bluuebunny/crossref_metadata_2025_split huggingface dataset:
Automated microscopy system for mosaic acquisition and processing
Authors: CHOW S. K. , HAKOZAKI H. , PRICE D. L. , MACLEAN N. A. B. , DEERINCK T. J. , BOUWER J. C. , MARTONE M. E. , PELTIER S. T. , ELLISMAN M. H. 
Published: June 2006

SummaryAn automatic mosaic acquisition and processing system for a multiphoton microscope is described for imaging large expanses of biological specimens at or near the resolution limit of light microscopy. In a mosaic, a larger image is created from a series of smaller images individually acquired systematically across a specimen. Mosaics allow wide‐field views of biological specimens to be acquired without sacrificing resolution, providing detailed views of biological specimens within context. The system is composed of a fast‐scanning, multiphoton, confocal microscope fitted with a motorized, high‐precision stage and custom‐developed software programs for automatic image acquisition, image normalization, image alignment and stitching. Our current capabilities allow us to acquire data sets comprised of thousands to tens of thousands of individual images per mosaic. The large number of individual images involved in creating a single mosaic necessitated software development to automate both the mosaic acquisition and processing steps. In this report, we describe the methods and challenges involved in the routine creation of very large scale mosaics from brain tissue labelled with multiple fluorescent probes.
Comparison of I5M and 4Pi‐microscopy
Authors: BEWERSDORF J. , SCHMIDT R. , HELL S. W. 
Published: June 2006

SummaryThe axial (z‐) resolution of ∼100 nm provided by 4Pi and I5M fluorescence microscopy relies on the coherent addition of spherical wavefronts of two opposing high aperture angle lenses. Both microscopes feature a point‐spread function (PSF) with a sharp central spot that is accompanied by axially shifted sidelobes which leads to replication artefacts in the raw image data. In a 4Pi‐microscope the sidelobes are less pronounced than in I5M and without relevant lateral (x,y) substructure, making their posterior removal in the image reliable and fast. On the other hand, high speeds of raw data acquisition are more easily gained by I5M. Moreover, I5M features a stronger signal as compared to the commonly employed two‐photon excitation (2PE) 4Pi‐imaging mode. We investigate here the capability of both techniques to image (aqueous) specimens without artefacts. To this end, we consider the optical transfer function (OTF) of the two microscopes in conjunction with the signal‐to‐noise‐ratio (SNR) of the object to be imaged. The imaging of E. coli bacteria with an interconvertable setup enabled a direct comparison of the two imaging modes. As both systems rely on high aperture angles, water‐immersion lenses of the largest numerical aperture available (NA = 1.2) were employed. The experimental results are corroborated by simulations assuming the signal strength encountered in the experiment. The comparison of the theoretical with the experimental PSFs/OTFs showed that our setup operated close to theory in both imaging modes. Although I5M provided about 10 times brighter raw image data as compared to (2PE) 4Pi‐microscopy, the I5M data could not be entirely cleared of artefacts. In conclusion, with the current aperture angles and fluorescence signal strengths, it is not advisable to trade in the suppression of the sidelobes for a larger image signal.
Epifluorescence, confocal and total internal reflection microscopy for single‐molecule experiments: a quantitative comparison
Authors: LANG E. , BAIER J. , KÖHLER J. 
Published: June 2006

SummaryEpifluorescence, confocal and total internal reflection microscopy are the most widely used techniques for optical single‐molecule experiments. Employing these methods, we recorded the emission intensity of the same single molecule as a function of the excitation rate under otherwise identical experimental conditions. Evaluation of these data provides a quantitative comparison of the signal‐to‐background ratios that can be achieved for the three microscopic techniques.
Phylogeography of the montane caddisfly Drusus discolor: evidence for multiple refugia and periglacial survival
Authors: PAULS STEFFEN U. , LUMBSCH H. THORSTEN , HAASE PETER 
Published: June 2006

AbstractWe studied the genetic population structure and phylogeography of the montane caddisfly Drusus discolor across its entire range in central and southern Europe. The species is restricted to mountain regions and exhibits an insular distribution across the major mountain ranges. Mitochondrial sequence data (COI) of 254 individuals from the entire species range is analysed to reveal population genetic structure. The data show little molecular variation within populations and regions, but distinct genetic differentiation between mountain ranges. Most populations are significantly differentiated based on FST and exact tests of population differentiation and most haplotypes are unique to a single mountain range. Phylogenetic analyses reveal deep divergence between geographically isolated lineages. Combined, these results suggest that past fragmentation is the prominent process structuring the populations across Europe. We use tests of selective neutrality and mismatch distributions, to study the demographic population history of regions with haplotype overlap. The high level of genetic differentiation between mountain ranges and estimates of demographic history provide evidence for the existence of multiple glacial refugia, including several in central Europe. The study shows that these aquatic organisms reacted differently to Pleistocene cooling than many terrestrial species. They persisted in numerous refugia over multiple glacial cycles, allowing many local endemic clades to form.
Geographic distribution of an extinct equid (Equus hydruntinus: Mammalia, Equidae) revealed by morphological and genetical analyses of fossils
Authors: ORLANDO LUDOVIC , MASHKOUR MARJAN , BURKE ARIANE , DOUADY CHRISTOPHE J. , EISENMANN VÉRA , HÄNNI CATHERINE 
Published: June 2006

AbstractEquus hydruntinusinhabited Europe and the Middle East for more than 300 000 years. For a long time, palaeontological data failed to placeE. hydruntinusinto the equid phylogenetic tree, confronted with the fact that it shares primitiveEquuscharacters with both zebras and asses, and derived characters with asses and hemiones. However, the study of a recently discovered skull points to a relationship with hemiones. Extraction of DNA from ancient samples from Crimea (E. hydruntinus) and Iran (E.cf.hydruntinus) yielded 134–288 bp of the mtDNA control region and 143 bp of the cytochromebgene. This DNA analysis supports the proximity ofE. hydruntinusandEquus hemionussuggested by skull and limb bone analyses, and rejects proximity to eitherEquus burchellior the asses suggested by tooth morphology. Dental morphology may thus be of poor taxonomical value if used alone for establishing equid phylogenetic relationships. Furthermore, the small genetic distance betweenE.cf.hydruntinusof Iran and the classicalE. hydruntinusof Crimea suggests that both samples belong to the same species. Accordingly, the geographic range ofE. hydruntinus— until now believed to be restricted to Europe, Israel, and Turkey — can be extended towards East as far as Iran.
Association of canine hypothyroidism with a common major histocompatibility complex DLA class II allele
Authors: Kennedy L. J. , Quarmby S. , Happ G. M. , Barnes A. , Ramsey I. K. , Dixon R. M. , Catchpole B. , Rusbridge C. , Graham P. A. , Hillbertz N. S. , Roethel C. , Dodds W. J. , Carmichael N. G. , Ollier W. E. R. 
Published: June 2006

AbstractDogs exhibit a range of immune‐mediated conditions including a lymphocytic thyroiditis which has many similarities to Hashimoto's thyroiditis in man. We have recently reported an association in Doberman Pinschers between canine hypothyroidism and a rare DLA class II haplotype that contains the DLA‐DQA1*00101 allele. We now report a further series of 173 hypothyroid dogs in a range of breeds where a significant association with DLA‐DQA1*00101 is shown.
Rat genotype influences quantitative and qualitative aspects of xenogeneic immune response to pig blood mononuclear cells
Authors: Bridle Byram W. , Wilkie Bruce N. , Jevnikar Anthony M. , Mallard Bonnie A. 
Published: June 2006

Abstract:  Background:  Xenotransplantation seeks to have cells with discordant genotypes co‐exist. The hypothesis that host genotype modulates xenogeneic immune response (IR) was tested.Methods:  Two inbred rat strains [Dark Agouti (DA) and Lewis (LEW)] representing diverse IR phenotypes were immunized with porcine blood mononuclear cells (BMC). Delayed‐type hypersensitivity (DTH), immunoglobulin (Ig), antibody (Ab) and isotype bias of Ab response were evaluated.Results:  DTH to pig BMC was greater in DA than in LEW rats. Natural Ab was qualitatively different between strains (IgM and IgA predominated in DA, IgM and IgG2a predominated in LEW). Twice as much IgG was elicited from DA than LEW rats and DA utilized all isotypes whereas LEW did not use IgG2a or IgG2c. IR bias was diametrically opposed; type 1 in DA but type 2 in LEW. Strains even differed in Ig profiles and dermal responses to saline injections and mitogen. The DA rats were the higher responders to pig BMC.Conclusions:  Recipient genotype had significant and broad effects on IR to porcine BMC and may influence xenograft rejection and xenotolerance induction. Moreover, this study suggests that caution should prevail when interpreting data derived from a single inbred strain, particularly given that humans, the target species, are genetically diverse.
Early up‐regulation of CXC‐chemokine expression is associated with strong cellular immune responses to murine skin xenografts
Authors: Lee Eun Mi , Park Joon Oh , Kim Donghee , Kim Jae Young , Oh Kook‐Hwan , Park Chung‐Gyu , Oh Byung Hee , Kim Suhnggwon , Ahn Curie 
Published: June 2006

Abstract:  Background:  The dynamic pattern of the cellular infiltration and mRNA expression of chemokines in rat‐to‐mouse skin xenografts were examined to gain an understanding of the possible role of chemokines in the stronger cellular immune responses to xenografts compared with the allo‐response.Methods:  The mean survival time of the xenografts was approximately 2 days less than that of allografts (10.7 ± 0.9 days vs. 8.9 ± 0.7 days, P < 0.05). In comparison with the allografts, the xenografts were characterized by a very early infiltration of monocytes/macrophages (day 3) and a larger number of CD4+ and CD8+ cells, as well as neutrophil infiltration in the early phase (day 5), and larger number of CD8+ and CD11b+ cells, as well as macrophage infiltration, in the later phase (day 7). Xenografts showed stronger interferon (IFN)‐inducible 10‐kDa protein (IP‐10) and monokine induced by IFN (MIG) mRNA expression levels, which appeared earlier than in the allografts. In the later phase, strong expression of regulated on activation, normal T cell expressed and secreted was observed. Cytokine mRNA expression in the xenografts could be summarized by higher expression of IFN‐γ, interleukin (IL)1β, IL6, and transforming growth factor ‐β1 mRNA than in the allografts. These results suggest that the early increased CXC‐chemokine expression, such as IP‐10 and MIG, which has been known to be mainly produced by macrophages, may play a critical role in the stronger cellular xenograft rejection compared with allograft rejection. Therefore, MIG antiserum or CXCR3 antiserum was administered to the rat skin‐engrafted mice every other day until rejection.Results:  Compared with the control normal rabbit serum‐treated mice, either the MIG antiserum‐ or CXCR3 antiserum‐treated mice showed a delayed rejection of approximately 2 days (8.3 ± 0.5 days vs. 10.6 ± 0.5 days or 10.8 ± 1.9 days, respectively, P < 0.05).Conclusion:  Overall, these results suggest that the more aggressive rejection of xenografts compared with allografts is due to the earlier expression of CXC‐chemokines, IP‐10 and MIG, and subsequent adjuvant effects of proinflammatory cytokines.
Has the evolution of complexity in the amphibian papilla influenced anuran speciation rates?
Authors: Richards C. L. 
Published: June 2006

Abstract
For anurans, increasing complexity of the inner ear has been correlated with speciation rates. The evolution of a complex amphibian papilla (AP) is thought to have facilitated speciation by extending the range of frequencies over which mating calls may diverge. Although this example has been proposed to represent a key innovation, the mechanism by which the AP is thought to promote speciation makes the questionable assumption that anurans generally use the AP for detection of their mating calls. This study uses mating calls from 852 species to test this assumption. Surprisingly, the calls of most species are not detected by the AP but by a second organ, the basilar papilla (BP). This refutes the role of AP complexity in facilitating call divergence and hence, speciation. Future research into the evolution of acoustically mediated reproductive isolation should focus instead on the BP as it may play a more critical role in anuran speciation.
Rampant host switching and multiple female body colour transitions in Philotrypesis (Hymenoptera: Chalcidoidea: Agaonidae)
Authors: Jiang Z. -F. , Huang D. -W. , Chen L.-L. , Zhen W. -Q. , Fu Y. -G. , Peng Z. -Q. 
Published: June 2006

Abstract
Figs (Ficus, Moraceae) and their associated fig waSPS (Hymenoptera, Chalcidoidea and Agaonidae) have attracted much attention and have been used as a model system for many studies. Fig waSPS belonging to the genus Philotrypesis are very common in most figs but their taxonomy, ecology and biology are currently poorly explored. A previous study on African Philotrypesis showed that their host association is phylogenetically conserved at subsection level. We reconstructed a molecular phylogeny with extended sampling from seven sections of figs. Our study suggested that the diversification of Philotrypesis is less constrained by host figs. Host switching is rampant between figs at species level and even at section level. We also investigated the evolution of the body colour forms in female Philotrypesis. Our study first suggested that female body colour is not evolutionarily stable and that there have been multiple transitions. Possible mechanisms for multiple colour transitions are expected to be determined in the near future.
Male Drosophila melanogaster have higher mating success when adapted to their thermal environment
Authors: Dolgin E. S. , Whitlock M. C. , Agrawal A. F. 
Published: June 2006

Abstract
Adaptation to new environments is a well-documented phenomenon. Individuals from populations maintained in a particular environment for multiple generations tend to be better able to survive and/or reproduce in that environment than their ancestors or other individuals adapted to alternative environments. A third major component of fitness, mating success, has not been well studied in replicated populations under selection in divergent environments. In this study, we used mating trials to compare the mating success of male Drosophila melanogaster adapted for 10 years to two different temperatures, 18 and 25°C. In competition for female partners, males had significantly higher mating success at their adapted temperature compared with males adapted to a different temperature. These results are consistent with the notion that those mutations favoured by natural selection also tend to be favoured by sexual selection.
Development of tinnitus‐related neuronal hyperactivity through homeostatic plasticity after hearing loss: a computational model
Authors: Schaette Roland , Kempter Richard 
Published: June 2006

AbstractTinnitus, the perception of a sound in the absence of acoustic stimulation, is often associated with hearing loss. Animal studies indicate that hearing loss through cochlear damage can lead to behavioral signs of tinnitus that are correlated with pathologically increased spontaneous firing rates, or hyperactivity, of neurons in the auditory pathway. Mechanisms that lead to the development of this hyperactivity, however, have remained unclear. We address this question by using a computational model of auditory nerve fibers and downstream auditory neurons. The key idea is that mean firing rates of these neurons are stabilized through a homeostatic plasticity mechanism. This homeostatic compensation can give rise to hyperactivity in the model neurons if the healthy ratio between mean and spontaneous firing rate of the auditory nerve is decreased, for example through a loss of outer hair cells or damage to hair cell stereocilia. Homeostasis can also amplify non‐auditory inputs, which then contribute to hyperactivity. Our computational model predicts how appropriate additional acoustic stimulation can reverse the development of such hyperactivity, which could provide a new basis for treatment strategies.
Chronic cocaine self‐administration is associated with altered functional activity in the temporal lobes of non human primates
Authors: Beveridge Thomas J. R. , Smith Hilary R. , Daunais James B. , Nader Michael A. , Porrino Linda J. 
Published: June 2006

AbstractPrevious studies utilizing a nonhuman primate model have shown that cocaine self‐administration in its initial stages is accompanied by alterations in functional activity largely within the prefrontal cortex and ventral striatum. Continued cocaine exposure may considerably change this response. The purpose of the present investigation was to characterize the effects of reinforcing doses of cocaine on cerebral metabolism in a nonhuman primate model of cocaine self‐administration, following an extended history of cocaine exposure, using the quantitative 2‐[14C]deoxyglucose (2‐DG) method. Rhesus monkeys were trained to self‐administer 0.03 mg/kg/injection (n = 4) or 0.3 mg/kg/injection (n = 4) cocaine and compared to monkeys trained to respond under an identical schedule of food reinforcement (n = 6). Monkeys received 30 reinforcers per session for a total of 100 sessions. Metabolic mapping was conducted at the end of the final session. After this extended history, cocaine self‐administration dose‐dependently reduced glucose utilization throughout the striatum and prefrontal cortex similarly to the initial stages of self‐administration. However, glucose utilization was also decreased in a dose‐independent manner in large portions of the temporal lobe including the amygdala, hippocampus and surrounding neocortex. The recruitment of temporal structures indicates that the pattern of changes in functional activity has undergone significant expansion beyond limbic regions into association areas that mediate higher order cognitive and emotional processing. These data strongly contribute to converging evidence from human studies demonstrating structural and functional abnormalities in temporal and prefrontal areas of cocaine abusers, and suggest that substance abusers may undergo progressive cognitive decline with continued exposure to cocaine.
Time is a rubberband: neuronal activity in monkey motor cortex in relation to time estimation
Authors: Renoult Louis , Roux Sébastien , Riehle Alexa 
Published: June 2006

AbstractAnticipation of predictable events is crucial for organizing motor performance. Using instructed delay tasks, it has been shown that even when delay duration is kept constant, reaction time fluctuates from trial to trial. As time estimation is at the core of anticipatory behavior, it is reasonable to speculate whether neuronal delay activity correlates with the subjective estimate of time. As a consequence of the scalar property of time estimation processes, the variability in time estimation increases continuously as time passes during the delay. This scalar property may then be reflected in the increasing variability in neuronal delay activity. We thus studied the influence of temporal prior information on neuronal delay activity in monkey motor cortex in two conceptually different tasks in which two equally probable delay durations were randomly presented. We hypothesized that if one considers the animal's subjective time as the time which elapses between the first (instruction) signal and movement onset, then, by suppressing this temporal variability, across‐trial variability in neuronal discharge should decrease. We thus defined a new time scale in each trial such that, after rescaling, the time between the instruction signal and movement onset was identical in all trials. Each spike was then displaced in time accordingly. As expected, the variability in the timing of neuronal peak discharges no longer increased during the trial. This suggests a direct link between the temporal profile of spiking activity and time estimation. The timing of motor cortical activity reflected the ‘elasticity’ of the animal's subjective time.
Galanin and galanin‐like peptide modulate neurite outgrowth via protein kinase C‐mediated activation of extracellular signal‐related kinase
Authors: Hawes Jessica J. , Narasimhaiah Roopashree , Picciotto Marina R. 
Published: June 2006

AbstractThe neuropeptide galanin is widely distributed in the central nervous system and plays a role in a number of processes in the adult brain. Galanin also has neurotrophic effects in the developing nervous system and after nerve injury. The current study investigated the mechanism by which galanin promotes neurite outgrowth in the neuronal cell line PC12 and in neurospheres derived from adult hippocampal progenitor cells. We demonstrated that galanin can induce extracellular signal‐related kinase (ERK) phosphorylation transiently in a concentration‐dependent manner in neurons. Galanin‐like peptide, which is thought to signal primarily through the GalR2 receptor subtype, induced ERK phosphorylation with similar kinetics to galanin. In functional studies, the ability of galanin and galanin‐like peptide to induce neurite outgrowth was dependent on activation of both protein kinase C and ERK. This study identified a novel physiological role for galanin‐induced ERK phosphorylation and identified ERK and protein kinase C as important signaling components in the galanin‐mediated modulation of neurite outgrowth.
Aquaporin 4 changes in rat brain with severe hydrocephalus
Authors: Mao Xiaoyan , Enno Terry L. , Del Bigio Marc R. 
Published: June 2006

AbstractHydrocephalus is characterized by impaired cerebrospinal fluid (CSF) flow with enlargement of the ventricular cavities of the brain and progressive damage to surrounding tissue. Bulk water movement is altered in these brains. We hypothesized that increased expression of aquaporins, which are water‐permeable channel proteins, would occur in these brains to facilitate water shifts. We used quantitative (real‐time) RT‐PCR, Western blotting and immunohistochemistry to evaluate the brain expression of aquaporins (AQP) 1, 4, and 9 mRNA and protein in Sprague–Dawley rats rendered hydrocephalic by injection of kaolin into cistern magna. AQP4 mRNA was significantly up‐regulated in parietal cerebrum and hippocampus 4 weeks and 9 months after induction of hydrocephalus (P < 0.05). Although Western blot analysis showed no significant change, there was more intense perivascular AQP4 immunoreactivity in cerebrum of hydrocephalic brains at 3–4 weeks after induction. We did not detect mRNA or protein changes in AQP1 (located in choroid plexus) or AQP9 (located in select neuron populations). Kir4.1, a potassium channel protein linked to water flux, exhibited enhanced immunoreactivity in the cerebral cortex of hydrocephalic rats; the perineuronal distribution was entirely different from that of AQP4. These results suggest that brain AQP4 up‐regulation might be a compensatory response to maintain water homeostasis in hydrocephalus.