bluuebunny/crossref_metadata_2025_split huggingface dataset:
Unjust, Cruel and Barbarous Proceedings: Japanese Mercenaries and the Amboyna Incident of 1623
Authors: Clulow Adam 
Published: March 2010

AbstractIn 1623, the Dutch governor of Amboyna, an important clove-producing island in modern-day Indonesia, executed a group of English merchants and Japanese mercenaries accused of plotting to seize control of the VOC castle on the island. After news of these events reached Europe, the Amboyna Massacre, as it came to be called in England, rapidly became invested with great consequences as English and Dutch leaders fought over the issues of blame and compensation. This article examines the Japanese mercenaries accused by the VOC, the silent participants whose cause was not taken up by any national government.
Controlling Water, Controlling People: Irrigation Engineering and State Formation in the Dutch East Indies
Authors: Ravesteijn Wim 
Published: March 2010

AbstractIn 1885, the Dutch East Indian state began a huge ‘civilisation offensive’ in the field of irrigation focussed on Java. It comprised creating modern irrigation works, regulating irrigation management and planning construction activities. This paper shows the successes and failures of this irrigation programme, which was part of the Dutch ‘colonial project’ as a whole. Particular attention is given to the question of why the colonial state made irrigation affairs one of its special missions. What emerges is that Dutch exploitation interests (sugar) were dominant, though the welfare interests of the native population (rice) clearly became more prominent. Another question to be dealt with is the issue of how the Dutch East Indian state realized its plans. As this paper argues, the engineers of the Public Works Department played a key part, but only in competition and cooperation with other relevant groups.
Perceptions of Nature in Early Modern Portuguese India
Authors: Smith Stefan Halikowski 
Published: March 2010

Portuguese perceptions of nature in the new worlds they encountered in Southeast Asia from the turn of the sixteenth century were a complex amalgam of inherited frameworks and the forging of a new gaze or vision. Grand claims that the Portuguese discoveries amount to the “construction of space” and the “invention of humanity” have been trumpeted, but are too overblown. From another perspective, Portuguese scholars have recently engaged in a philosophical debate aroundexperiencialismo—the distinction between “scientific experience” and the supposedly pre- or non-scientific “lived” experience of the senses (experiência vivencial), suggesting that the Portuguese Discoveries fall at a critical juncture between these two hermeneutic paradigms. But what did this amount to in concrete terms?I would prefer to turn to other scholars like the Belgian historian Albert Deman, who has stipulated that the perception of Indian nature in the European imaginary, was locked in three unchanging tropes that even first-hand experience could not easily undo. These tropes were exuberance, superabundance and luxury, and go right back to the first encounters between East and West in antiquity, notably Alexander the Great's adventures of the fourth century B.C., which impressed upon Westerners the East's “superior forms of life” and what Pliny, for example, dutifully acknowledged as “the wonder of the victorious expedition of Alexander the Great, when that part of the world was first revealed.” Why wonder, and what does Deman allude to when he writes of “superior forms of life”? The common impression was that everything grew more forcefully, and in greater profusion in the East. There were, for example, two flowerings a year of some plants; the colours and tastes were stronger; the smells were beguiling. What the Portuguese noted as “thefumos da India” merely drew on biblical reference in the Book of Proverbs to the “spicy breezes of the East”. From these basic conceptions had sprung compilations of all the fabulous stories of the East, texts such as those produced by Ktesias the Knidian and Megasthenes whose ideas were passed down through Pliny into the genre of the marvellous, ormirabilia, fanciful speculations and fables developed along the lines of half-truths reported by returning merchants and travellers, and sometimes fictions spread by Arab middlemen keen to retain their long-standing monopoly of purveyance to Christian consumers.
Saint-Joseph University of Beirut: An Enclave of the French-Speaking Communities in the Levant, 1875–1914
Authors: Herzstein Rafael 
Published: March 2010

The origin of the Saint-Joseph University of Beirut, or USJ, dates back to the Seminar of Ghazir founded by the Jesuit Fathers in 1843. The College of Ghazir, established with the intention of training the local Maronite clergy, was transferred to Beirut in 1875. This centre for higher studies was named Saint-Joseph University. In his audience of 25 February 1881, Pope Leo XIII conferred the title of Pontifical University on the USJ.This article deals with the history of the USJ, the first great French-speaking Jesuit institution in the area which, at the time, bore the name of “Syria”. (The term Syria is used henceforth to represent the geographical entity of the nineteenth and early twentieth centuries, which includes Syria and Lebanon of the present.) The underlying reasons for the creation of Saint-Joseph University of Beirut have to do with its being located in a province of the Ottoman Empire coveted by the future mandatory power, France. By the 1870s, the Ottoman Empire was being preserved chiefly by the competition between the European powers, all of whom wanted chunks of it. The Ottoman territory, like the territory of the Austro-Hungarian Empire, encompassed a great many ethnic groups whose own nationalism was also stirring. Under Ottoman rule, the region of the Levant developed economic and religious ties with Europe. Open to the West, it became a hotbed of political strife between various foreign nations including France, Russia and Britain. These powerful countries assumed the protection of certain ethnic and religious groups, with France supporting the Christian Maronites and Britain supporting the Druzes.
Use of serology and urine antigen detection to estimate the proportion of adult community-acquired pneumonia attributable toStreptococcus pneumoniae
Authors: WATT J. P. , MOÏSI J. C. , DONALDSON R. L. A. , REID R. , FERRO S. , WHITNEY C. G. , SANTOSHAM M. , O'BRIEN K. L. 
Published: March 2010

SUMMARYStreptococcus pneumoniaeis a common cause of community-acquired pneumonia (CAP) but existing diagnostic tools have limited sensitivity and specificity. We enrolled adults undergoing chest radiography at three Indian Health Service clinics in the Southwestern United States and collected acute and convalescent serum for measurement of PsaA and PspA titres and urine for pneumococcal antigen detection. Blood and sputum cultures were obtained at the discretion of treating physicians. We compared findings in clinical and radiographic CAP patients to those in controls without CAP. Urine antigen testing showed the largest differential between CAP patients and controls (clinical CAP 13%, radiographic CAP 17%, control groups 2%). Serological results were mixed, with significant differences between CAP patients and controls for some, but not all changes in titre. Based on urine antigen and blood culture results, we estimated that 11% of clinical and 15% of radiographic CAP cases were due to pneumococcus in this population.
The influence of sperm concentration, length of the gamete co-culture and the evolution of different sperm parameters on the in vitro fertilization of prepubertal goat oocytes
Authors: Palomo M.J. , Mogas T. , Izquierdo D. , Paramio M.T. 
Published: March 2010

SummaryThe aims of the present study were: (1) to evaluate the influence of sperm concentration (ranging from 0.5 × 106 to 4 × 106 spermatozoa/ml) and length of the gamete co-incubation time (2, 4, 6, 8, 10, 12, 16, 20, 24 or 28 h) on in vitro fertilization (IVF), assessing the sperm penetration rate; (2) to investigate the kinetics of different semen parameters as motility, viability and acrosome status during the co-culture period; and (3) to analyse the effect of the presence of cumulus–oocytes complexes (COCs) on these parameters. To achieve these objectives, several experiments were carried out using in vitro matured oocytes from prepubertal goats. The main findings of this work are that: (1) in our conditions, the optimum sperm concentration is 4 × 106 sperm/ml, as this sperm:oocyte ratio (approximately 28,000) allowed us to obtain the highest penetration rate, without increasing polyspermy incidence; (2) the highest percentage of viable acrosome-reacted spermatozoa is observed between 8–12 h of gamete co-culture, while the penetration rate is maximum at 12 h of co-incubation; and (3) the presence of COCs seems to favour the acrosome reaction of free spermatozoa on IVF medium, but not significantly. In conclusion, we suggest that a gamete co-incubation for 12–14 h, with a concentration of 4 × 106 sperm/ml, would be sufficient to obtain the highest rate of penetration, reducing the exposure of oocytes to high levels of reactive oxygen species produced by spermatozoa, especially when a high sperm concentration is used to increase the caprine IVF outcome.
Policy approaches to energy and resource use in US agriculture
Authors: Sorensen Ann , Daukas Jimmy 
Published: March 2010

AbstractImproving energy and resource use in US agriculture begins with the soil. Healthy soils improve air and water quality, increase land productivity, help resist the effects of drought and floods, improve energy efficiency and enhance the ability to mitigate climate change. In 1993, the US Board on Agriculture concluded that national policy should seek to: conserve and enhance soil quality as a fundamental first step to improve the environment; increase the efficiency of nutrient, pesticide and irrigation use in farming systems; increase the resistance of farming systems to erosion and runoff; and make greater use of field and landscape buffer zones, all delivered through farm system management plans. Despite their detailed analysis and thoughtful approach, only a few of their recommendations were implemented. But now, calls from the scientific community to improve resource and energy use in agriculture are becoming more urgent in tone and could help drive policy reform. We review the reasons behind this rising sense of urgency, highlight some of the potential policy drivers along with policy ‘game changers’ and offer policy options. We argue to expand our view of agriculture as a source not only of food, fiber, biofuels and renewable energy but also of other critical ecosystem services, like cleaner water, carbon sequestration and wildlife habitat, and to adjust policies to realize this potential on all agricultural lands. We recommend undertaking a second National Agricultural Land Study as a basis to develop a clear national strategy to help US agriculture meet the challenges it will face in the coming decades. For the short term, we offer incremental policies to improve energy and resource use and, for the long term, we offer a vision of what that national strategy might include once the necessary analyses are completed and consensus is reached.
All together now: integrating customer data with MasterVision
Authors: CULLING James 
Published: March 2010

ABSTRACTA publisher's customer and user data typically comes in many forms and from many specialized repositories and systems. For sales and marketing staff in particular, there is considerable insight to be gained from analysing all of this data closely. However, achieving an integrated and complete ‘single customer view’ via a data warehouse solution can be a costly, time‐consuming and challenging undertaking. In this case study report, DataSalon's MasterVision is described as an alternative approach to solving this problem for publishers. Key to the solution is a dynamic data modelling philosophy, with both the underlying database and product interface configured for each publisher around the specific customer data supplied. A number of real‐life 'use cases' are explained and the value of Ringgold's Identify database of organizations, in addressing a number of integration challenges but also in adding to the intelligence that can be gleaned from source data, is discussed.
Write when hot — submit when not: seasonal bias in peer review or acceptance?
Authors: SHALVI Shaul , BAAS Matthijs , HANDGRAAF Michel J. J. , DE DREU Carsten K.W. 
Published: March 2010

ABSTRACTAt a top psychology journal, Psychological Science (PS), submissions peak during the summer months. We tested whether this seasonal submission bias decreases the likelihood of a paper being accepted in that period. Month of submission data was obtained for all 575 publications in PS for the period 2003–2006. Whereas submissions to PS were higher in the summer, there was no evidence that most accepted publications were originally submitted in the summer. Thus, contributors submit to PS when the likelihood of acceptance is the lowest – creating their own entrance barrier. A similar seasonal pattern was not identified for Personality and Social Psychology Bulletin, another top psychology journal. Using the Web of Knowledge database, we further assessed whether overcoming the seasonal entrance barrier influences the number of citations a paper receives in subsequent years. We discuss the possibility that the different rejections policies in the two journals, employing desk rejections or not, may explain this discrepancy, and explore a range of alternative hypotheses.
Reliability of reviewers' ratings when using public peer review: a case study
Authors: BORNMANN L. , DANIEL H.‐D. 
Published: March 2010

ABSTRACTIf a manuscript meets scientific standards and contributes to the advancement of science, it can be expected that two or more reviewers will agree on its value. Manuscripts are rated reliably when there is a high level of agreement between independent reviewers. This study investigates for the first time whether inter‐rater reliability, which is low with the traditional model of closed peer review, is also low with the new system of public peer review or whether higher coefficients can be found for public peer review. To investigate this question we examined the peer‐review process practiced by the interactive open access journal Atmospheric Chemistry and Physics (based on 465 manuscripts submitted between 2004 and 2006 receiving 1,058 reviews in total). The results of the study show that inter‐rater reliability is low (kappa coefficient) or reasonable (Intraclass Correlation Coefficient) in public peer review.
The economic downturn and libraries: an international survey
Authors: ROWLANDS Ian , NICHOLAS David 
Published: March 2010

ABSTRACTThere is some concern that libraries, particularly university libraries, are facing a very bleak future because of the word‐wide economic downturn. Much of the evidence regarding the economic problems and consequent impacts is parochial, far from robust, and there is a suspicion of stakeholders talking the situation up. This paper presents robust and independent evidence on the extent to which libraries from around the world are experiencing financial hardship, the impacts that result, and what the future looks like. Comparative analyses are made on the grounds of country, sector, and size of institution. The particular situation of university libraries is highlighted and the implications of the findings are examined from the perspective of scholarly publishers.
EBImage—an R package for image processing with applications to cellular phenotypes
Authors: Pau Grégoire , Fuchs Florian , Sklyar Oleg , Boutros Michael , Huber Wolfgang 
Published: March 2010

Abstract
Summary: EBImage provides general purpose functionality for reading, writing, processing and analysis of images. Furthermore, in the context of microscopy-based cellular assays, EBImage offers tools to segment cells and extract quantitative cellular descriptors. This allows the automation of such tasks using the R programming language and use of existing tools in the R environment for signal processing, statistical modeling, machine learning and data visualization.
Availability: EBImage is free and open source, released under the LGPL license and available from the Bioconductor project (http://www.bioconductor.org/packages/release/bioc/html/EBImage.html).
Contact: gregoire.pau@ebi.ac.uk
PathWave: discovering patterns of differentially regulated enzymes in metabolic pathways
Authors: Schramm Gunnar , Wiesberg Stefan , Diessl Nicolle , Kranz Anna-Lena , Sagulenko Vitalia , Oswald Marcus , Reinelt Gerhard , Westermann Frank , Eils Roland , König Rainer 
Published: March 2010

Abstract
Motivation: Gene expression profiling by microarrays or transcript sequencing enables observing the pathogenic function of tumors on a mesoscopic level.
Results: We investigated neuroblastoma tumors that clinically exhibit a very heterogeneous course ranging from rapid growth with fatal outcome to spontaneous regression and detected regulatory oncogenetic shifts in their metabolic networks. In contrast to common enrichment tests, we took network topology into account by applying adjusted wavelet transforms on an elaborated and new 2D grid representation of curated pathway maps from the Kyoto Enzyclopedia of Genes and Genomes. The aggressive form of the tumors showed regulatory shifts for purine and pyrimidine biosynthesis as well as folate-mediated metabolism of the one-carbon pool in respect to increased nucleotide production. We spotted an oncogentic regulatory switch in glutamate metabolism for which we provided experimental validation, being the first steps towards new possible drug therapy. The pattern recognition method we used complements normal enrichment tests to detect such functionally related regulation patterns.
Availability and Implementation: PathWave is implemented in a package for R (www.r-project.org) version 2.6.0 or higher. It is freely available from http://www.ichip.de/software/pathwave.html
Contact: r.koenig@dkfz.de; r.eils@dkfz.de
Supplementary information: Supplementary data are available at Bioinformatics online.
Development and Testing of a CD‐ROM Program for Improving Adolescent Knowledge of Inflammatory Bowel Disease
Authors: Boamah Lynelle M , Bohren Janet R , Pentiuk Scott , Baker Raymond , Yi Michael , Moyer M Susan 
Published: March 2010

ABSTRACTObjective:The aim of this study was to design a theory‐based educational program for adolescents with inflammatory bowel disease (IBD) using an interactive multimedia CD‐ROM and to test its effectiveness in improving knowledge in IBD.Materials and Methods:Curriculum‐based instruction using educational theory and principles was designed for adolescents on an interactive multimedia CD‐ROM. Twenty subjects completed summative evaluation of the CD‐ROM measuring gain in knowledge about IBD immediately and 9 months after instruction.Results:Subjects found the CD‐ROM to be informative, appealing, and easy to use. The mean baseline score of the adolescents on the Crohn's and Colitis Knowledge questionnaire was 12.2 (standard deviation 5.14, range 3–24). After an average of 30 minutes of self‐directed learning, adolescent subjects increased their posttest score to a mean of 19.8, a gain of 7.6 points over baseline (95% confidence interval 5.2–10.1, P < 0.0001). Knowledge of medications, disease complications, and gastrointestinal structure and function was gained and retained upon retesting at 9 months with a mean Crohn's and Colitis Knowledge questionnaire score of 17.5 (standard deviation 3.9, range 12–26), which was still an improvement over the mean pretest knowledge score of 12.2 (P < 0.001).Conclusions:Adolescents with IBD have low baseline knowledge about their disease. A rigorously developed interactive educational tool is now available for instructing adolescent patients about their IBD.
Immune Suppression by Cyclosporin A Inhibits Phytohemagglutinin‐induced Precocious Gut Maturation in Suckling Rats
Authors: Prykhod'ko Olena , Pierzynowski Stefan G , Weström Björn R 
Published: March 2010

ABSTRACTObjectives:Enteral exposure to the lectin phytohemagglutinin (PHA) provokes precocious gut maturation in suckling rats coinciding with an early expansion of intestinal mucosal T and B lymphocytes. Here, the role of the immune system in neonatal gut growth and maturation was further studied.Materials and Methods:The effects of immunosuppression by cyclosporine A (CyA), 7.5 μg/g of body weight, injected 12 hours before and then daily after the intragastric gavage of PHA, 100 μg/g body weight, to 14‐day‐old suckling rats were studied after 4 and 12 hours and later after 72 hours.Results:At 4 hours after PHA feeding, an early rapid increase in the intestinal levels of the proinflammatory cytokines interleukin‐6, interleukin‐1β, and tumor necrosis factor was obtained, and the CyA treatment did not prevent the temporary PHA‐induced intestinal disturbance seen at 12 hours. Later, at 72 hours after PHA gavage the CyA treatment significantly counteracted the PHA‐induced gut changes with a decrease in small intestinal growth, a delay in the appearance of adult‐phenotype enterocytes in the distal small intestinal, and total inhibition of the PHA‐induced pancreas development. Additionally, the increase in plasma level of the acute phase protein, haptoglobin, after PHA feeding was dampened by CyA.Conclusions:The results indicate that proinflammatory cytokines are involved in the early recruitment of lymphocytes to the gut after PHA challenge, and that the ensuing precocious gut maturation is dependent on activation of the immune system, presumably T cells, in suckling rats.
Supplementation With Fatty Acids Influences the Airway Nitric Oxide and Inflammatory Markers in Patients With Cystic Fibrosis
Authors: Keen Christina , Olin Anna‐Carin , Eriksson Susanne , Ekman Anna , Lindblad Anders , Basu Samar , Beermann Christopher , Strandvik Birgitta 
Published: March 2010

ABSTRACTObjectives:To obtain a balance in the fatty acid (FA) metabolism is important for the inflammatory response and of special importance in cystic fibrosis (CF), which is characterized by impaired FA metabolism, chronic inflammation, and infection in the airways. Nitric oxide (NO) has antimicrobial properties and low nasal (nNO) and exhaled NO (FENO), commonly reported in CF that may affect bacterial status. The present study investigates the effect of different FA blends on nNO and FENO and immunological markers in patients with CF.Patients and Methods:Forty‐three patients with CF and “severe” mutations were consecutively enrolled in a randomized double‐blind placebo‐controlled study with 3 FA blends containing mainly n‐3 or n‐6 FA or saturated FA acting as placebo. FENO, nNO, serum phospholipid concentrations of FA, and biomarkers of inflammation were measured before and after 3 months of supplementation.Results:Thirty‐five patients in clinically stable condition completed the study. The serum phospholipid FA pattern changed significantly in all 3 groups. An increase of the n‐6 FA, arachidonic acid, was associated with a decrease of FENO and nNO. The inflammatory biomarkers, erythrocyte sedimentation rate, and interleukin‐8 decreased after supplementation with n‐3 FA and erythrocyte sedimentation rate increased after supplementation with n‐6 FA.Conclusions:This small pilot study indicated that the composition of dietary n‐3 and n‐6 FA influenced the inflammatory markers in CF. FENO and nNO were influenced by changes in the arachidonic acid concentration, supporting previous studies suggesting that both the lipid abnormality and the colonization with Pseudomonas influenced NO in the airways.