bluuebunny/crossref_metadata_2025_split huggingface dataset:
INTERNATIONAL CRIMINAL COURTS ROUND-UP
Authors: Guellai Amna , Rojo Enrique Carnero 
Published: February 2009

AbstractThe International Criminal Courts Round-Up reports on the most interesting judgements and decisions rendered by international(ized) criminal courts and tribunals during the reporting period. In addition, important developments within the various organs of the courts are highlighted, such as the appointment of new judges and significant amendments to the procedural rules of the courts. The Round-Up presently covers issues concerning the International Criminal Court, the International Criminal Tribunal for the former Yugoslavia, the International Criminal Tribunal for Rwanda and the Special Court for Sierra Leone.
Aliens are us. An innovative course in astrobiology
Authors: Oliveira Carlos F. , Barufaldi James P. 
Published: February 2009

AbstractWe live in a scientific world; paradoxically, the scientific literacy of the population is minimal at best. Science is an ongoing process, a human endeavour; paradoxically, students tend to believe that science is a finished enterprise. Many non-science major students are not motivated in science classes; paradoxically, there is a public fascination with the possibility of life in the Universe, which is nowadays a scientific endeavour. An astrobiology course was developed at the Center for Science and Mathematics Education at The University of Texas at Austin to address these paradoxes and includes the following objectives: (a) to improve scientific literacy; (b) to demonstrate that science is a work in progress; (c) to enhance the inherent interdisciplinary aspect of science; (d) to demonstrate that science is embedded in society and relates with several social sciences; (e) to improve the content knowledge about the nature of science; (f) to illustrate how engaging learning science can be; and (g) to draw from the intrinsic motivation already incorporated in the general population. The course has been offered, taught and revised for the past three years. The informal course student feedback has been very positive and encouraging. The purpose of this paper is to provide a general overview of the course. In addition, the course's background, content, themes and mode of delivery are outlined, discussed and analysed in this paper. This paper subscribes to an educational philosophy that focuses on the multidisciplinary nature of science and includes critical thinking-based teaching strategies using the dynamic discipline of astrobiology.
JOHANN SIGISMUND COUSSER, WILLIAM III AND THE SERENATA IN EARLY EIGHTEENTH-CENTURY DUBLIN
Authors: OWENS SAMANTHA 
Published: February 2009

ABSTRACTAmong the holdings of Hamburg’s Staats- und Universitätsbibliothek Carl von Ossietzky is an anonymous fifty-two-page score headed ‘Serenata à 4’, described in the corresponding catalogue entry by its former owner, German musicologist Friedrich Chrysander (1826–1901), as a ‘cantata for the funeral of the English king William III of Orange, 1702’. But both the work’s text and the recent identification of the manuscript as being in the hand of Johann Sigismund Cousser (1660–1727) call for a reassessment of this serenata’s provenance, situating it in either England or Ireland between Cousser’s arrival in London on Christmas Day 1704 and the end of Queen Anne’s reign in 1714. Over the course of the two decades he resided in Ireland, from 4 July 1707 until his death, Cousser was responsible for the composition and musical direction of one ode and more than twenty serenatas, the majority of which were commissioned by the viceregal court at Dublin Castle for state celebrations of the reigning monarch’s birthday. Taking printed librettos, contemporary newspaper reports, Cousser’s own commonplace book and two further surviving manuscript scores as its primary evidence, this study seeks to establish a likely location and occasion for the performance of the ‘William III’ serenata within Dublin’s musical life during the early eighteenth century. In their choice of terminology, compositional style and performance practices, Cousser’s serenatas, which may have incorporated elements of theatrical staging and dancing, reveal his extensive Continental experience, and they can be seen to have functioned in part as an operatic substitute, presumably reflecting the limited financial resources of Dublin high society.
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.
Accurate identification of orthologous segments among multiple genomes
Authors: Hachiya Tsuyoshi , Osana Yasunori , Popendorf Kris , Sakakibara Yasubumi 
Published: February 2009

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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

Abstract
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.
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

AbstractA 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

AbstractThis 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.