bluuebunny/crossref_metadata_2025 huggingface dataset:
Choosing BLAST options for better detection of orthologs as reciprocal best hits
Authors: Moreno-Hagelsieb Gabriel , Latimer Kristen
Published: November 2007

Motivation: The analyses of the increasing number of genome sequences requires shortcuts for the detection of orthologs, such as Reciprocal Best Hits (RBH), where orthologs are assumed if two genes each in a different genome find each other as the best hit in the other genome. Two BLAST options seem to affect alignment scores the most, and thus the choice of a best hit: the filtering of low information sequence segments and the algorithm used to produce the final alignment. Thus, we decided to test whether such options would help better detect orthologs.

Results: Using Escherichia coli K12 as an example, we compared the number and quality of orthologs detected as RBH. We tested four different conditions derived from two options: filtering of low-information segments, hard (default) versus soft; and alignment algorithm, default (based on matching words) versus Smith–Waterman. All options resulted in significant differences in the number of orthologs detected, with the highest numbers obtained with the combination of soft filtering with Smith–Waterman alignments. We compared these results with those of Reciprocal Shortest Distances (RSD), supposed to be superior to RBH because it uses an evolutionary measure of distance, rather than BLAST statistics, to rank homologs and thus detect orthologs. RSD barely increased the number of orthologs detected over those found with RBH. Error estimates, based on analyses of conservation of gene order, found small differences in the quality of orthologs detected using RBH. However, RSD showed the highest error rates. Thus, RSD have no advantages over RBH.

Availability: Orthologs detected as Reciprocal Best Hits using soft masking and Smith–Waterman alignments can be downloaded from http://popolvuh.wlu.ca/Orthologs.

Contact:  gmoreno@wlu.ca
Agency and Change: Berlioz in Britain, 1870–1920
Authors: Langley Leanne
Published: November 2007

Far from being always unjustly neglected until the late twentieth century, as a recent view would have it, Berlioz's music enjoyed dedicated attention and considerable admiration a century earlier. His orchestral works, in particular, were taken up by a range of skilful players and conductors in Britain from the 1870s, yielding performances in the English regions, the London suburbs and in Scotland that impressed ordinary listeners much more than many experienced ones. I argue that structural change and professional competition within the British concert industry to 1920 assisted this remarkable reception – largely ignored in the historiography of Berlioz's reputation as well as in that of British musical culture – while imaginative musicians, astute promoters, writers and thousands of listeners continued to benefit from contact with his work. Berlioz's challenging music indeed became an agent of aesthetic change in Britain – a benchmark, and a calling-card, of modern orchestral presentation that was both standard and commonly accessible before the First World War.
Islands in the sea: extreme female natal site fidelity in the Australian sea lion,Neophoca cinerea
Authors: Campbell R.A , Gales N.J , Lento G.M , Baker C.S
Published: November 2007

Pinnipeds (seals, fur seals, sea lions and walrus) form large breeding aggregations with females often remaining faithful to a natal site or area. In these cases, females are philopatric to regional areas on broad geographical scales of hundreds to thousands of kilometres. An investigation of variation in a control region sequence of mtDNA in the Australian sea lion (Neophoca cinerea) has shown a case of extreme female natal site fidelity that has resulted in almost fixed population differentiation across its range (ΦST=0.93). This high level of population subdivision over short geographical distances (approx. 60 km) is unparalleled in any social marine mammal and reflects the unique life-history traits of this rare species. The high level of population subdivision and exclusive female natal site fidelity has important ramifications for conservation management, and poses many interesting questions of both academic and applied interest.
Filling the gap between identified neuroblasts and neurons in crustaceans adds new support for Tetraconata
Authors: Ungerer Petra , Scholtz Gerhard
Published: November 2007

The complex spatio-temporal patterns of development and anatomy of nervous systems play a key role in our understanding of arthropod evolution. However, the degree of resolution of neural processes is not always detailed enough to claim homology between arthropod groups. One example is neural precursors and their progeny in crustaceans and insects. Pioneer neurons of crustaceans and insects show some similarities that indicate homology. In contrast, the differentiation of insect and crustacean neuroblasts (NBs) shows profound differences and their homology is controversial. ForDrosophilaand grasshoppers, the complete lineage of several NBs up to formation of pioneer neurons is known. Apart from data on median NBs no comparable results exist for Crustacea. Accordingly, it is not clear where the crustacean pioneer neurons come from and whether there are NBs lateral to the midline homologous to those of insects. To fill this gap, individual NBs in the ventral neuroectoderm of the crustaceanOrchestia cavimanawere labelledin vivowith a fluorescent dye. A partial neuroblast map was established and for the first time lineages from individual NBs to identified pioneer neurons were established in a crustacean. Our data strongly suggest homology of NBs and their lineages, providing further evidence for a close insect–crustacean relationship.
Functional flexibility of human cyclin‐dependent kinase‐2 and its evolutionary conservation
Authors: Bártová Iveta , Koča Jaroslav , Otyepka Michal
Published: November 2007

Cyclin‐dependent kinase 2 (CDK2) is the most thoroughly studied of the cyclin‐dependent kinases that regulate essential cellular processes, including the cell cycle, and it has become a model for studies of regulatory mechanisms at the molecular level. This contribution identifies flexible and rigid regions of CDK2 based on temperature B‐factors acquired from both X‐ray data and molecular dynamics simulations. In addition, the biological relevance of the identified flexible regions and their motions is explored using information from the essential dynamics analysis related to conformational changes of CDK2 and knowledge of its biological function(s). The conserved regions of CMGC protein kinases' primary sequences are located in the most rigid regions identified in our analyses, with the sole exception of the absolutely conserved G13 in the tip of the glycine‐rich loop. The conserved rigid regions are important for nucleotide binding, catalysis, and substrate recognition. In contrast, the most flexible regions correlate with those where large conformational changes occur during CDK2 regulation processes. The rigid regions flank and form a rigid skeleton for the flexible regions, which appear to provide the plasticity required for CDK2 regulation. Unlike the rigid regions (which as mentioned are highly conserved) no evidence of evolutionary conservation was found for the flexible regions.
Unsuspected osteomyelitis is frequent in persistent diabetic foot ulcer and better diagnosed by MRI than by 18F‐FDG PET or 99mTc‐MOAB
Authors: Schwegler B. , Stumpe K. D. M. , Weishaupt D. , Strobel K. , Spinas G. A. , Von Schulthess G. K. , Hodler J. , Böni T. , Donath M. Y.
Published: November 2007

Aim.  Prevalence, optimal diagnostic approach and consequences of clinically unsuspected osteomyelitis in diabetic foot ulcers are unclear. Early diagnosis of this infection may be crucial to ensure correct management.

Methods.  We conducted a prospective study in 20 diabetic patients with a chronic foot ulcer (>8 weeks) without antibiotic pretreatment and without clinical signs for osteomyelitis to assess the prevalence of clinically unsuspected osteomyelitis and to compare the value of magnetic resonance imaging (MRI), 18F‐fluorodeoxyglucose positron emission tomography (18F‐FDG PET) and 99mTc‐labelled monoclonal antigranulocyte antibody scintigraphy (99mTc‐MOAB). Those with suggestive scans underwent bone biopsy for histology (n = 7).

Results.  Osteomyelitis was confirmed by biopsy in seven of the 20 clinically unsuspected foot ulcers. Presence of osteomyelitis was not related to age, ulcer size, ulcer duration, duration of diabetes or HbA1c. C‐reactive protein was slightly elevated in patients with osteomyelitis (35.1 ± 16.0 mg L−1 vs. 12.2 ± 2.6 mg L−1 in patients with and without osteomyelitis respectively; P = 0.07). MRI was positive in six of the seven patients with proven osteomyelitis, whereas 18F‐FDG PET and 99mTc‐MOAB were positive only in (the same) two patients. Of the seven patients with osteomyelitis, five had lower limb amputation and in one patient the ulcer was persisting after 24 months of follow‐up. In contrast, of the 13 patients without detectable signs of osteomyelitis on imaging modalities only two had lower limb amputation and two persisting ulcers.

Conclusions.  Clinically unsuspected osteomyelitis is frequent in persisting foot ulcers and is a high risk factor for adverse outcome. MRI appears superior to 18F‐FDG PET and 99mTc‐MOAB in detecting foot ulcer‐associated osteomyelitis and might be the preferred imaging modality in patients with nonhealing diabetic foot ulcers.
Social semantics: how useful has group selection been?
Authors: WEST S. A. , GRIFFIN A. S. , GARDNER A.
Published: November 2007

In our social semantics review (J. Evol. Biol., 2007, 415–432), we discussed some of the misconceptions and sources of confusion associated with group selection. Wilson (2007, this issue) claims that we made three errors regarding group selection. Here, we aim to expand upon the relevant points from our review in order to refute this claim. The last 45 years of research provide clear evidence of the relative use of the kin and group selection approaches. Kin selection methodologies are more tractable, allowing the construction of models that can be applied more easily to specific biological examples, including those chosen by Wilson to illustrate the utility of the group selection approach. In contrast, the group selection approach is not only less useful, but also appears to frequently have negative consequences by fostering confusion that leads to wasted effort. More generally, kin selection theory allows the construction of a unified conceptual overview that can be applied across all taxa, whereas there is no formal theory of group selection.
Orthotopic transplantation of immortalized mesencephalic progenitors (CSM14.1 cells) into the substantia nigra of hemiparkinsonian rats induces neuronal differentiation and motoric improvement
Authors: Haas Stefan Jean‐Pierre , Petrov Stanislav , Kronenberg Golo , Schmitt Oliver , Wree Andreas
Published: November 2007

Neural progenitor cell grafting is a promising therapeutic option in the treatment of Parkinson's disease. In previous experiments we grafted temperature‐sensitive immortalized CSM14.1 cells, derived from the ventral mesencephalon of E14‐rats, bilaterally in the caudate putamen of adult hemiparkinsonian rats. In these studies we were not able to demonstrate either a therapeutic improvement or neuronal differentiation of transplanted cells. Here we examined whether CSM14.1 cells grafted bilaterally orthotopically in the substantia nigra of hemiparkinsonian rats have the potential to differentiate into dopaminergic neurons. Adult male rats received 6‐hydroxydopamine into the right medial forebrain bundle, and successful lesions were evaluated with apomorphine‐induced rotations 12 days after surgery. Two weeks after a successful lesion the animals received bilateral intranigral grafts consisting of either about 50 000 PKH26‐labelled undifferentiated CSM14.1 cells (n = 16) or a sham‐graft (n = 9). Rotations were evaluated 3, 6, 9 and 12 weeks post‐grafting. Animals were finally perfused with 4% paraformaldehyde. Cryoprotected brain slices were prepared for immunohistochemistry using the freeze‐thaw technique to preserve PKH26‐labelling. Slices were immunostained against neuronal epitopes (NeuN, tyrosine hydroxylase) or glial fibrillary acidic protein. The CSM14.1‐cell grafts significantly reduced the apomorphine‐induced rotations 12 weeks post‐grafting compared to the sham‐grafts (P < 0.05). There was an extensive mediolateral migration (400–700 µm) of the PKH26‐labelled cells within the host substantia nigra. Colocalization with NeuN or glial fibrillary acidic protein in transplanted cells was confirmed with confocal microscopy. No tyrosine hydroxylase‐immunoreactive grafted cells were detectable. The therapeutic effect of the CSM14.1 cells could be explained either by their glial cell‐derived neurotrophic factor‐expression or their neural differentiation with positive effects on the basal ganglia neuronal networks.
Reduced calcium‐dependent mitochondrial damage underlies the reduced vulnerability of excitotoxicity‐tolerant hippocampal neurons
Authors: Pivovarova Natalia B. , Stanika Ruslan I. , Watts Charlotte A. , Brantner Christine A. , Smith Carolyn L. , Andrews S. Brian
Published: November 2007

J. Neurochem.(2008)104,1686–1699.

In central neurons, over‐stimulation of NMDA receptors leads to excessive mitochondrial calcium accumulation and damage, which is a critical step in excitotoxic death. This raises the possibility that low susceptibility to calcium overload‐induced mitochondrial damage might characterize excitotoxicity‐resistant neurons. In this study, we have exploited two complementary models of preconditioning‐induced excitotoxicity resistance to demonstrate reduced calcium‐dependent mitochondrial damage in NMDA‐tolerant hippocampal neurons. We have further identified adaptations in mitochondrial calcium handling that account for enhanced mitochondrial integrity. In both models, enhanced tolerance was associated with improved preservation of mitochondrial membrane potential and structure. In the first model, which exhibited modest neuroprotection, mitochondria‐dependent calcium deregulation was delayed, even though cytosolic and mitochondrial calcium loads were quantitatively unchanged, indicating that enhanced mitochondrial calcium capacity accounts for reduced injury. In contrast, the second model, which exhibited strong neuroprotection, displayed further delayed calcium deregulation and reduced mitochondrial damage because downregulation of NMDA receptor surface expression depressed calcium loading. Reducing calcium entry also modified the chemical composition of the calcium‐buffering precipitates that form in calcium‐loaded mitochondria. It thus appears that reduced mitochondrial calcium loading is a major factor underlying the robust neuroprotection seen in highly tolerant cells.
Proteolysis of multiple myelin basic protein isoforms after neurotrauma: characterization by mass spectrometry
Authors: Ottens Andrew K. , Golden Erin C. , Bustamante Liliana , Hayes Ronald L. , Denslow Nancy D. , Wang Kevin K. W.
Published: November 2007

Neurotrauma, as in the case of traumatic brain injury, promotes protease over‐activation characterized by the select fragmentation of brain proteins. The resulting polypeptides are indicators of biochemical processes, which can be used to study post‐injury dynamics and may also be developed into biomarkers. To this end, we devised a novel mass spectrometry approach to characterize post‐injury calpain proteolytic processing of myelin basic protein (MBP), a biomarker of brain injury that denotes white matter damage and recovery. Our approach exceeds conventional immunological assays in its deconvolution of multiple protein isoforms, its absolute quantification of proteolytic fragments and its polypeptide selectivity. We quantified and characterized post‐injury proteolytic processing of all MBP isoforms identified in adult rat cortex. Further, the translation of calpain‐cleaved MBP into CSF was verified following brain injury. We ascertained that the exon‐6 sequence of MBP resulted in a characteristic shift in gel migration for intact and fragmented protein alike. We also found evidence for a second post‐TBI cleavage event within exon‐2 and for the dimerization of the post‐TBI 4.3 kDa fragment. Ultimately, the novel methodology described here can be used to study MBP dynamics and other similar proteolytic events of relevance to brain injury and other CNS processes.
The effects of deer browsing on woodland structure and songbirds in lowland Britain
Authors: GILL ROBIN M. A. , FULLER ROBERT J.
Published: November 2007

The effects of deer in woodlands are known to result in habitat changes which can be detrimental to songbirds. In the first part of the paper we review the effects that deer may have on critical resources for woodland birds. The principal mechanism by which deer may affect habitat quality is through the reduction of low woody vegetation, which forms a key element of the preferred habitat of several species – this may be associated with loss of nest‐sites, increased exposure to predators and reduction of food. The second part of the paper presents new evidence for the impacts of deer on vegetation structure, and how they may be contributing to the declines of some woodland songbirds in Britain. Results from extensive studies of deer at 13 woodland sites in England and Wales reveal that understorey foliage density decreases significantly with increasing deer density. Reduction of foliage was greatest at below 1.5 m above ground. We also report preliminary results of an experimental comparison of songbird densities between deer‐fenced and unfenced areas of young coppice woodland in eastern England. In this study, deer browsing caused extensive impacts on vegetation structure in young coppice, though there was considerable variation between plots. Deer browsing resulted in reduction of canopy cover, reduction in density and cover of understorey vegetation, and an increase in grass cover. Abundance of bird species using the understorey, including all migrants, was significantly higher in coppice where deer were excluded. These results lend support to the hypothesis that deer are at least partly responsible for causing declines in some British bird populations, but they do not eliminate the possibility that increased shading is also responsible for changes in woodland structure. At present there is much spatial variation in deer densities in Britain so that impacts on low vegetation and habitat quality for birds are not expected to be the same in all regions. However, with continuing increases in deer numbers it is to be expected that such impacts will become more widespread.
Self‐Regulation, Ego Depletion, and Motivation
Authors: Baumeister Roy F. , Vohs Kathleen D.
Published: November 2007

Motivation is underappreciated in self‐regulation theories (as is true in social personality psychology at large). This paper reviews the role of motivation in the context of the strength, or limited‐resource, model of self‐control in several domains. Sacrificing one desire in order to pursue another is more difficult when the incipient response is strongly motivated, a notion that highlights the struggle between urges and restraints. A reduction in ego resources can be temporarily overcome by strong motivation – nevertheless, ego depletion is not solely a loss of motivation: Recent experiments indicate that regulatory resources are rooted in physical energy stores. Motivational conflicts, especially the clash between selfish motives and behaviors that promote social acceptance, set the stage for the necessity of self‐regulation and the circumstances in which ego depletion is most likely.
Quantifying a within-lake gradient of wave energy in Gillfillan Lake, Nova Scotia
Authors: Keddy Paul A.
Published: November 2007

The zonation patterns of shoreline plants vary greatly within lakes and exposure to waves may be an important cause of this variation. The principal objective of this study was to find a method for ranking lakeshores from low to high exposure. Two methods for ranking were tried. The first was simply the percent of the substrate composed of silt and clay and the second was calculated based on fetch values from aerial photographs and wind data from a nearby weather station. Field data were collected from 30 points chosen at random along the shoreline of Gillfillan Lake in Yarmouth County, Nova Scotia. Each was sampled for the proportion of silt and clay in the substrate and the zone widths occupied by shoreline plants. Exposure values were calculated for all 30 points, using 16 different methods of calculation. The proportion of silt and clay in the substrate was negatively correlated with exposure, whichever method of calculation was used. Principal components analysis was then used to summarize the zonation patterns of 64 plant species. The positions of transects on the first principal component (PC1, 18.7% of variation) were not correlated with any measure of exposure; they appear to reflect two types of glacial till found in Gillfillan Lake. The positions of transects on PC2 and PC3 (12.9 and 9.6% of the variation, respectively) were strongly correlated with the percent of the substrate consisting of silt and clay but not significantly with the calculated exposure measure. Thus percent silt and clay is a more appropriate axis for gradient analysis of zonation patterns. Species such as Calamagrostis canadensis, Carex stricto, and Pontederia cordata had zone widths which were negatively correlated with exposure, whereas the widths of the zones occupied by Aster novi-belgii, Agrostis perennans, and Aster tradescanti were positively correlated with exposure. While exposure affects the zonation patterns of some species, these patterns are apparently superimposed upon those produced by different types of glacial till.
Changes of protein patterns in winter rye following cold acclimation and desiccation stress
Authors: Cloutier Y.
Published: November 2007

A comparative study on the electrophoretic patterns of proteins from rye protoplasts has been carried out using a two-dimensional electrophoretic gel system. Rye was cold hardened by cold acclimation or desiccation stress. The two treatments did not induce similar protein pattern changes indicating different metabolic and physiological responses of the cell to these two stresses. A protein band with an apparent molecular weight of 46 000 increased upon hardening by both treatments and was correlated to freezing tolerance. Proteins in this band may play a role in the expression of freezing tolerance of the cell.
SOME ASPECTS OF GOLD–GOLD COLLISIONS AT RHIC AT $\sqrt{s_{NN}} = 200~{\rm GeV}$ AND A VERSION OF THE SEQUENTIAL CHAIN MODEL
Authors: GUPTAROY P. , DE BHASKAR , SAU GOUTAM , BISWAS S. K. , BHATTACHARYYA S.
Published: November 2007

Experimental studies on gold–gold collisions at RHIC at [Formula: see text] have produced a vast amount of data and results to be analyzed in the light of various competing models in the domain of multiparticle production scenario. We have chosen to analyze here the measured data on the pT-spectra of various light and nonstrange secondaries and some of their very important ratio-behaviors at the various centralities of the collision in the light of a version of the sequential chain model. The agreements between measured data and theoretical plots are found to be modestly satisfactory.
Sharing common ground: Nery Delgado (1835–1908) in Spain in 1878
Authors: Carneiro A.
Published: November 2007

The Geological Survey of Portugal (Comissão dos Serviços Geológicos), was created in 1857, as a section of the Geodesic Division of the Ministry of Public Works, Trade and Industry. It benefited greatly from the workings of the ministry, which in trying to modernize the country was concerned to keep up with the latest technical and scientific developments occurring elsewhere in Europe. Since its foundation, the Geological Survey of Portugal showed a clear drive towards its participation in an international scientific dialogue and cooperation. This strategy encompassed subscription to specialized foreign books and journals; intense correspondence with foreign specialists; the regular publication of monographs and memoirs in French; occasional or permanent collaboration with foreign experts; and travelling. The main outcome of the ‘travel of negotiation’ undertaken in 1878 to Spain by the Portuguese geologist J. F. Nery Delgado, then adjunct to the Director of the Portuguese Geological Survey, in addition to improving relationships with the geologists of the neighbouring country, was the collection of field data that was useful for the geological characterization of the southern Portuguese regions. He was also able to negotiate and look for data which could persuade his Spanish colleagues to subscribe to interpretations consistent with the Portuguese geological map, published in 1876.
Théodore Andre Monod and the lost
Fer de Dieu
meteorite of Chinguetti, Mauritania
Authors: Marvin U. B.
Published: November 2007

Théodore Monod (1902–2000), of the Muséum National d'Histoire Naturelle in Paris, was a natural scientist with an extraordinarily wide range of interests and expertise. His early researches were chiefly in marine zoology, which he continued to pursue throughout his career. However, in 1923 he began to work in the Sahara Desert and travelled through it for thousands of kilometres on foot and camel-back collecting samples for the museum and keeping detailed journals of the geology, palaeontology, flora, fauna, prehistoric artefacts, and the customs and cultures of the peoples he met. Monod published nearly 700 technical articles in scientific journals and numerous books for general readers. He won innumerable honours in France and internationally, but only one of his books, few of his articles, and no biographical accounts of Monod's activities have been published in English. This paper focuses on his search for the
Fer de Dieu
, an iron meteorite said to be 40 metres high and 100 metres long, lying in the desert of Mauritania. He found no trace of it, but the meteorite remains legendary in the history of meteoritics.
The geological travels of Sir Charles Lyell in Madeira and the Canary Islands, 1853–1854
Authors: WILSON L. G.
Published: November 2007

Throughout his life, Lyell travelled extensively, always as a keen observer. He viewed the Earth's geological history as continuous with and subject to the same processes of change as at present. Leopold von Buch's theory of craters of elevation contradicted Lyell's view of Earth history. Thus Lyell travelled to Madeira and the Canary Islands in 1853 to see von Buch's evidence. Lyell found the islands formed by a long series of volcanic eruptions, not by the single explosive upheaval that von Buch had described. Nevertheless, Lyell still accepted Léonce Élie de Beaumont's claim that lava flows could not form compact rock on steep slopes. In 1855, Lyell learned from Eilhard Mitscherlich that on Stromboli contemporary steeply inclined lava flows were forming solid rock. In 1857, Lyell went to Sicily where unmistakable evidence contradicted Élie de Beaumont. In the walls of the Valle del Bove, steeply inclined layers of lava were intersected by dykes that pointed towards a former centre of eruption at Trifoglietto, later buried by volcanic rocks emitted from the present centre of eruption at the summit of Etna, proving that the Valle del Bove could not have originated as a crater of elevation.
Two Tyrrells cross the Barren Lands of Canada, 1893
Authors: Spalding D. A. E.
Published: November 2007

In May 1893 Joseph and James Tyrrell, sons of an Irish immigrant to Canada, left Edmonton in Canada's Northwest Territories with a group of voyageurs, partly aided by an aboriginal map and First Nations guides. By January 1894 the team had reached Winnipeg, Manitoba, completing the first expedition through the last large unexplored area of the mainland of Canada. The travellers suffered from many dangers, and the expedition was more than three months overdue when its members arrived at York Factory.

Some specimens were lost, but records and photographs acquired on the expedition form an important record of northern exploration. Joe Tyrrell identified the Keewatin centre of glaciation, and the post-glacial extension of the Hudson Bay basin is now known as the Tyrrell Sea. There was criticism at the apparent lack of economic benefit, but Tyrrell located iron ore and a possible copper-bearing area, and his work led indirectly to a productive nickel mine and the present working of diamonds. Tyrrell also documented the huge caribou herds, and the lives of the Inuit that depended on them.
In the footsteps of Thomas Livingstone Mitchell (1792–1855): soldier, surveyor, explorer, geologist, and probably the first person to compile geological maps in Australia
Authors: Oldroyd D.
Published: November 2007

The Scotsman, Thomas Mitchell, was one of Australia's leading pioneers and explorers. Trained as a military surveyor, he travelled to Sydney in 1827, and was soon in charge of the mapping of New South Wales, an important position as it was vital to get the new colony surveyed, so that land could be apportioned correctly and fairly. In addition, Mitchell had responsibility for laying out the plans for the early road system of New South Wales, in which work he displayed excellent judgement, selecting a viable route for a road across the Blue Mountains, and directing the construction work. But Mitchell also had ambitions to be a proper explorer and to make original scientific contributions. He undertook four major expeditions, and later wrote them up in what are now classics of early Australian geographical writing. His Department's masterly ‘Nineteen Counties’ topographic map of the Sydney region and its hinterland, produced in 1834, was a milestone for the development of NSW. Mitchell had no formal training in geology, but on learning that he was to take up an appointment in NSW he rapidly made the acquaintance of London geologists and acquired the rudiments of the subject. While in the field in 1834, he was fortunate to be an early visitor to Wellington Caves, west of the Blue Mountains, where he excavated, collected, and dispatched many new mammalian specimens to experts in Britain. These attracted great interest in Edinburgh, London, and Paris, where the study of cave remains had been attracting attention for several years. Also in 1834, Mitchell coloured the outcrops of the main rock types of the Sydney region onto his ‘Nineteen Counties’ map, thus producing what was probably the first geological map of any part of Australia. This is reproduced here in colour for the first time. His later, published, geological maps of the Wellington area and a locality near Bathurst are also reproduced. The paper discusses the possible sources of information for the 1834 map. Mitchell wrote up his Wellington observations and submitted them to the Geological Society of London, but only an abstract was published and the full paper was refused publication (for unknown reasons). He eventually wrote up his findings, with illustrations, in a book describing his explorations (1838); but following his ‘rejection’ he did little further work in geology other than a hasty examination of a goldfield near Bathurst at the time of the NSW gold rush (1852). The present paper seeks to give a comprehensive account of Mitchell's geological work, which was an important adjunct to his career as a ‘traveller/explorer’ and cartographer.
Nineteenth-century observations of the Dun Mountain Ophiolite Belt, Nelson, New Zealand and trans-Tasman correlations
Authors: Johnston M. R.
Published: November 2007

The Nelson Mineral Belt, part of the Dun Mountain Ophiolite Belt of Permian age, in the north of the South Island of New Zealand, was the subject of intense interest soon after the European settlement of New Zealand owing to the discovery of copper and chromite mineralization. The first geologist to survey the Mineral Belt in east Nelson was Thomas Ridge Hacket (
c
. 1830–1884), who arrived from Britain in 1857, although he was primarily interested in the mineralization. The first scientific description of the belt followed the visit in 1859 of the geologist Ferdinand von Hochstetter (1829–1884) of the Austrian Geological Survey who regarded the belt as a sill. He recognized that Dun Mountain was not serpentinite, like the rest of the belt, but an olivine-rich rock that he named dunite. von Hochstetter tentatively considered that thick mafic rocks of the Brook Street Volcanics, that were then considered to be intrusives rather than sedimentary, may have been a correlative of the Mineral Belt. Between the belt and the Brook Street rocks he mapped the Wooded Peak Limestone and Maitai Slates. von Hochstetter tentatively assigned a Mesozoic age to all of the above rocks and for nearly 100 years Mesozoic sedimentary rocks in many parts of New Zealand were regarded as a correlative of the Maitai Slates.

Both Hacket and von Hochstetter confirmed an abundance of chromite in the Mineral Belt, a finding that resulted in the building of New Zealand's first railway. Mining was short-lived but hopes were raised that gold might be found following Hacket's move to Queensland in the late 1860s. He recognized that the Gympie gold-fields had many similarities with Dun Mountain and reasoned that east Nelson might also be auriferous. This was taken up by men in Nelson such as Sir David Monro (1813–1877) and William Wells (1810–1893) who were keen geological observers, and by Monro's son in law Dr, later Sir James, Hector (1834–1907) who was director of the New Zealand Geological Survey. In 1870, Hector arranged for Edward Heydelbach Davis (1845–1871) to undertake a detailed examination of the Permo-Triassic rocks of east Nelson. Davis, like Hacket, regarded the Mineral Belt as metamorphosed Maitai rocks. As well as demonstrating that the east Nelson rocks did not contain economic concentrations of gold, copper or chromite, Davis showed that they were distinct from what had been thought to be similar rocks in the Coromandel gold-fields in North Island of New Zealand. This was the first, if not fully appreciated, step to limit the Maitai rocks. Hacket's correlation of the Gympie and Dun Mountain rocks was forgotten until the advent of plate tectonics. The various major rock units in Nelson are now recognized as terranes that accumulated as a result of convergent plate tectonics along the Mesozoic margin of Gondwanaland.
Writing, ‘inscription’ and fact: eighteenth century mineralogical books based on travels in the Habsburg regions, the Carpathian Mountains
Authors: Klemun M.
Published: November 2007

In the second half of the eighteenth century there was an explosion in travel literature in the German-speaking countries. Travel literature became an important medium for broadening of people's horizons. When transferring travel experiences into the written word the traveller had a wealth of literary forms at their disposal: the diary, the letter, the narrative structured according to the chronology of the journey. Moreover, topography, ‘statistics’ in the contemporary sense and ‘apodemics’ (the art of travelling) as a professional basis for travelling offered the potential for a scientific approach. The scientific interest in ‘mineralogical’ journeys aimed at acquiring reliable empirical data, and required formal strategies to counter the superficiality and selectivity of fieldwork. The choice of one strategy of description, and that is the thesis presented here, is based on epistemological factors. This paper looks at three works of travel literature, in which the chosen form of writing correlates with the central scientific findings of the respective authors: Belsazar de la Motte Hacquet (1739–1815), Ignaz von Born (1742–1791) and Ehrenbert von Fichtel (1732–1795) all of whom wrote ‘mineralogical’ books based on extensive travelling in the eastern Habsburg territories.
Geological travellers in view of their philosophical and economical intentions: Johann Wolfgang von Goethe (1749–1832) and Caspar Maria Count Sternberg (1761–1838)
Authors: Schweizer C.
Published: November 2007

Two geological travellers, who clearly differ in their approach to scientific questions and their interpretation, are presented. Goethe was mainly interested in natural phenomenon and linking the interpretation of his observations in a deductive approach to a philosophically and psychologically influenced, more general view of natural mechanisms. Sternberg, on the other hand, chose an inductive approach in his conclusions from geological observations and never inclined to any philosophical explanations behind them. Goethe's natural philosophy behind his scientific concepts was strongly formed by Baruch de Spinoza (1632–1677) and led to his own subjective approach of interpreting scientific phenomena. However, Sternberg's knowledge of geognosy along the formations in the Habsburg region and in Germany is based on numerous observations at various locations and on the comparison of his findings, having a vast general knowledge on the geology of a wide area. Goethe and Sternberg's correspondence between 1820–1832 gives insight into the specific differences between these two travellers and their individual methods of geological investigation.
Efficacy of Salbutamol and Ipratropium Bromide in the Management of Acute Bronchiolitis – A Clinical Trial
Authors: Karadag Bulent , Ceran Omer , Guven Gulsah , Dursun Esengul , Ipek Ilke Ozahi , Karakoc Fazilet , Ersu Refika Hamutcu , Bozaykut Abdulkadir , Inan Savas , Dagli Elif
Published: November 2007

Background: A wide range of drugs are commonly used to treat bronchiolitis, but evidence of their effectiveness is limited. Objectives: To investigate the efficacy of ipratropium bromide and salbutamol in the treatment of patients with moderate-severe bronchiolitis. Methods: Sixty-nine infants with moderate-severe bronchiolitis hospitalized at their first episode of wheezing or crepitations in the chest were enrolled in a prospective, double-blind, placebo-controlled trial. Patients were randomly assigned to receive nebulized salbutamol, ipratropium bromide or placebo. Main outcome measures were changes in oxygen saturation rates and clinical scores and duration of hospitalization. Results: In the bronchodilator groups, clinical scores were better compared to the placebo group at 30 min (8.4 ± 1.3 vs. 7.5 ± 0.8, p < 0.05). Bronchodilator groups had also significantly lower clinical scores (7.3 ± 1.2 vs. 5.9 ± 1.1, p < 0.0001, and 5.3 ± 1.4 vs. 4.5 ± 1.6, p = 0.006, respectively) and higher oxygen saturation rates compared to the placebo group at 8 and 24 h (89.6 ± 2.4 vs. 94.3 ± 4.4, and 92.2 ± 2.6 vs. 95.9 ±4.4, respectively, p < 0.0001). Improvement rates and duration of hospitalization were not statistically different among groups. Conclusions: Clinical scores and oxygen saturation levels improved more rapidly in the bronchodilator groups than in the placebo group up to 24 h, but these drugs did not have a sufficient effect to change the natural course of the disease.
Potential Options to Optimize Therapy of Gastroesophageal Reflux Disease with Proton Pump Inhibitors
Authors: Tonini M. , Vigneri S. , Neri M. , Cuomo R. , Savarino V. , Pace F.
Published: November 2007

Proton pump inhibitors (PPIs) are antisecretory agents that are widely used in the short- and long-term management of gastroesophageal reflux disease (GERD) to relieve symptoms, heal esophagitis, and prevent complications, such as strictures and Barrett’s esophagus. The total healthcare costs of GERD are high, especially for maintenance treatment. Therefore, the choice of cost-effective therapeutic options is an ineluctable challenge for public health authorities, third-party payers, and patients. In some European Union countries, a recent trend of public health authorities is to promote the choice of less expensive PPIs, regardless of their antisecretory potency – this in spite of the evidence that newer PPIs provide superior symptom relief and esophageal erosion healing compared to earlier drugs. Several large clinical trials have demonstrated the superiority of esomeprazole over other PPIs at standard doses for both initial and continuous maintenance therapy in patients with moderate/severe erosive esophagitis. The non-erosive GERD poses a major challenge as this condition appears more frequently to be less responsive to PPIs. The use of PPIs with the strongest antisecretory properties might reveal to be more adequate and cost-effective, particularly for this indication.
Bayesian Model Comparison in Nonlinear BOLD fMRI Hemodynamics
Authors: Jacobsen Daniel J. , Hansen Lars Kai , Madsen Kristoffer Hougaard
Published: November 2007

Nonlinear hemodynamic models express the BOLD (blood oxygenation level dependent) signal as a nonlinear, parametric functional of the temporal sequence of local neural activity. Several models have been proposed for both the neural activity and the hemodynamics. We compare two such combined models: the original balloon model with a square-pulse neural model (Friston, Mechelli, Turner, & Price, 2000) and an extended balloon model with a more sophisticated neural model (Buxton, Uludag, Dubowitz, & Liu, 2004). We learn the parameters of both models using a Bayesian approach, where the distribution of the parameters conditioned on the data is estimated using Markov chain Monte Carlo techniques. Using a split-half resampling procedure (Strother, Anderson, & Hansen, 2002), we compare the generalization abilities of the models as well as their reproducibility, for both synthetic and real data, recorded from two different visual stimulation paradigms. The results show that the simple model is the better one for these data.
A Sensorimotor Approach to Sound Localization
Authors: Aytekin Murat , Moss Cynthia F. , Simon Jonathan Z.
Published: November 2007

Sound localization is known to be a complex phenomenon, combining multisensory information processing, experience-dependent plasticity, and movement. Here we present a sensorimotor model that addresses the question of how an organism could learn to localize sound sources without any a priori neural representation of its head-related transfer function or prior experience with auditory spatial information. We demonstrate quantitatively that the experience of the sensory consequences of its voluntary motor actions allows an organism to learn the spatial location of any sound source. Using examples from humans and echolocating bats, our model shows that a naive organism can learn the auditory space based solely on acoustic inputs and their relation to motor states.
Dynamics of Learning Near Singularities in Layered Networks
Authors: Wei Haikun , Zhang Jun , Cousseau Florent , Ozeki Tomoko , Amari Shun-ichi
Published: November 2007

We explicitly analyze the trajectories of learning near singularities in hierarchical networks, such as multilayer perceptrons and radial basis function networks, which include permutation symmetry of hidden nodes, and show their general properties. Such symmetry induces singularities in their parameter space, where the Fisher information matrix degenerates and odd learning behaviors, especially the existence of plateaus in gradient descent learning, arise due to the geometric structure of singularity. We plot dynamic vector fields to demonstrate the universal trajectories of learning near singularities. The singularity induces two types of plateaus, the on-singularity plateau and the near-singularity plateau, depending on the stability of the singularity and the initial parameters of learning. The results presented in this letter are universally applicable to a wide class of hierarchical models. Detailed stability analysis of the dynamics of learning in radial basis function networks and multilayer perceptrons will be presented in separate work.
Valuations for Spike Train Prediction
Authors: Itskov Vladimir , Curto Carina , Harris Kenneth D.
Published: November 2007

The ultimate product of an electrophysiology experiment is often a decision on which biological hypothesis or model best explains the observed data. We outline a paradigm designed for comparison of different models, which we refer to as spike train prediction. A key ingredient of this paradigm is a prediction quality valuation that estimates how close a predicted conditional intensity function is to an actual observed spike train. Although a valuation based on log likelihood (L) is most natural, it has various complications in this context. We propose that a quadratic valuation (Q) can be used as an alternative to L. Q shares some important theoretical properties with L, including consistency, and the two valuations perform similarly on simulated and experimental data. Moreover, Q is more robust than L, and optimization with Q can dramatically improve computational efficiency. We illustrate the utility of Q for comparing models of peer prediction, where it can be computed directly from cross-correlograms. Although Q does not have a straightforward probabilistic interpretation, Q is essentially given by Euclidean distance.
Population Coding with Motion Energy Filters: The Impact of Correlations
Authors: Klam F. , Zemel R. S. , Pouget A.
Published: November 2007

The codes obtained from the responses of large populations of neurons are known as population codes. Several studies have shown that the amount of information conveyed by such codes, and the format of this information, is highly dependent on the pattern of correlations. However, very little is known about the impact of response correlations (as found in actual cortical circuits) on neural coding. To address this problem, we investigated the properties of population codes obtained from motion energy filters, which provide one of the best models for motion selectivity in early visual areas. It is therefore likely that the correlations that arise among energy filters also arise among motion-selective neurons. We adopted an ideal observer approach to analyze filter responses to three sets of images: noisy sine gratings, random dots kinematograms, and images of natural scenes. We report that in our model, the structure of the population code varies with the type of image. We also show that for all sets of images, correlations convey a large fraction of the information: 40% to 90% of the total information. Moreover, ignoring those correlations when decoding leads to considerable information loss—from 50% to 93%, depending on the image type. Finally we show that it is important to consider a large population of motion energy filters in order to see the impact of correlations. Study of pairs of neurons, as is often done experimentally, can underestimate the effect of correlations.
Chaotic Frequency Scaling in a Coupled Oscillator Model for Free Rhythmic Actions
Authors: Raftery Aaron , Cusumano Joseph , Sternad Dagmar
Published: November 2007

The question of how best to model rhythmic movements at self-selected amplitude-frequency combinations, and their variability, is a long-standing issue. This study presents a systematic analysis of a coupled oscillator system that has successfully accounted for the experimental result that humans' preferred oscillation frequencies closely correspond to the linear resonance frequencies of the biomechanical limb systems, a phenomenon known as resonance tuning or frequency scaling. The dynamics of the coupled oscillator model is explored by numerical integration in different areas of its parameter space, where a period doubling route to chaotic dynamics is discovered. It is shown that even in the regions of the parameter space with chaotic solutions, the model still effectively scales to the biomechanical oscillator's natural frequency. Hence, there is a solution providing for frequency scaling in the presence of chaotic variability. The implications of these results for interpreting variability as fundamentally stochastic or chaotic are discussed.