects from nutrient enrichment and can help elucidate the causes and consequences of ecological patterns and processes in rivers.
Sink habitats can alter ecological outcomes for competing species
Authors: SCHREIBER SEBASTIAN J. , KELTON MOLLY
Published: October 2005

Species often compete for breeding sites in heterogeneous landscapes consisting of sources and sinks. To understand how the presence or absence of sink breeding sites influence ecological outcomes, we extend Pulliam's source–sink model to competing species.

In a homogeneous landscape consisting of source sites, we prove that one species, the ‘superior’ competitor, competitively excludes the other. Dominance is determined by a simple rule: the species that at equilibrium acquires new breeding sites at a faster rate dominates.

We prove that the inclusion of sink sites can alter this ecological outcome by either mediating coexistence, reversing competitive dominance, or facilitating a priority effect.

Sink‐mediated coexistence requires the species to exhibit asymmetries in acquiring sink sites, the ‘inferior’ species to have a competitive advantage on sink sites and the ratio of sink to source sites be sufficiently low.

For example, if the sink breeding sites are competitive refuges for the ‘inferior’ competitor and not too low in quality, coexistence occurs if the number of sink sites lies below a threshold. Alternatively, when the number of sink sites exceeds this threshold, competitive dominance is reversed and the ‘superior’ competitor is displaced.

Counter‐intuitively, despite being unable to support species in isolation, sink habitats embedded in a geographical mosaic of sources and sinks can enhance biodiversity by mediating coexistence or alter species composition by reversing competitive interactions.
Predation of beech seed by mice: effects of numerical and functional responses
Authors: RUSCOE WENDY A. , ELKINTON JOSEPH S. , CHOQUENOT DAVID , ALLEN ROBERT B.
Published: October 2005

The functional response of post‐dispersal seed predators (house mouse,Mus musculus) to absolute densities of southern beech seed (Nothofagus solandrivar.cliffortioides) was studied in laboratory and field trials. House mice showed a Type II (hyperbolic) functional response to seed availability and this was not modified by the presence of an alternative food source.

Maximum daily intake rate of beech seeds during field trials averaged 1042 seeds mouse−1. This is sufficient to provide house mice with both the energy and protein required for growth and reproduction.

We explicitly incorporated the functional response into the numerical response of house mice to beech seed, measured for field populations monitored in a New Zealand beech forest. House mice showed a strong numerical response to beech seed intake rate that was modified by some density‐dependent mechanism(s).

We developed a model that simulated seedfall, house mouse population growth and seed reserve depletion over one year. We found that the previously reported decline in house‐mouse populations in beech forests during spring and summer is likely to be related to spring beech seed germination that renders seed no longer available as a food source for house mice.

From our simulation model it does not appear that house‐mouse populations can completely eat‐out beech seed reserves prior to germination in a year of large seedfall. ‘Masting’ behaviour in New Zealand native beech trees is therefore sufficient to satiate an eruptive population of an exotic mammalian omnivore, despite the lack of a long co‐evolutionary interaction.
Quantifying the impact of environmental factors on arthropod communities in agricultural landscapes across organizational levels and spatial scales
Authors: SCHWEIGER O. , MAELFAIT J. P. , VAN WINGERDEN W. , HENDRICKX F. , BILLETER R. , SPEELMANS M. , AUGENSTEIN I. , AUKEMA B. , AVIRON S. , BAILEY D. , BUKACEK R. , BUREL F. , DIEKÖTTER T. , DIRKSEN J. , FRENZEL M. , HERZOG F. , LIIRA J , ROUBALOVA M. , BUGTER R.
Published: October 2005

In landscapes influenced by anthropogenic activities, such as intensive agriculture, knowledge of the relative importance and interaction of environmental factors on the composition and function of local communities across a range of spatial scales is important for maintaining biodiversity.

We analysed five arthropod taxa covering a broad range of functional aspects (wild bees, true bugs, carabid beetles, hoverflies and spiders) in 24 landscapes (4 × 4 km) across seven European countries along gradients of both land‐use intensity and landscape structure. Species–environment relationships were examined in a hierarchical design of four main sets of environmental factors (country, land‐use intensity, landscape structure, local habitat properties) that covered three spatial scales (region, landscape, local) by means of hierarchical variability partitioning using partial canonical correspondence analyses.

Local community composition and the distribution of body size classes and trophic guilds were most affected by regional processes, which highly confounded landscape and local factors. After correcting for regional effects, factors at the landscape scale dominated over local habitat factors. Land‐use intensity explained most of the variability in species data, whereas landscape characteristics (especially connectivity) accounted for most of the variability in body size and trophic guilds.

Synthesis and applications.Our results suggest that management effort should be focused on land‐use intensity and habitat connectivity in order to enhance diversity in agricultural landscapes. Since these factors are largely independent, specific conservation programmes may be developed with regards to socio‐economic and agri‐environmental requirements. Changes in either of these factors will enhance diversity but will also result in specific effects on local communities related to dispersal ability and the resource use of species.
Effects of slash harvest on bryophytes and vascular plants in southern boreal forest clear‐cuts
Authors: ÅSTRÖM MARCUS , DYNESIUS MATS , HYLANDER KRISTOFFER , NILSSON CHRISTER
Published: October 2005

Slash harvesting from forests to provide bioenergy reduces the amount of woody debris in the managed forest landscape and changes the physical and chemical environment in clear‐cuts. We examined previously unstudied effects of commercial (i.e. non‐experimental) slash harvest on species composition and richness of liverworts, mosses and vascular plants. The results call for modification of commercial slash harvest practices.

Differences between conventionally harvested (i.e. slash left) and slash‐harvested stands were investigated 5–10 years after clear‐cutting through analysis of 28 paired stands, with one 0·1‐ha plot divided into five 0·02‐ha subplots in each stand.

The species composition of mosses and liverworts in 0·1‐ha plots was significantly affected by slash harvest, whereas the composition of vascular plant species was not.

The species richness of liverworts was significantly reduced by slash harvest in plots of both sizes, whereas moss richness was reduced only in 0·02‐ha plots. The loss of liverwort species was largest, with approximately one‐third of the species disappearing. The species richness of vascular plants was not significantly affected by slash harvest in either plot size.

Slash harvest reduced species richness of forest bryophytes and of bryophytes typically growing on organic substrates in open habitats. Species richness of non‐forest bryophytes on inorganic substrates remained unchanged.

Synthesis and applications. Our results show that slash harvest reduces shelter and woody substrates, which changes species composition and reduces species richness of liverworts and mosses in clear‐cuts. Increased mechanical disturbance that removes remnant vegetation and exposes mineral soil may also play a role. In order to conserve bryophytes, we advocate mitigation of adverse ecological effects through enhanced environmental care within slash‐harvested stands. Leaving more tree clusters, and creating and protecting large woody debris would be especially important in these stands, and would also improve the habitat for other organisms.
Effect of bur type and conditioning on the surface and interface of dentine
Authors: BARROS J. A. , MYAKI S. I. , NÖR J. E. , PETERS M. C.
Published: October 2005

summary  The purpose of this in vitro study was to evaluate the surface and resin–dentine interface characteristics of permanent tooth dentine cut with diamond or carbide burs and treated with phosphoric acid (PA) or an acidic conditioner. Labial surfaces of permanent incisors were prepared into dentine with high‐speed carbide or diamond burs and divided into two halves. Phosphoric acid 36% was applied on one half and non‐rinse conditioner (NRC) was applied on the other half. Ten randomly selected scanning electron microscopy (SEM) fields from each specimen (n = 15) were evaluated. Occlusal surfaces of third molars were divided in two halves for evaluation of the resin–dentine interface. The halves were randomly assigned to one of each conditioner and restored with Prime & Bond NT/Spectrum. Ten specimens were analysed by SEM to evaluate hybrid layer formation and interfacial seal. We observed that surfaces prepared with carbide bur presented less residual smear plugs (P < 0·05) than surfaces prepared with diamond burs. Surfaces conditioned with NRC, which is a smear layer modifier, presented more residual smear plugs than surfaces conditioned with PA (P < 0·05). Treatment with PA resulted in more sealed interfaces than specimens treated with NRC. Within the limitations of this study the results showed that carbide burs leave a surface that is more conducive to bonding than diamond burs.
The lamp effect of laser Doppler flowmetry on teeth
Authors: POLAT S. , ER K. , POLAT N. T.
Published: October 2005

summary  The aim of this study is to analyse the intra and extracoronal scattering of laser light. Twelve vital teeth from 12 volunteer individuals (aged 22–29 years) were used. The camera removing the charge coupled device's infrared cut filter was used for imaging the laser Doppler flowmetry light during pulpal blood flow measurement. When the obtained photos were analysed, it was seen that the laser beam caused the tooth to shine like a lamp and it also illuminated the tissues inside the mouth (tongue, lips, adjacent teeth, etc.). As a result, it was shown that when the necessary cautions were not taken, the laser could scatter all around the tissues surrounding the tooth. Because of the conductive characteristic of the fibre and the optical characteristics of the tooth, we think that the beam is inevitably scattered onto the tissues outside the pulp and together with the isolation of the gingiva, crown should be isolated, as well.
The prevalence of temporomandibular disorders in patients with psoriasis with or without psoriatic arthritis
Authors: DERVIS E. , DERVIS E.
Published: October 2005

summary  Psoriasis is a chronic, genetic, non‐contagious skin disorder that appears in many different forms and can affect any part of the body, including the nails and scalp. It may affect the quality of life by causing psychosocial stress. Psoriatic arthritis (PA) is considered to be a spondyloarthropathy, and has spinal and peripheral joint involvement associated with psoriasis. The purpose of this study was to evaluate the prevalence of signs and symptoms of temporomandibular disorders (TMD) in patients with psoriasis without PA and in patients with PA and compare with a healthy group. Signs and symptoms of TMD were evaluated by means of Helkimo's Anamnestic (Ai) and Dysfunction indices (Di). In the present study, patients with psoriasis without arthritis did not report TMD signs and symptoms significantly more often than healthy subjects. A statistically significant increase was found in patients with PA when compared with psoriasis patients without arthritis and healthy patients in Di. In patients with PA, muscle tenderness on palpation, temporomandibular joint sounds and stiffness/tiredness in jaws in the morning were the most frequent findings. It is concluded that the signs and symptoms of TMD in PA is caused mainly by related joint involvement that directly affects the masticatory system.
Evolutionary history of the European whitefishCoregonus lavaretus(L.) species complex as inferred from mtDNA phylogeography and gill‐raker numbers
Authors: ØSTBYE K. , BERNATCHEZ L. , NÆSJE T. F. , HIMBERG K.‐J. M. , HINDAR K.
Published: October 2005

We compared mitochondrial DNA and gill‐raker number variation in populations of the European whitefishCoregonus lavaretus(L.) species complex to illuminate their evolutionary history, and discuss mechanisms behind diversification. Using single‐strand conformation polymorphism (SSCP) and sequencing 528 bp of combined parts of the cytochrome oxidaseb(cytb) and NADH dehydrogenase subunit 3 (ND3) mithochondrial DNA (mtDNA) regions, we documented phylogeographic relationships among populations and phylogeny of mtDNA haplotypes. Demographic events behind geographical distribution of haplotypes were inferred using nested clade analysis (NCA) and mismatch distribution. Concordance between operational taxonomical groups, based on gill‐raker numbers, and mtDNA patterns was tested. Three major mtDNA clades were resolved in Europe: a North European clade from northwest Russia to Denmark, a Siberian clade from the Arctic Sea to southwest Norway, and a South European clade from Denmark to the European Alps, reflecting occupation in different glacial refugia. Demographic events inferred from NCA were isolation by distance, range expansion, and fragmentation. Mismatch analysis suggested that clades which colonized Fennoscandia and the Alps expanded in population size 24 500–5800 years before present, with minute female effective population sizes, implying small founder populations during colonization. Gill‐raker counts did not commensurate with hierarchical mtDNA clades, and poorly with haplotypes, suggesting recent origin of gill‐raker variation. Whitefish designations based on gill‐raker numbers were not associated with ancient clades. Lack of congruence in morphology and evolutionary lineages implies that the taxonomy of this species complex should be reconsidered.
The colonization of Europe by the freshwater crustaceanAsellus aquaticus(Crustacea: Isopoda) proceeded from ancient refugia and was directed by habitat connectivity
Authors: VEROVNIK R. , SKET B. , TRONTELJ P.
Published: October 2005

Recent continental‐scale phylogeographic studies have demonstrated that not all freshwater fauna colonized Europe from the classic Mediterranean peninsular refugia, and that northern or central parts of the continent were occupied before, and remained inhabited throughout the Pleistocene. The colonization history of the ubiquitous aquatic isopod crustaceanAsellus aquaticuswas assessed using mitochondrial COI and a variable part of nuclear 28S rDNA sequences. Phylogeographic analysis of the former suggested that dispersion proceeded possibly during late Miocene from the western part of the Pannonian basin. Several areas colonized from here have served as secondary refugia and/or origins of dispersion, well before the beginning of the Pleistocene. Postglacial large‐scale range expansion was coupled with numerous separate local dispersions from different refugial areas. Connectivity of the freshwater habitat has played an important role in shaping the current distribution of genetic diversity, which was highest in large rivers. The importance of hydrographic connections for the maintenance of genetic contact was underscored by a discordant pattern of mtDNA and nuclear rDNA differentiation. Individuals from all over Europe, differing in their mtDNA to a level normally found between species or even genera (maximal within population nucleotide divergence reached 0.16 ± 0.018), shared the same 28S rRNA gene sequence. Only populations from hydrographically isolated karst water systems in the northwestern Dinaric Karst had distinct 28S sequences. Here isolation seemed to be strong enough to prevent homogenization of the rRNA gene family, whereas across the rest of Europe genetic contact was sufficient for concerted evolution to act.
Water flow through junctions in Douglas‐fir roots
Authors: SCHULTE PAUL J.
Published: October 2005

Roots are important conduits for the redistribution of water within the rooting zone. Root systems are often highly branched, and water flow between regions undoubtedly involves passage through junctions between individual roots. This study considered junctions in the roots of Douglas‐fir with regard to the resistances encountered by water flow through the xylem. Flow into the root branch distally along the main root encountered much greater resistance than flow into the branch and proximally along the main root (toward the plant stem). When the main root proximal to the junction was gradually shortened, the resistance to flow in the branch root and distally along the main root increased dramatically. Thus, flow in this manner appears to depend on lateral flow within the root over many centimetres proximal to the junction and not just within the direct connection at the junction. These results suggest that the hydraulic nature of junctions is an important aspect of hydraulic redistribution of water within the soil utilizing flow through roots.
Assessment of frequency, transmission, and genitourinary complications of enterobiasis (pinworms)
Authors: Burkhart Craig N. , Burkhart Craig G.
Published: October 2005

Background  Pinworms are the most common helminth infection in the USA and Western Europe, with prevalence rates in some communities of as high as 30–50%. Pinworms generally live in the gastrointestinal tract, and helminth infestations have been noted in over one‐quarter of acute appendectomies on histologic examination.

Results & Conclusions  Although transmission is often attributed to the ingestion of infective eggs by nail biting and inadequate hand washing, inhalation and ingestion of airborne eggs also occur. The female Enterobius vermicularis migrates nightly to the perianal area to deposit her eggs, but some worms find their way into adjacent orifices, most commonly the female genitourinary tract, producing an array of symptoms. More consideration of this entity is justified in patients presenting with genitourinary complaints not responding to normal therapies. In the treatment of pinworms affecting genitourinary organs, treatment with possibly two oral agents, namely mebendazole and ivermectin, and a topical therapy for the eggs may be warranted.
Iatrogenic Mycobacterium abscessus infection associated with acupuncture: clinical manifestations and its treatment
Authors: Ryu Hwa Jung , Kim Woo Joo , Oh Chil Hwan , Song Hae Jun
Published: October 2005

Background  Mycobacterial infections transmitted by acupuncture are an emerging problem. There have been two reports of mycobacterial infections complicating acupuncture in the English literature.

Aim  To describe the clinical manifestations and treatment of patients who acquired localized Mycobacterium abscessus infection in the process of acupuncture.

Methods  Clinical manifestations and responses to different methods of treatment were reviewed in 40 patients who developed various skin lesions after acupuncture at a Korean oriental medicine clinic.

Results  The morphology of the lesions which developed at the acupuncture sites varied. Although the lesions disappeared with the combined administration of clarithromycin and amikacin for 3 months in most cases, five out of 25 patients (20%) showed residual lesions at the end of treatment, and had to be treated with a higher dosage of clarithromycin or alternative antibiotics based on sensitivity tests.

Conclusions  We recommend at least 3 months of treatment with clarithromycin for treating skin infections caused by M. abscessus, with supplementary antibiotics selected based on patients’ drug sensitivity tests.
A case of pemphigus vulgaris accompanied by multiple myeloma
Authors: Kurokawa Motoki , Koketsu Hideki , Oda Yujiro , Nagamine Hidehiro , Toyama Takanori , Hashimoto Takashi , Setoyama Mitsuru
Published: October 2005

Pemphigus is a mucocutaneous intraepithelial blistering disease caused by autoantibodies to epithelial cell adhesion molecules (desmoglein). The association between pemphigus and malignant neoplasm is well recognized. We present the case of a 62‐year‐old woman with pemphigus vulgaris accompanied by multiple myeloma. To the best of our knowledge, this is the first report of a case of pemphigus vulgaris concomitant with multiple myeloma. From the results of immunoblotting using normal human epidermal extracts and indirect immunofluorescence using rat bladder sections, and her clinical manifestations, our case does not seem to be one of paraneoplastic pemphigus.
Anti‐agalactosyl immunoglobulin G antibodies in localized scleroderma
Authors: Mimra Yoshihiro , Ihn Hronobu , Jinnin Masatoshi , Asano Yoshihide , Yamane Kenichi , Yazawa N , Tamaki Kunihiko
Published: October 2005

Background  Anti‐agalactosyl immunoglobulin G (IgG) antibodies (anti‐AG IgG) have been reported to be detected and correlated with disease activity in some collagen diseases.

Method  Forty‐seven serum samples from patients with localized scleroderma were examined using an enzyme‐linked immunosorbent assay.

Results  Anti‐AG IgG were positive in 19% of patients with localized scleroderma. The frequency of anti‐AG IgG in generalized morphea was much higher than that in linear scleroderma or that in morphea. There was a significant correlation between anti‐AG IgG levels and the number of the sclerotic lesions and between anti‐AG IgG levels and the number of involved areas. The levels of anti‐AG IgG were significantly higher in patients with antinuclear antibody, antisingle‐stranded DNA antibody or rheumatoid factor than in those without.

Conclusion  Anti‐AG IgG can be an indicator of the severity of localized scleroderma.
Prevalence of asthma, allergic rhinoconjunctivitis and allergic sensitization in Mongolia
Authors: Viinanen A. , Munhbayarlah S. , Zevgee T. , Narantsetseg L. , Naidansuren Ts. , Koskenvuo M. , Helenius H. , Terho E. O.
Published: October 2005

Background:  Studies in countries, such as Mongolia, which are in transition from farming to industrial society permit evaluation of the impact of environmental change on atopic diseases.

Methods:  In the screening study, questionnaire data were obtained from 9453 subjects aged 10–60 years. In the clinical study, a subsample of 869 subjects (participation rate 50.0%) was examined. A questionnaire‐based interview, clinical examination, skin prick tests, spirometry and bronchodilation test or methacholine challenge test were used to define the clinical diagnoses. The prevalences of atopic diseases were evaluated at the population level using two‐phase data and sampling weights.

Results:  The prevalences of asthma, allergic rhinoconjunctivitis and allergic sensitization with 95% confidence intervals were 1.1% (0.3–2.0%), 9.3% (4.0–14.6%) and 13.6% (7.4–19.9%) in Mongolian villages, 2.4% (1.4–3.5%), 12.9% (8.2–17.7%) and 25.3% (17.1–33.6%) in rural towns and 2.1% (1.3–3.0%), 18.4% (13.3–23.4%) and 31.0% (24.5–37.5%) in Ulaanbaatar city, respectively. The prevalence of allergic rhinoconjunctivitis (P = 0.02) and allergic sensitization (P = 0.003) increased significantly with increasing urbanization.

Conclusions:  The prevalences of atopic diseases were low in rural Mongolia and increased with increasing urbanization suggesting that rural living environment protects against atopy.
Effect of suplatast tosilate on goblet cell metaplasia in patients with asthma
Authors: Hoshino M. , Fujita Y. , Saji J. , Inoue T. , Nakagawa T. , Miyazawa T.
Published: October 2005

Background:  Goblet cell metaplasia is a pathologic characteristic of asthma, associated with excess mucus secretion. Interleukin (IL)‐4 and IL‐13 plays an important role in mucus hypersecretion. Suplatast tosilate (suplatast), an antiallergic agent, is a Th2 cytokine inhibitor that suppresses the synthesis of IL‐4, IL‐5, IL‐13, and eosinophilic airway inflammation.

Objective:  We examined the effects of suplatast on mucus production in bronchial biopsy specimens taken from asthmatic subjects.

Methods:  Oral suplatast 300 mg daily, or placebo was administered for 3 months in a double‐blind, parallel‐group study in 25 patients with asthma. Biopsy specimens were evaluated at before and after treatment for alcian blue/period acid‐Schiff (AB/PAS), MUC5AC staining in bronchial epithelium and IL‐4+, IL‐13+ cells as well as inflammatory cells in lamina propria.

Results:  There were significant decreases in the percentage of AB/PAS (P < 0.01) and MUC5AC (P < 0.01) stained area in the suplatast group. These changes were accompanied by significant decreases in IL‐4+ and IL‐13+ cells in suplatast‐treated subjects. Additionally, we have observed that the number of infiltrating eosinophils and CD4+ T cells significantly decreased.

Conclusions:  These findings suggest that suplatast prevents goblet cell metaplasia through modulation of Th2 cytokine production and the recruitment of eosinophils and CD4+ T cells in the asthmatic airways.
Exaled nitric oxide and air trapping correlation in asthmatic children
Authors: Mappa L. , Cardinale F. , Camodeca R. , Tortorella M. L. , Pietrobelli A. , Armenio L. , Boner A. L.
Published: October 2005

Exhaled nitric oxide (eNO) levels have been shown to correlate with atopy and with airway hyperresponsiveness but not with standard spirometry. The aim of our study was to evaluate the correlation between eNo levels and functional residual capacity (FRC), residual volume (RV), RV to total lung capacity (TLC) ratio, and pulmonary resistances in asthmatic children ages 6–13 years. Forty‐nine patients (35 males) were enrolled in the study. Nineteen of them were not receiving inhaled corticosteroids. The eNO levels were measured by chemiluminescence's analyzer and lung function study were performed by body box plethysmography. As expected, there was no correlation between eNO levels and forced vital capacity (FVC); forced expiratory volume in the first second (FEV1); mid respiratory flow between 25 and 75% of the vital capacity (MEF25‐‐75), FEV1/FVC, and pulmonary resistances. Instead a correlation was found between eNO level and RV both considering all the study population together (r = 0.51, P = 0.001) and separately the asthmatic children not receiving ICS (r = 0.6, P = 0.003). In the patients receiving ICS the correlation was still present (r = 0.43, P = 0.01). The correlation between eNo levels and RV may reflect the effect of airway inflammation on NO production and diffusion as well as peripheral airway trapping and consequent RV.