bluuebunny/crossref_metadata_2025 huggingface dataset:
Comparison of QuantiFERON-TB Gold In-Tube Test and Tuberculin Skin Test for Identification of LatentMycobacterium tuberculosisInfection in Healthcare Staff and Association Between Positive Test Results and Known Risk Factors for Infection
Authors: Vinton Paul , Mihrshahi Seema , Johnson Paul , Jenkin Grant A. , Jolley Damien , Biggs Beverley-Ann
Published: February 2009

Objective.

We compared a whole-blood interferon-γ release assay (QuantiFERON-TB Gold In-Tube test, hereafter “QFT-in tube test”) with a tuberculin skin test (TST) to determine which test more accurately identified latentMycobacterium tuberculosisinfection in healthcare staff.

Methods.

A total of 481 hospital staff members were recruited from 5 hospitals in Melbourne, Australia. They provided information about demographic variables and tuberculosis (TB) risk factors (ie, birth or travel in a country with a high prevalence of TB, working in an occupation likely to involve contact withM. tuberculosisor individuals with TB, or being a household contact of an individual with a proven case of pulmonary TB). The QFT-in tube test and the TST were administered in accordance with standardized protocols. Concordance between the test results and positive risk factors was analyzed using theкstatistic, the McNemar test, and logistic regression.

Results.

A total of 358 participants had both a TST result and a QFT-in tube test result available for comparison. There were fewer positive QFT-in tube test results than positive TST results (6.7% vs. 33.0%;P< .001). Agreement between the tests was poor (71%;к= 0.16). A positive QFT-in tube test result was associated with birth in a country with a high prevalence of TB, the number of years an individual had lived in a country with a high prevalence of TB (ie, the effect of each additional year, treated as a continuous variable), and high-risk occupational contact. A positive TST result was associated with older age, receipt of bacille Calmette-Guérin (BCG) vaccination, and working in an occupation that involved patient contact. Receipt of BCG vaccination was most strongly associated with discordant results in instances in which the TST result was positive and the QFT-in tube test result was negative.

Conclusion.

In a population of healthcare staff with a low prevalence of TB and a significant rate of BCG vaccination, a positive QFT-in tube test result was associated with the presence of known risk factors for TB exposure, whereas a positive TST result was more strongly associated with a prior history of BCG vaccination.
Determination of error field sources by accurate mapping of the magnetic geometry of the H-1 heliac
Authors: Kumar Santhosh T.A. , Blackwell Boyd D. , Harris Jeffrey H.
Published: February 2009

High precision mapping of the vacuum flux surfaces of the H-1NF heliac is carried out using electron-beam multi-wire tomography for various magnetic configurations and field strengths. The extreme accuracy of this technique has been exploited to understand the nature of error fields and to determine the best-fit empirical values for the H-1NF coil parameters, by point-by-point matching experimental surface data with computer modelling results. This has helped in developing a highly accurate computer model for H-1NF magnetic configurations.
Codeposition of deuterium with ITER materials
Authors: Doerner R.P. , Baldwin M.J. , De Temmerman G. , Hanna J. , Nishijima D. , Roth J. , Schmid K. , Tynan G.R. , Umstadter K.
Published: February 2009

The levels of retention in codeposited layers of each of the three ITER materials (C, Be and W) are compared. Scaling laws, based on the conditions during the codeposition process (surface temperature, incident particle energy and ratio of the depositing fluxes), are presented to allow prediction of expected retention under ITER conditions. Retention in carbon codeposits scales inversely with incident particle energy, whereas in the metallic codeposits the retention level scales proportionally to increasing particle energy. The differing scaling of retention with incident particle energy provides insights into which material may impact the global retention in ITER depending on where it may form codeposits. In addition to the amount of retention, the release behaviour of tritium from codeposits will influence the tritium accumulation rate within ITER. The thermal release behaviour of T (or D) from codeposits can be used to evaluate the effectiveness of baking at different temperatures as a means of tritium removal. Finally, the desorption kinetics from Be and W codeposits are contrasted. In the case of W codeposits, the duration of the baking cycle is important in determining the removal efficiency, whereas with Be codeposited layers, the maximum achievable bake temperature plays the leading role in determining removal efficiency.
Geodesic excursions into an embedded disc on a hyperbolic Riemann surface
Authors: Haas Andrew
Published: February 2009

We calculate the asymptotic average rate at which a generic geodesic on a finite area hyperbolic

2
2

-orbifold returns to an embedded disc on the surface, as well as the average amount of time it spends in the disc during each visit. This includes the case where the center of the disc is a cone point.
Tessellation and Lyubich–Minsky laminations associated with quadratic maps, II: Topological structures of 3-laminations
Authors: Kawahira Tomoki
Published: February 2009

According to an analogy to quasi-Fuchsian groups, we investigate the topological and combinatorial structures of Lyubich and Minsky’s affine and hyperbolic33-laminations associated with hyperbolic and parabolic quadratic maps.

We begin by showing that hyperbolic rational maps in the same hyperbolic component have quasi-isometrically the same33-laminations. This gives a good reason to regard the main cardioid of the Mandelbrot set as an analogue of the Bers slices in the quasi-Fuchsian space. Then we describe the topological and combinatorial changes of laminations associated with hyperbolic-to-parabolic degenerations (and parabolic-to-hyperbolic bifurcations) of quadratic maps. For example, the differences between the structures of the quotient33-laminations of Douady’s rabbit, the Cauliflower, andz↦z2z \mapsto z^2are described.

The descriptions employ a new method oftessellationinside the filled Julia set introduced in Part I [Ergodic Theory Dynam. Systems29(2009), no. 2] that works like external rays outside the Julia set.
Accurate identification of orthologous segments among multiple genomes
Authors: Hachiya Tsuyoshi , Osana Yasunori , Popendorf Kris , Sakakibara Yasubumi
Published: February 2009

Motivation: The accurate detection of orthologous segments (also referred to as syntenic segments) plays a key role in comparative genomics, as it is useful for inferring genome rearrangement scenarios and computing whole-genome alignments. Although a number of algorithms for detecting orthologous segments have been proposed, none of them contain a framework for optimizing their parameter values.

Methods: In the present study, we propose an algorithm, named OSfinder (Orthologous Segment finder), which uses a novel scoring scheme based on stochastic models. OSfinder takes as input the positions of short homologous regions (also referred to as anchors) and explicitly discriminates orthologous anchors from non-orthologous anchors by using Markov chain models which represent respective geometric distributions of lengths of orthologous and non-orthologous anchors. Such stochastic modeling makes it possible to optimize parameter values by maximizing the likelihood of the input dataset, and to automate the setting of the optimal parameter values.

Results: We validated the accuracies of orthology-mapping algorithms on the basis of their consistency with the orthology annotation of genes. Our evaluation tests using mammalian and bacterial genomes demonstrated that OSfinder shows higher accuracy than previous algorithms.

Availability: The OSfinder software was implemented as a C++ program. The software is freely available at http://osfinder.dna.bio.keio.ac.jp under the GNU General Public License.

Contact:  hacchy@dna.bio.keio.ac.jp

Supplementary information:  Supplementary data are available at Bioinformatics online.
High-performance gene name normalization with GeNo
Authors: Wermter Joachim , Tomanek Katrin , Hahn Udo
Published: February 2009

Motivation: The recognition and normalization of textual mentions of gene and protein names is both particularly important and challenging. Its importance lies in the fact that they constitute the crucial conceptual entities in biomedicine. Their recognition and normalization remains a challenging task because of widespread gene name ambiguities within species, across species, with common English words and with medical sublanguage terms.

Results: We present GeNo, a highly competitive system for gene name normalization, which obtains an F-measure performance of 86.4% (precision: 87.8%, recall: 85.0%) on the BioCreAtIvE-II test set, thus being on a par with the best system on that task. Our system tackles the complex gene normalization problem by employing a carefully crafted suite of symbolic and statistical methods, and by fully relying on publicly available software and data resources, including extensive background knowledge based on semantic profiling. A major goal of our work is to present GeNo's architecture in a lucid and perspicuous way to pave the way to full reproducibility of our results.

Availability: GeNo, including its underlying resources, will be available from www.julielab.de. It is also currently deployed in the Semedico search engine at www.semedico.org.

Contact:  joachim.wermter@uni-jena.de
Square-mesh codend circumference and selectivity
Authors: Broadhurst Matt K. , Millar Russell B.
Published: February 2009

Broadhurst, M. K., and Millar, R. B. 2009. Square-mesh codend circumference and selectivity. – ICES Journal of Marine Science, 66: 566–572. Despite the wide-scale assessment and the use of square-mesh codends in demersal trawls, relatively few studies have tested the effects of configurations other than mesh size on their selectivity. We investigated the consequences of increasing the circumference of square-mesh codends used in an Australian penaeid fishery from the expected optimal configuration of ∼33% of maximum diamond-mesh extension to ∼56 and 75%. Three square-mesh designs comprised 27-mm polyamide mesh throughout and had the same length (100 bars, B), but different circumferences (90, 150, and 200 B, respectively). Paired simultaneous comparisons (using twin trawls) of each treatment codend against a small-meshed control revealed significant effects of circumference on the efficiency of the trawl for a small teleost (pink-breasted siphonfish, Siphamia roseigaster) and commercial size classes of school prawns (Metapenaeus macleayi). Compared with the 90 codend, pink-breasted siphonfish catches and prawn count (numbers per 500 g) were both significantly greater in the codends of larger circumference, and these effects are attributed to concomitant (i) convoluted or reduced lateral openings of meshes and (ii) lesser probabilities of organisms encountering meshes in the posterior section. These differences would not preclude the use of codends of larger circumference in the fishery, but they do highlight the need to select appropriate configurations in future studies to reduce the potential for including the confounding effects of different geometries.
Bomb dating and age determination of skates (family Rajidae) off the eastern coast of Canada
Authors: McPhie Romney P. , Campana Steven E.
Published: February 2009

McPhie, R. P., and Campana, S. E. 2009. Bomb dating and age determination of skates (family Rajidae) off the eastern coast of Canada. – ICES Journal of Marine Science, 66: 546–560. Recent declines in abundance of skates off the eastern coast of Canada have heightened the need for validated age and growth estimates in the region. In all, 502 winter (Leucoraja ocellata), little (Leucoraja erinacea), thorny (Amblyraja radiata), and smooth (Malacoraja senta) skate vertebral centra collected seasonally between 1999 and 2004 were sectioned using a mass processing method, then used to reconstruct growth in each species. Bomb radiocarbon (Δ14C) analysis was used to provide evidence of annual band-pair deposition in thorny skates. Estimates of L∞ from traditional von Bertalanffy growth models (VBGM) ranged from 60.6 cm (little skate) to 89.7 cm (thorny skate), and K estimates from 0.07 (thorny skate) to 0.19 (little skate). A modified two-parameter VBGM (Lmax = 94.1 cm) fitted to winter skate length-at-age data yielded a value of K of 0.15. Maximum observed ages ranged from 12 (little skate) to 19 years in both winter and thorny skates. The year-specific incorporation of Δ14C milled from thorny and winter skate vertebral sections closely resembled shark-derived reference chronology values from the Northwest Atlantic. Pre-bomb Δ14C in a thorny skate collected in 1988 and aged at 23 years appeared to validate age interpretations and suggested that thorny skate reach an absolute age of at least 28 years, the oldest validated age reported for any species of batoid.
Kernel methods for the detection and classification of fish schools in single-beam and multibeam acoustic data
Authors: Buelens Bart , Pauly Tim , Williams Raymond , Sale Arthur
Published: February 2009

Buelens, B., Pauly, T., Williams, R., and Sale, A. 2009. Kernel methods for the detection and classification of fish schools in single-beam and multibeam acoustic data. – ICES Journal of Marine Science, 66: 1130–1135. A kernel method for clustering acoustic data from single-beam echosounder and multibeam sonar is presented. The algorithm is used to detect fish schools and to classify acoustic data into clusters of similar acoustic properties. In a preprocessing routine, data from single-beam echosounder and multibeam sonar are transformed into an abstracted representation by multidimensional nodes, which are datapoints with spatial, temporal, and acoustic features as components. Kernel methods combine these components to determine clusters based on joint spatial, temporal, and acoustic similarities. These clusters yield a classification of the data in groups of similar nodes. Including the spatial components results in clusters for each school and effectively detects fish schools. Ignoring the spatial components yields a classification according to acoustic similarities, corresponding to classes of different species or age groups. The method is described and two case studies are presented.
On the target strength of Baltic clupeids
Authors: Fässler Sascha M. M. , Gorska Natalia
Published: February 2009

Fässler, S. M. M., and Gorska, N. 2009. On the target strength of Baltic clupeids. – ICES Journal of Marine Science, 66: 1184–1190. The acoustic backscattering of Baltic clupeids, herring and sprat, is explored to improve biomass estimation of these ecologically and commercially important species. Modelling approaches that account for the complexity of fish morphology are used to compute the mean backscattering cross section. The input data for modelling are based on X-ray radiographs of Baltic herring and sprat. The backscatter sensitivity to fish morphology and to other biological (fat content), acoustic (frequency), behavioural (orientation pattern), and environmental (depth and salinity) parameters is also analysed. The effect of various parameters on the TS–L relationship of Baltic clupeids is studied, and the possibility of using the same TS–L relationships for Baltic herring and sprat is discussed. The results improve the understanding of the spatial and temporal variability of the measured target strength of clupeids in the Baltic Sea.
Management of Transplant House Spread of Acidovorax avenae subsp. citrulli on Cucurbits with Bactericidal Chemicals in Irrigation Water
Authors: Hopkins Donald L. , Thompson Constance M. , Lovic Branko
Published: February 2009

Bacterial fruit blotch (BFB), caused by Acidovorax avenae subsp. citrulli, is a seed-borne disease of cucurbits that spreads rapidly in the warm, humid environment of the transplant house, often resulting in high numbers of infected plants going into the field. The only control options for BFB once it gets into a transplant house are crop destruction or multiple applications of a copper-containing bactericide/fungicide. In this study, various treatments were compared with the standard foliar spray application of cupric hydroxide for BFB control under transplant house conditions. Peroxyacetic acid at 80 μg/ml and ionized copper at 1.0 and 1.5 μg/ml applied through the daily irrigation water were more effective than cupric hydroxide in reducing spread of A. avenae subsp. citrulli. Combining ionized copper or peroxyacetic acid in the irrigation water with a weekly foliar application of acibenzolar-S-methyl was most effective in reducing spread. The utilization of these transplant house treatments along with the elimination of all transplants with symptoms or near plants with symptoms should greatly reduce the chances of introducing BFB into fields on transplants.

Accepted for publication 14 November 2008. Published 29 January 2009.
CAPS Analysis: A Possible Tool to Detect and Group Geminiviruses Infecting Some Fibre Crops and Weeds
Authors: Chatterjee Arpita , Roy Anirban , Ghosh Subrata K.
Published: February 2009

Some fibre crops and weeds, showing typical symptoms caused by begomoviruses, were subjected to PCR amplification using different sets of primers specific for DNA A and DNA β molecules of begomoviruses. Restriction digestion of full length DNA A and DNA β using different enzymes revealed variation in restriction profiles amongst the virus isolates in the present study. Moreover, variation in the restriction profile of different DNA β molecule with that of their corresponding reported sequences were also noticed. Cleaved amplified polymorphic sequence (CAPS) analysis of DNA β revealed little or no genetic distance between the begomoviruses infecting Sida acuminata and S. rhombifolia and also among the begomoviruses infecting Urena, Hibiscus cannabinus, and H. sabdariffa. But the same analysis with full length DNA A showed close phylogenetic relationships between begomoviruses infecting H. cannabinus and H. sabdariffa. Hence, for wide spread variation and unavailability of any sequence information CAP analysis might be a useful tool to detect and group begomoviruses.

Accepted for publication 9 October 2008. Published 2 February 2009.
Negative (and very low) thermal expansion in ReO3from 5 to 300 K
Authors: Dapiaggi Monica , Fitch Andy N.
Published: February 2009

This paper reports the accurate measurement of the ReO3cell parameter as a function of temperature. The thermal expansion is confirmed to be negative over most of the temperature range from 5 to 300 K. The main problems with the measurements are the very small variations (in the range of 10−5 Å) in the cell parameter at each temperature, requiring tight control of the stability and reliability of instrumental effects. In particular, achieving monochromator stability over time might be challenging with the high energy and high beam current variations of a third-generation synchrotron facility. On the other hand, such effects are usually checked by the addition of silicon as an internal standard, but the accuracy (and precision) of the published thermal expansion (which is not certified) might not be sufficient for its use when dealing with very small cell parameter variations.
Phase relations in the Ba–Sr–Co–Fe–O system at 1273 K in air
Authors: Yáng Zhèn , Harvey Ashley S. , Infortuna Anna , Gauckler Ludwig J.
Published: February 2009

Selected compositions of the Ba–Sr–Co–Fe–O system were synthesized from powders by the solid-state reaction method. Samples were equilibrated at 1273 K for 36 000 s in air. The resulting powders were characterized by X-ray diffraction (XRD) at room temperature and by high-temperaturein situXRD. The phases present in the BaxSr1−xCoyFe1−yO3−δsystem are outlined for 1273 K in air. For most of the quaternary compositions, the cubic perovskite is formed, except for the compositions withx= 1 (excludingy= 0.4),y= 1 andx,y= 0.8, where the phases mainly show hexagonal distortions, andx, y= 0, for which a predominant cubic phase is mixed with other phases.
Irena: tool suite for modeling and analysis of small-angle scattering
Authors: Ilavsky Jan , Jemian Peter R.
Published: February 2009

Irena, a tool suite for analysis of both X-ray and neutron small-angle scattering (SAS) data within the commercialIgor Proapplication, brings together a comprehensive suite of tools useful for investigations in materials science, physics, chemistry, polymer science and other fields. In addition to Guinier and Porod fits, the suite combines a variety of advanced SAS data evaluation tools for the modeling of size distribution in the dilute limit using maximum entropy and other methods, dilute limit small-angle scattering from multiple non-interacting populations of scatterers, the pair-distance distribution function, a unified fit, the Debye–Bueche model, the reflectivity (X-ray and neutron) using Parratt's formalism, and small-angle diffraction. There are also a number of support tools, such as a data import/export tool supporting a broad sampling of common data formats, a data modification tool, a presentation-quality graphics tool optimized for small-angle scattering data, and a neutron and X-ray scattering contrast calculator. These tools are brought together into one suite with consistent interfaces and functionality. The suite allows robust automated note recording and saving of parameters during export.
Behaviour and performance of juvenile shortnose sturgeon Acipenser brevirostrum at different water velocities
Authors: Kieffer J. D. , Arsenault L. M. , Litvak M. K.
Published: February 2009

Critical swimming speeds (mean ±s.e.) for juvenile shortnose sturgeon Acipenser brevirostrum were 34·4 cm s−1± 1·7 (2·18 ± 0·09 body lengths, BL s−1). Swimming challenges at 10, 20 and 30 cm s−1 revealed that juvenile A. brevirostrum are relatively poor swimmers, and that the fish did not significantly modify their swimming behaviour, although they spent more time substratum skimming (i.e. contact with flume floor) at 30 cm s−1 relative to 10 cm s−1. When present, these behavioural responses are probably related to morphological features, such as flattened rostrum, large pectoral fins, flattened body shape and heterocercal tail, and may be important to reduce the costs of swimming.
Morphology–diet relationships in four killifishes (Teleostei, Cyprinodontidae,Orestias) from Lake Titicaca
Authors: Maldonado E. , Hubert N. , Sagnes P. , De MÉrona B.
Published: February 2009

This study explores the relationship between morphology and diet in four Andean killifishes (Orestias) from Lake Titicaca that are known to differ in habitat use. Species that fed preferentially on amphipods (Orestias albus) or molluscs (Orestias luteus) separated in multivariate space from other species that feed on cladocera and algae (Orestias agassiiandOrestias jussiei). Generally, specimens feeding on cladocera were characterized by a short, blunt nose with a small mouth; whereas, specimens feeding on amphipods exhibited a long snout with a large mouth. Specimens including molluscs in their diet tended to have a larger posterior part of the head and the larger opercles than others; while the occurrence of substratum in gut content was generally related to a short but deep head. The present analysis suggests that the littoralO. jussieihas an intermediate phenotype and diet between the pelagic (O. agassii) and benthic (O. albusandO. luteus) species. Results suggest that resource partitioning was occurring and that several morphological traits relate to characteristics of the diet, and it is inferred that the benthic, the pelagic and the littoral zones in the lake host different prey communities constituting distinct adaptive landscapes.
Heart rate and ventilation in Antarctic fishes are largely determined by ecotype
Authors: Campbell H. , Davison W. , Fraser K. P. P. , Peck L. S. , Egginton S.
Published: February 2009

Extrinsic neural and humoral influences on heart rate (fH) and ventilation frequency (fV) were examined following varying periods of post‐surgical recovery in eight related Antarctic fish species inhabiting an array of inshore niches. Resting fH after recovery from handling was lower than previous reports, and the novel measurement of routine fH in free‐swimming Dissostichus mawsoni (6·14 beats min−1, bpm) is the lowest recorded for any fish. The extent of cardio‐depressive cholinergic (vagal) tonus explained the large range of fH among species and varied with behavioural repertoire, being lower in the more active species, apart from Notothenia coriiceps. Adrenergic tonus was low compared with cholinergic tonus, with the exception of Trematomus newnesi. Hence, high cardiac cholinergic tonus may be a genotypic trait of the notothenioids that diverged with ecotype. Power spectral analysis showed that the vagal influence produced comparable spectra among species of similar morphology and ecotype. Removal of autonomic tonus resulted in a remarkably similar intrinsic fH between species. Simultaneous measurements of cardio‐respiratory variables and oxygen consumption () were made in the benthic Trematomus bernacchii and cryopelagic Pagothenia borchgrevinki. The slopes of the relationship between fH and were similar. Trematomus bernacchii, however, had a higher for a given fH than P. borchgrevinki, and P. borchgrevinki required a two‐fold larger range in fH to reach a similar maximum , suggesting that there is a difference in cardiovascular fitness between the two species. Overall, the data suggest that cardio‐respiratory control in Antarctic nototheniids is largely determined by activity levels associated with a given ecotype.
Metabolic rate, growth and aggressiveness in three Atlantic salmon Salmo salar populations
Authors: SeppÄnen E. , Tiira K. , Huuskonen H. , Piironen J.
Published: February 2009

Standard metabolic rate (RS), specific growth rate (G) and aggressiveness were investigated in three Finnish populations of Atlantic salmon Salmo salar (Neva, Saimaa and Teno), which were reared in identical hatchery conditions. The populations differed in their geographical origin and native habitat. There was a significant difference between populations in RS: the southernmost Neva population had higher values in RS than the northernmost Teno population. No difference was found in G or aggressiveness between the populations. G was found to have a significant positive association with aggressiveness and RS among the three populations, however, these results were not statistically significant after correction for multiple tests. There was no significant association between RS and aggressiveness. Higher metabolic rate of the most southern population Neva is suggested to be an adaptation to the more abundant food sources of the southern stream.
Energy density of anchovy Engraulis encrasicolus in the Bay of Biscay
Authors: Dubreuil J. , Petitgas P.
Published: February 2009

The energy density (ED) of anchovy Engraulis encrasicolus in the Bay of Biscay was determined by direct calorimetry and its evolution with size, age and season was investigated. The water content and energy density varied seasonally following opposite trends. The ED g−1 of wet mass (MW) was highest at the end of the feeding season (autumn: c. 8 kJ g−1MW) and lowest in late winter (c. 6 kJ g−1MW). In winter, the fish lost mass, which was partially replaced by water, and the energy density decreased. These variations in water content and organic matter content may have implications on the buoyancy of the fish. The water content was the major driver of the energy density variations for a MW basis. A significant linear relationship was established between ED g−1 (y) and the per cent dry mass (MD; x): y =−4·937 + 0·411x. In the light of the current literature, this relationship seemed to be not only species specific but also ecosystem specific. Calibration and validation of fish bioenergetics models require energy content measurements on fish samples collected at sea. The present study provides a first reference for the energetics of E. encrasicolus in the Bay of Biscay.
The ‘egg sandwich’: a method for linking spatially resolved salmonid hatching rates with habitat variables in stream ecosystems
Authors: Pander J. , Schnell J. , Sternecker K. , Geist J.
Published: February 2009

This paper describes the development of the ‘egg sandwich’, a system for assessing stream substratum quality by linking measurements of depth‐specific salmonid egg hatching success and physico‐chemical water variables from the same sites within the interstitial zone.
Effect of Flavobacterium columnare inoculation, antibiotic treatments and resident bacteria on rainbow trout Oncorhynchus mykiss eyed egg survival and external membrane structure
Authors: Barnes M. E. , Bergmann D. , Jacobs J. , Gabel M.
Published: February 2009

This study was conducted to evaluate the potential pathogenicity of the bacterium Flavobacterium columnare on rainbow trout Oncorhynchus mykiss eyed eggs. Survival to hatching was unaffected by the inclusion in the incubation water of either 300 colony‐forming units (CFU) ml−1 or 3000 CFU ml−1 of F. columnare at either 10 or 12° C in either McConaughy or Shasta strain eyed eggs. Bacterial numbers, obtained via scanning electron microscopy or culture, and external membrane morphology were also not significantly different among eggs receiving different concentrations of F. columnare. Initial F. columnare burdens were significantly and positively correlated to the presence of biofilm on the egg external membrane, and biofilm was in turn significantly correlated with increased membrane degradation. The use of either streptomycin or tetracyclin antibiotics significantly reduced bacterial numbers on McConaughy strain eggs, and more eggs survived to hatch in those dishes treated with antibiotics.
Latitudinal variation in egg size and number in anadromous masu salmon Oncorhynchus masou
Authors: Morita K. , Tamate T. , Sugimoto Y. , Tago Y. , Watanabe T. , Konaka H. , Sato M. , Miyauchi Y. , Ohkuma K. , Nagasawa T.
Published: February 2009

Latitudinal variation in egg size and number in anadromous masu salmon Oncorhynchus masou was examined. Relatively greater variation in egg size occurred among rivers than among females within rivers or within females. Egg size was generally greater and egg number generally lower at more northerly latitudes.
Increased expression of centrosomal α, γ‐tubulin in atypical ductal hyperplasia and carcinoma of the breast
Authors: Niu Yun , Liu Tieju , Tse Gary M. K. , Sun Baocun , Niu Ruifang , Li Hiu‐ming , Wang Hui , Yang Yi , Ye Xue , Wang Ying , Yu Qi , Zhang Fei
Published: February 2009

Centrosomal abnormalities have been found in various cancer types. We sought to determine whether centrosomal dysfunctions occur in the atypical ductal hyperplasia (ADH)–carcinoma sequence of breast cancer. As α and γ‐tubulins are the structural components of centrosomes, we performed real time quantitative polymerase chain reaction (qPCR), in situ hybridization (ISH) and immunnohistochemistry (IHC) to determine the DNA copy levels, messenger RNA (mRNA) expression, and protein expression of α and γ‐tubulins respectively. γ‐tubulin staining was used for the localization and quantification of centrosomes. We found that α‐tubulin or γ‐tubulin mRNA was increasingly expressed from normal breast tissue (NBT) to ADH, ductal carcinoma in situ (DCIS), and infiltrative ductal carcinoma (IDC), respectively, with the highest expressions being found in DCIS. The expression profiles of α, γ‐tubulin proteins were concordant with that of mRNA, except that the highest expression was found in IDC. Similarly, DNA copies of α, γ‐tubulins showed a rising tendency, with the highest level for γ‐tubulin attained in IDC and that for α‐tubulin was found in DCIS. However, there was no significant difference of α, γ‐tubulin DNA copy levels, mRNA expression, and protein expression between DCIS and IDC. Our results demonstrate that centrosomal aberrations may play key roles in the early stage of breast tumorogenesis. The malignant transformation sequence is probably attributable to the amplification of centrosomal DNA leading to mRNA and protein over‐expression of these centrosomal proteins. Furthermore, determination of α, γ‐tubulins using combined qPCR with ISH may be useful in assisting the diagnosis of premalignant lesions of the breast. (Cancer Sci 2009; 100: 580–587)
Increased susceptibility to spontaneous lung cancer in mice lacking LIM‐domain only 7
Authors: Tanaka‐Okamoto Miki , Hori Keiko , Ishizaki Hiroyoshi , Hosoi Akihiro , Itoh Yu , Wei Min , Wanibuchi Hideki , Mizoguchi Akira , Nakamura Hiroyuki , Miyoshi Jun
Published: February 2009

LIM‐domain only (LMO) 7 is a multifunctional protein that is predicted to regulate the actin cytoskeleton, assembly of adherens junctions in epithelial cells, and gene expression. LMO7 was highly expressed in the mouse lung and predominantly localized to the apical membrane domain of bronchiolar epithelial cells. Although mice lacking LMO7 were viable and fertile in specific pathogen‐free conditions, they developed protruding epithelial lesions in the terminal and respiratory bronchioles and alveolar ducts at 14–15 weeks of age. Furthermore, they tended to develop spontaneous adenocarcinoma in the lung at over 90 weeks of age. The cumulative incidence ratios of lung cancer were 22% in LMO7−/– mice and 13% in LMO7+/– mice whereas no primary lung cancer was observed in wild‐type mice. Ex vivo analyses of the cancer cells showed numerical chromosome abnormalities and tumorigenicity in nude mice. These results suggest that LMO7 can act as a tumor suppressor whose deficiency confers a genetic predisposition to naturally occurring lung cancer. (Cancer Sci 2009; 100: 608–616)
Vegetation dynamics in western Uganda during the last 1000 years: climate change or human induced environmental degradation?
Authors: Lejju Julius B.
Published: February 2009

A multi‐proxy analysis of microfossils from sedimentary records, together with evidence from historical and archaeological data, has provided evidence of vegetation dynamics and human environment interactions in western Uganda for the last 1000 years. Pollen, fungal spores and phytoliths extracted from sediment cores obtained from a papyrus swamp at Munsa archaeological site indicate a relatively wet and forested environment in western Uganda prior to ca 1000 yr bp (cal 977–1159 ad). A subsequent decline in forest vegetation occurred from ca 920 yr bp (cal 1027–1207 ad). However, the deforestation period occurred during a wet period as registered in the River Nile water records, suggesting a human induced deforestation at Munsa rather than reduced precipitation. Increased numbers of herbivores, presumably domesticated cattle, postdeforestation are evidenced by the presence of dung fungal spores and broad accord with the archaeological evidence for initial occupation of the site at Munsa and the establishment of a mixed economy based on crops, cattle and iron working between 1000 and 1200 ad. From ca 200 yr bp (cal 1647–1952 ad), forest recovery occurred at Munsa site and appears to reflect abandonment of the site, as suggested by archaeological evidence, possibly following a period of prolonged drought and famine between 1600 and 1800 ad, as recounted in the oral rich traditions of western Uganda and also reflected by low water levels of River Nile.
Ecological gradients as a framework for analysis of land‐use change in East Africa
Authors: Majule A. E. , Mbonile M. J. , Campbell D. J.
Published: February 2009

This paper discusses the ecological gradient as an organizing framework to assist understanding the complex interactions between societal and ecological processes underlying land‐use change in East Africa. Detailed case studies on the gradients of the slopes of Mt Kilimanjaro, Kenya show how land‐use change is responsive to the dynamics of both local and external driving forces. The study has shown that the distinct ecological conditions at the extremities of gradients are associated with specific land uses which may be different within livelihood systems such as for wet and dry season grazing. Access to water for cultivation, domestic use, livestock and wildlife is critical in determining the nature and distribution of livelihood systems. Land‐use systems interact across the different ecological zones of the gradients characterized by vigorous spatial, cultural and economic interactions. Sometime conflicts occur between or within land‐use/livelihood systems. There is strong evidence that the areas of higher economic potential remain advantaged compared with areas lower on the gradient. The ecological characteristics have been found to influence human activities and distribution. Interactions between societies are important in terms of trade, social relations and access to resources.
Bush encroachment under three contrasting land‐use practices in a mesic South African savanna
Authors: Wigley B. J. , Bond W. J. , Hoffman M. T.
Published: February 2009

This study determined the effects of land‐use practice had on the rate and extent of bush encroachment in a mesic savanna in KwaZulu‐Natal, South Africa. Changes in woody cover were measured for 1 km2 sites in areas under communal, commercial and conservation land‐use systems for the period between 1937 and 2000. Land users from each area were interviewed to gain the histories of each area and to determine how the changes in woody cover had impacted them and whether anything was being done to counteract the spread of trees and shrubs on their land. Bush encroachment occurred across all three of the land‐use types in the 67‐year period between 1937 and 2000. The results showed that land‐use practice had enormous impacts on the process of bush encroachment. The communal site showed a decrease in grass (21%) and tree (5%) cover and an increase in shrub cover (13%). At the commercial site, there was a considerable decrease in grass cover (46%) and moderate increase in shrub cover (10%) and a massive increase in tree cover (36%). The area under conservation showed a substantial decrease in grass cover (47%), a slight decrease in shrub cover (19%) and a massive increase in tree cover (66%). The perceived causes of these changes were fairly similar amongst the different land users. The changes were mostly not perceived to be a problem for the communal land users. The main advantages mentioned were increased woody resources for building and firewood and increased browse availability. The commercial and conservation land users perceived the changes to have significant negative connotations including the loss of grazing land and biodiversity and secondary invasion of encroached areas by alien plant species. Despite these perceptions, very little has been done to combat bush encroachment in the commercial and conservation land use systems.
Assessing the impacts of fire on the vegetation resources that are available to the local communities of the seasonal wetlands of the Okavango, Botswana, in the context of different land uses and key government policies
Authors: Tacheba Budzanani , Segosebe Eagilwe , Vanderpost Cornelis , Sebego Reuben
Published: February 2009

The Okavango wetlands in north western Botswana are the most fire‐prone environment in Botswana. Most of these fires are anthropogenic. The fires in this environment are thought to impact the environment negatively and therefore practices that are associated with extensive use of fire have been strongly criticized. Despite this, there has been little work done to understand how these fires impact the wetlands environment and its dynamics, especially the vegetation resources that are used by the local communities in the wetlands. The objective of the study was to identify fire spatial and temporal trends in relation to settlement distribution, through the use of remote sensing, socio‐economic and phytosociological surveys. The fire history results show that geographically there has not been any significant change in vegetation structure and that in fact fires may have promoted biodiversity. The results of analysis show an overall variance on vegetation structure of 23% whereas the rest are unaccounted for. There is a strong association between settlements, ethnicities, literacy and fire occurrences. The most fire‐prone areas are inhabited by communities that have used fire in the past for various resource use practices.
An overview of environmental issues in Southern Africa
Authors: Darkoh Michael Bernard Kwesi
Published: February 2009

This paper provides an overview of some of the significant environmental problems in the Southern African region. The key problems highlighted are global warming and climate variability, loss of biodiversity, deforestation, desertification‐land degradation, waste and littering, population growth, urbanization, pollution, poverty and health hazards. These problems present a challenge to governments and other players within and outside Southern Africa to seek for long‐term solutions by addressing the root causes of these problems. The paper notes that although the environmental problems facing the Southern African region are being tackled at national, regional and international levels, there is more that can be done. At the national level, the different agencies and players, both within and outside government need to strengthen coordination and implementation of key interventions in different sectors in both rural and urban areas. At the African regional and international levels, there is a need to address geopolitical forces and issues that contribute to the underdevelopment of the African region. Among the major issues are poor terms of international trade, political instability, poverty, declining economic performance and international debt.
Assessment of spring water quality and quantity, and health implications in Tongaren division, Nzoia River catchment, Kenya
Authors: Simiyu G. M. , Ngetich J. , Esipila T. A.
Published: February 2009

Spring water is the common source of public water supply in most rural communities of developing countries such as Kenya. The water quality and quantity may be altered due to catchments degradation. This study was carried out in Tongaren division, Nzoia River catchment. The aim of this study was to investigate and map the occurrence and distribution of springs and to determine their water quality and quantity. This study determined the spring water discharge, conductivity, turbidity, total and thermotolerant (faecal) coliforms to assess suitability and sustainability of spring water for safe drinking. Twenty‐eight springs were identified and their locations mapped using Global Positioning System (GPS) geo‐reference data. Discharge ranged from 0.1 to 3 l s−1, with some drying up during dry season. Total coliform was innumerable in most of the studied springs while thermotolerant (faecal) coliform counts occurred in eight springs, including four protected springs. This poses high risks of water‐borne diseases. The water should be filtered and boiled prior to use for drinking. Facilitation of communities enabled development of seven springs to enhance water yield and quality. This study established high potential in the communities to develop springs and utilize the spring water as alternative source of livelihoods.
Environmental variability and the fishery dynamics of the Okavango delta, Botswana: the case of subsistence fishing
Authors: Mmopelwa G. , Mosepele K. , Mosepele B. , Moleele N. , Ngwenya B.
Published: February 2009

The hydrological regime of the Okavango River Basin is the main driver of ecological change in the delta. The delta supports a small‐scale fishery which is a source of livelihood for communities within its fringes. The fish resource is particularly important to subsistence fishers, who have limited access to socio‐economic opportunities. However, fish availability is subject to ‘concentration and dilution’ effects because of the hydrological regime. As a copying strategy, fishers use a variety of fishing methods to effectively harvest the delta’s fish community across all its trophic levels. This exploitation regime helps to maintain the delta’s species diversity and only reduces fish biomass proportionally across the different trophical levels. Furthermore, fishers have developed different fish‐processing techniques to preserve their harvest for low fishing season periods to cope with low food availability. The aim of this paper therefore, was to explore spatio‐temporal variations in fish availability and to show how the delta’s subsistence fishers cope with this dynamicity.
Livelihood diversification and implications on dryland resources of central Tanzania
Authors: Liwenga Emma T.
Published: February 2009

The concern over sustainable livelihoods in African drylands is an issue that has received considerable attention from researchers and policy makers alike. Over the past two decades African rural areas have undergone rapid changes, whereby, rural income diversification has become the most salient feature. With a particular focus on dryland ecosystems, among the major challenges facing communities in these areas is recurrent drought leading to conditions of food insecurity. This paper draws on experience on coping mechanisms for food insecurity from an agro‐pastoral community in Mvumi, located in the semiarid areas of central Tanzania. An understanding of livelihoods of people in this area has involved examining how communities have managed to adjust their livelihood in the midst of challenges resulting not only from drought but also from various forces such as socio–economic, political and ecological factors. It has been found out that, despite profound food crisis in this area, people are not always desperate and that there are possibilities for realizing some hidden potentials of dryland resources for livelihood diversification. The issue of sustainable natural resource management in such areas is, however, questionable because of some adverse environmental effects associated with some of the coping mechanisms.
Participatory planning, management and alternative livelihoods for poor wetland‐dependent communities in Kampala, Uganda
Authors: Kabumbuli Robert , Kiwazi Frederick William
Published: February 2009

The paper is based on an on‐going 3‐year study in the wetland communities of Kampala. The study uses participatory methods and aims to contribute to (i) the development of low‐income wetland communities, (ii) to prepare these communities to become less dependent on wetlands without receding into poverty, and (iii) the better management of the wetlands. The communities in direct dependence and intimate interaction with Nakivubo wetlands are mainly poor, live and work under hazardous conditions, and their activities pose a threat to the ecological function of the wetlands. Yet these wetlands are important for filtering the city’s waste and storm water before it flows into Lake Victoria’s Murchison Bay, which is Kampala’s source of piped water. Government approaches to the problem of wetland encroachment have largely failed because they are confrontational, and are not consistent or participatory. The study has in the first year conducted a series of activities including stakeholder analysis, resource analysis, livelihood analysis, a questionnaire survey and action planning. Preliminary data show that wetland dependency is very high among the poor nearby communities. They practice cultivation, brick‐making and harvesting of wetland vegetation. However, these activities are under threat because wetland resources are dwindling due to increasing population and over‐use. Livelihoods are threatened not only by the decreasing productivity of the wetland, but also by the ever‐present government threat to evict wetland encroachers to restore its ecology. The study therefore works with communities to prepare for less dependence on wetlands so that they do not suddenly recede into worse poverty if they are evicted. They formulate strategies to enhance alternative livelihood, and for management of the wetland. Action plans have been formulated to address the situation through a newly created association.