bluuebunny/crossref_metadata_2025 huggingface dataset:
Testing the predictive adaptive response in a host‐parasite system
Authors: Devevey Godefroy , Bize Pierre , Fournier Sara , Person Emilie , Christe Philippe
Published: July 2009

1. Harsh environmental conditions experienced during development can reduce the performance of the same individuals in adulthood. However, the ‘predictive adaptive response’ hypothesis postulates that if individuals adapt their phenotype during development to the environments where they are likely to live in the future, individuals exposed to harsh conditions in early life perform better when encountering the same harsh conditions in adulthood compared to those never exposed to these conditions before.

2. Using the common vole (Microtus arvalis) as study organism, we tested how exposure to flea parasitism during the juvenile stage affects the physiology (haematocrit, resistance to oxidative stress, resting metabolism, spleen mass, and testosterone), morphology (body mass, testis mass) and motor performance (open field activity and swimming speed) of the same individuals when infested with fleas in adulthood. According to the ‘predictive adaptive response’ hypothesis, we predicted that voles parasitized at the adult stage would perform better if they had already been parasitized with fleas at the juvenile stage.

3. We found that voles exposed to fleas in adulthood had a higher metabolic rate if already exposed to fleas when juvenile, compared to voles free of fleas when juvenile and voles free of fleas in adulthood. Independently of juvenile parasitism, adult parasitism impaired adult haematocrit and motor performances. Independently of adult parasitism, juvenile parasitism slowed down crawling speed in adult female voles.

4. Our results suggest that juvenile parasitism has long‐term effects that do not protect from the detrimental effects of adult parasitism. On the contrary, experiencing parasitism in early‐life incurs additional costs upon adult parasitism measured in terms of higher energy expenditure, rather than inducing an adaptive shift in the developmental trajectory.

5. Hence, our study provides experimental evidence for long term costs of parasitism. We found no support for a predictive adaptive response in this host‐parasite system.
Are competitive effect and response two sides of the same coin, or fundamentally different?
Authors: Wang Ping , Stieglitz Tara , Zhou Dao Wei , Cahill Jr James F
Published: July 2009

1. The ability to suppress neighbour growth and the ability to withstand growth suppression are widely viewed as two forms of competition, competitive effect and competitive response.

2. We conducted a greenhouse experiment to determine whether these two forms of competition were functionally linked, and to determine which plant traits are associated with effect and response competitive abilities among seedlings of 22 perennial North American prairie species. We further explored the trait‐function relationship by growing plants under different soil fertilities and with different neighbour species.

3. To determine competitive abilities, we used a phytometer approach with two phytometer species: Poa pratensis and Achillea millefolium grown in competition with each of the 22 focal species under low and high fertility. Root and shoot morphological traits were measured and principal component analyses were used to reduce the dimensionality of the data. Three axes were extracted, which roughly corresponded to size, root and shoot architecture.

4. The hierarchy of competitive effect ability of the target species did not vary with either soil fertility or neighbour identity, while the hierarchies of competitive response abilities were highly variable among the treatments. Competitive effect ability was closely associated with size‐related traits under high nutrient conditions, and with root‐related traits under low nutrient conditions. In contrast, few plant traits axes were related to competitive response.

5. These findings indicate significant differences between competitive effect and response ability. We suggest competitive effect ability is a consistent trait of a species, linked to specific plant traits. In contrast, we found little evidence to support the idea that competitive response ability is itself a species trait, and instead it appears this may be simply a collection of different ways of avoiding or tolerating competition and/or low nutrient conditions. Supporting this argument was a lack of any consistency in which traits were associated with competitive response ability.

6. We recognize the limitations of a single study of seedlings under greenhouse conditions. However, we suggest these findings indicate a need to critically examine current assumptions about plant competition, how it is defined, and the traits which control a species’ competitive ability.
Field tests reveal genetic variation for performance at low temperatures in Drosophila melanogaster
Authors: Overgaard Johannes , Sørensen Jesper Givskov , Jensen Louise Toft , Loeschcke Volker , Kristensen Torsten Nygaard
Published: July 2009

1. Physiological and evolutionary responses underlying thermal adaptation and acclimation are often investigated under controlled laboratory conditions. Such studies may fail to assess ecologically relevant parameters as they do not account for the complexity of the natural environment.

2. We investigated a population of Drosophila melanogaster for performance at low temperature conditions in the field using release recapture assays and in the laboratory using standard cold resistance assays. The aim of the study was to get a better understanding of the nature and underlying mechanisms of the trait measured in field recapture studies and the association between field performance and fitness measures estimated in the laboratory.

3. We performed one generation of selection on the ability to reach a resource at low temperature under field conditions. Flies that reached a resource (‘mobile’) and those that never left the release site (‘stationary’) were reared to the F1 and F2 generation in the laboratory. Subsequent field releases with these flies demonstrated a clear genetic differentiation between mobile and stationary flies in their ability to reach resources at low temperatures in the field. This indicates that mobility at low temperature is under additive genetic influence. In contrast mobile and stationary flies were generally indistinguishable when tested in standard laboratory tests of cold performance. The genetic differentiation between the two sub‐populations was not linked to allelic variation in known candidate genes for cold adaptation. However, using transcriptomics we identified new candidate genes (transcripts) and pathways that differed between the mobile and stationary flies.

4. The current study reveals an irregular relationship between cold performance in the field and in the laboratory. Based on these results, we suggest that the ecological relevance of laboratory assays should be evaluated more critically in studies of thermal adaptation and hardening/acclimation.
Paoay Lake, northern Luzon, the Philippines: a record of Holocene environmental change
Authors: STEVENSON JANELLE , SIRINGAN FERNANDO , FINN JAN , MADULID DOMINGO , HEIJNIS HENK
Published: July 2009

The last 7000 years of environmental history for Paoay Lake and its surrounding landscape is examined through the analysis of pollen, diatoms, charcoal, mineral magnetics and AMS dating. Basal sediments contain shells of Cerithiidae and the saline‐tolerant diatom Diploneis indicating that this was an estuarine environment before becoming a freshwater lake after 6000 bp. Pollen analysis shows that submontane forests, characterized by Pinus pollen, underwent a major disturbance around 5000 years ago, recovering to previous levels by 1000 years ago. Charcoal as an indicator of fire is abundant throughout record, although the highest levels occur in the earlier part of the record, between 6500 and 5000 years ago. An aspect of the project was to examine whether there is evidence of land clearance and agricultural development in the region during the late Holocene. While a clear signal of human impact in the record remains equivocal, there appears to be a correspondence between submontane forest decline and mid‐Holocene ocean data that depict warmer and possibly drier conditions for the region. The study highlights the vulnerability of these montane forests to forecasts of a warmer and drier climate in the near future.
Thermal adaptation of heterotrophic soil respiration in laboratory microcosms
Authors: BRADFORD MARK A. , WATTS BRIAN W. , DAVIES CHRISTIAN A.
Published: July 2009

Respiration of heterotrophic microorganisms decomposing soil organic carbon releases carbon dioxide from soils to the atmosphere. In the short term, soil microbial respiration is strongly dependent on temperature. In the long term, the response of heterotrophic soil respiration to temperature is uncertain. However, following established evolutionary trade‐offs, mass‐specific respiration (Rmass) rates of heterotrophic soil microbes should decrease in response to sustained increases in temperature (and vice‐versa). Using a laboratory microcosm approach, we tested the potential for theRmassof the microbial biomass in six different soils to adapt to three, experimentally imposed, thermal regimes (constant 10, 20 or 30 °C). To determineRmassrates of the heterotrophic soil microbial biomass across the temperature range of the imposed thermal regimes, we periodically assayed soil subsamples using similar approaches to those used in plant, animal and microbial thermal adaptation studies. As would be expected given trade‐offs between maximum catalytic rates and the stability of the binding structure of enzymes, after 77 days of incubationRmassrates across the range of assay temperatures were greatest for the 10 °C experimentally incubated soils and lowest for the 30 °C soils, with the 20 °C incubated soils intermediate. The relative magnitude of the difference inRmassrates between the different incubation temperature treatments was unaffected by assay temperature, suggesting that maximum activities and notQ10were the characteristics involved in thermal adaptation. The time taken for changes inRmassto manifest (77 days) suggests they likely resulted from population or species shifts during the experimental incubations; we discuss alternate mechanistic explanations for those results we observed. A future research priority is to evaluate the role that thermal adaptation plays in regulating heterotrophic respiration rates from field soils in response to changing temperature, whether seasonally or through climate change.
The terminology and use of species–area relationships: a response to Dengler (2009)
Authors: Scheiner Samuel M.
Published: July 2009

Dengler (Journal of Biogeography, 2009, 36, 728–744) addresses issues regarding species–area relationships (SARs), but fails to settles those issues. He states that only certain types of sampling schemes should be used to construct SARs, but is not consistent in the criteria that he uses to include some sampling schemes but not others. He argues that a sampling scheme of contiguous plots will be more accurate in extrapolating beyond the sampled area, but logic tells us that a dispersed sampling scheme is likely to be more accurate. Finally, he concludes that the ‘true’ SAR is a power function, but this conclusion is inconsistent with his results and with the results of others. Rather than defining a narrow framework for SARs, we need to recognize that the relationship between area and species richness is scale‐ and system‐dependent. Different sampling schemes serve different purposes, and a variety of functional relationships are likely to hold. Further theoretical and empirical work is needed to resolve these issues fully.
Phylogeography and genetic structure of the orchid Himantoglossum hircinum (L.) Spreng. across its European central–marginal gradient
Authors: Pfeifer Marion , Schatz Bertrand , Xavier Picó F. , Passalacqua Nicodemo G. , Fay Michael F. , Carey Pete D. , Jeltsch Florian
Published: July 2009

Aim  This study aims to link demographic traits and post‐glacial recolonization processes with genetic traits in Himantoglossum hircinum (L.) Spreng (Orchidaceae), and to test the implications of the central–marginal concept (CMC) in Europe.

Location  Twenty sites covering the entire European distribution range of this species.

Methods  We employed amplified fragment length polymorphism (AFLP) markers and performed a plastid microsatellite survey to assess genetic variation in 20 populations of H. hircinum located along central–marginal gradients. We measured demographic traits to assess population fitness along geographical gradients and to test for correlations between demographic traits and genetic diversity. We used genetic diversity indices and analyses of molecular variance (AMOVA) to test hypotheses of reduced genetic diversity and increased genetic differentiation and isolation from central to peripheral sites. We used Bayesian simulations to analyse genetic relationships among populations.

Results  Genetic diversity decreased significantly with increasing latitudinal and longitudinal distance from the distribution centre when excluding outlying populations. The AMOVA revealed significant genetic differentiation among populations (FST = 0.146) and an increase in genetic differentiation from the centre of the geographical range to the margins (except for the Atlantic group). Population fitness, expressed as the ratio NR/N, decreased significantly with increasing latitudinal distance from the distribution centre. Flower production was lower in most eastern peripheral sites. The geographical distribution of microsatellite haplotypes suggests post‐glacial range expansion along three major migratory pathways, as also supported by individual membership fractions in six ancestral genetic clusters (C1–C6). No correlations between genetic diversity (e.g. diversity indices, haplotype frequency) and population demographic traits were detected.

Main conclusions  Reduced genetic diversity and haplotype frequency in H. hircinum at marginal sites reflect historical range expansions. Spatial variation in demographic traits could not explain genetic diversity patterns. For those sites that did not fit into the CMC, the genetic pattern is probably masked by other factors directly affecting either demography or population genetic structure. These include post‐glacial recolonization patterns and changes in habitat suitability due to climate change at the northern periphery. Our findings emphasize the importance of distinguishing historical effects from those caused by geographical variation in population demography of species when studying evolutionary and ecological processes at the range margins under global change.
All this happened, more or less: thoughts on ‘truth’, the role of fiction and its potential application in mental health and psychiatric nursing research
Authors: BILEY F. C.
Published: July 2009

Accessible summary

This paper explores history and historical research from different perspectives.

It explores the role of fiction in the construction of historical work and how there may be elements of fiction in history, and, similarly, historical ‘fact’ in works of fiction.

A number of texts that explore the 1960's counterculture are interrogated.

A conclusion is drawn that works of fiction can be used, with caution, to inform our understanding of the past.

Fundamental differences in the philosophy of history as an academic discipline are briefly explored, primarily from two perspectives. The traditional psychiatric and mental health nursing historian objectively uses primary sources in order to be able to make ‘truth’ claims about the past. The post‐modern psychiatric nursing historian, on the other hand, constructs truth claims, rather than discovers them, and in the process of doing so creates historical discourses that are different from the past. To the postmodern psychiatric nursing historian, all histories are fictions, created with the use of imagination, and have characteristics that are similar to the literary constructions that are more traditionally identified as fiction. A variety of literature is used in order to explore such claims, and the conclusion is drawn that, with caution and careful attention to the rigorous use of historical method, fiction can be used as a valid source for historical research in psychiatric and mental health nursing.
Prevalence, comorbidities and risk factors of restless legs syndrome in the Korean elderly population – results from the Korean Longitudinal Study on Health and Aging
Authors: KIM KI WOONG , YOON IN‐YOUNG , CHUNG SEOCKHOON , SHIN YOON‐KYUNG , LEE SEOK BUM , CHOI EUN AE , PARK JOON HYUCK , KIM JONG‐MIN
Published: July 2009

The aim of this study was to determine the prevalence, neuropsychiatric comorbidities, iron metabolism and potential risk factors of restless legs syndrome (RLS) in the elderly Korean population. As a community‐based epidemiological study, a simple random sample of 1118 was drawn from a roster of 61 730 adult individuals aged 65 years and older and 714 participated. The diagnosis of RLS was established in face‐to‐face interviews using the four minimal diagnostic criteria for RLS recommended by National Institute of Health. Depressive symptoms, nocturnal sleep disturbances, daytime sleepiness and quality of life were evaluated. Laboratory tests of iron metabolism, markers of inflammation, renal and endocrine function, hormones and vitamins were performed. A total of 59 patients (42 women and 17 men) were diagnosed as RLS with a prevalence of 8.3% (95% confidence interval: 6.2–10.3%), with an almost twofold higher prevalence in women (10.2%) than in men (5.7%). Depression was more prevalent among the subjects with RLS than without RLS and poor nocturnal sleep and quality of life were also observed in subjects with RLS. Daytime sleepiness was observed in 32.8% of subjects with RLS. No significant differences were found in iron metabolism or other risk factors between the subjects with and without RLS. The prevalence of RLS in the Korean elderly population was comparable with that in the Caucasian population. RLS had undesirable effects on mood, sleep quality and general wellbeing of elderly individuals.
NsrR targets in the Escherichia coli genome: new insights into DNA sequence requirements for binding and a role for NsrR in the regulation of motility
Authors: Partridge Jonathan D. , Bodenmiller Diane M. , Humphrys Michael S. , Spiro Stephen
Published: July 2009

The Escherichia coli NsrR protein is a nitric oxide‐sensitive repressor of transcription. The NsrR‐binding site is predicted to comprise two copies of an 11 bp motif arranged as an inverted repeat with 1 bp spacing. By mutagenesis we confirmed that both 11 bp motifs are required for maximal NsrR repression of the ytfE promoter. We used chromatin immunoprecipitation and microarray analysis (ChIP‐chip) to show that NsrR binds to 62 sites close to the 5′ ends of genes. Analysis of the ChIP‐chip data suggested that a single 11 bp motif (with the consensus sequence AANATGCATTT) can function as an NsrR‐binding site in vivo. NsrR binds to sites in the promoter regions of the fliAZY, fliLMNOPQR and mqsR‐ygiT transcription units, which encode proteins involved in motility and biofilm development. Reporter fusion assays confirmed that NsrR negatively regulates the fliA and fliL promoters. A mutation in the predicted 11 bp NsrR‐binding site in the fliA promoter impaired repression by NsrR and prevented detectable binding in vivo. Assays on soft‐agar confirmed that NsrR is a negative regulator of motility in E. coli K12 and in a uropathogenic strain; surface attachment assays revealed decreased levels of attached growth in the absence of NsrR.
Speech therapy in patients with excessive supragastric belching – a pilot study
Authors: Hemmink G. J. M. , Ten Cate L. , Bredenoord A. J. , Timmer R. , Weusten B. L. A. M. , Smout A. J. P. M.
Published: July 2009

Abstract  In patients whose main symptom is excessive belching, supragastric belching appears to be the predominant mechanism. This belch pattern is characterized by a rapid influx of air into the oesophagus, immediately followed by rapid air expulsion. The rate at which supragastric belching occurs is influenced by attention and distraction, suggesting a behavioural disorder and speech therapy may be of benefit to these patients. In 17 consecutive patients with excessive belching, concurrent impedance monitoring and high‐resolution manometry were performed to ascertain the mechanism of belching. Patients with supragastric belches were referred to a speech therapist, who was familiar with the concept of supragastric belching. Before and after treatment by the speech therapist, patients filled out a VAS scale regarding the severity of their symptoms. In all patients, supragastric belches were identified with impedance monitoring. Eleven patients were referred to a speech therapist, six patients were not able or willing to undergo repetitive treatments. Eleven patients completed treatment by the speech therapist consisting of 10 (8–10) sessions. Overall, the VAS scales showed a significant improvement of the severity of symptoms (P < 0.05). Six of the 11 patients reported a large decrease (>30%) in their symptoms and four patients reported a modest decrease (<30%). In one patient, the VAS scores indicated an increase in symptoms. Speech therapy performed by a well‐informed speech pathologist leads to a significant symptom reduction in patients with excessive supragastric belching. This is the first study indicating benefit of a treatment for excessive belching.
Quality and equality in obstetric care: racial and ethnic differences in caesarean section delivery rates
Authors: Bryant Allison S. , Washington Sierra , Kuppermann Miriam , Cheng Yvonne W. , Caughey Aaron B.
Published: July 2009

We sought to examine racial/ethnic differences in deliveries by caesarean section (CS) over time, particularly among women at low risk for this procedure. To do so, we conducted a retrospective cohort study at the University of California, San Francisco, a tertiary care academic centre. Births occurring between 1980 and 2001 were included in the analyses. Women with multiple gestations, fetuses in other than the cephalic presentation or with other known contraindications to vaginal birth were excluded. A total of 28 493 African American, Asian, Latina and White women were studied. Risk‐adjusted models were created to explore differences in CS risk by race/ethnicity. We also performed analyses of subgroups of women at relatively low risk of CS, and explored changes in observed disparities over time.

The overall CS rate was 15.8%. The absolute rate was highest among Latinas (16.7%) and lowest among Asians (14.7%). After adjustment for known risk factors, African American women had a 1.48 times greater odds of having a CS than did White women [95% confidence interval (CI) 1.31, 1.68], and Latina women had a 1.19 times greater odds [95% CI 1.05, 1.34]. Stepwise adjustment for confounders showed that this variation is not entirely explained by known risk factors. These differences exist even for women at low risk of CS, and have persisted over time. We conclude that racial and ethnic disparities in CS delivery exist, even among women presumed to be at lower risk of CS; rates have not improved with time. Disparities in risk‐adjusted CS should be considered as a quality metric for obstetric care, whether at the national, state, hospital or provider level.
Treatment of New World cutaneous leishmaniasis – a systematic review with a meta‐analysis
Authors: Tuon Felipe Francisco , Amato Valdir Sabbaga , Graf Maria Esther , Siqueira Andre Machado , Nicodemo Antonio Carlos , Neto Vicente Amato
Published: July 2009

Background  New World leishmaniasis is an important endemic disease and public health problem in developing countries. The increase in ecologic tourism has extended this problem to developed countries. Few drugs have emerged over the past 50 years, and drug resistance has increased, such that the cure rate is no better than 80% in large studies. Despite these data, there has been no systematic review with a meta‐analysis of the therapy used in this important tropical disease. The aim of this study was to determine the best drug management in the treatment of cutaneous leishmaniasis (CL) in Latin America based on the best studies published in the medical literature.

Methods  MEDLINE, LILACS, EMBASE, Web of Science, and Cochrane Library databases were searched to identify articles related to CL and therapy. Articles with adequate data on cure and treatment failure, internal and external validity information, and more than four patients in each treatment arm were included.

Results  Fifty‐four articles met our inclusion criteria and 12 were included in the meta‐analysis. Pentavalent antimonials were the most studied drugs, with a total of 1150 patients, achieving a cure rate of 76.5%. The cure rate of pentamidine was similar to that of pentavalent antimonials. Other drugs showed variable results, and all demonstrated an inferior response.

Conclusion  Although pentavalent antimonials are the drugs of choice in the treatment of CL, pentamidine showed similar results. Nevertheless, several aspects, such as cost, adverse effects, local experience, and availability of drugs to treat CL, must be considered when determining the best management of this disease, especially in developing countries where resources are scarce.
Non‐invasive ventilation in prone position for refractory hypoxemia after bilateral lung transplantation
Authors: Feltracco Paolo , Serra Eugenio , Barbieri Stefania , Persona Paolo , Rea Federico , Loy Monica , Ori Carlo
Published: July 2009

Abstract:  Temporary graft dysfunction with gas exchange abnormalities is a common finding during the postoperative course of a lung transplant and is often determined by the post‐reimplantation syndrome. Supportive measures including oxygen by mask, inotropes, diuretics, and pulmonary vasodilators are usually effective in non‐severe post‐reimplantation syndromes. However, in less‐responsive clinical pictures, tracheal intubation with positive pressure ventilation, or non‐invasive positive pressure ventilation (NIV), is necessary. We report on the clinical course of two patients suffering from refractory hypoxemia due to post‐reimplantation syndrome treated with NIV in the prone and Trendelenburg positions. NIV was well tolerated and led to resolution of atelectactic areas and dishomogeneous lung infiltrates. Repeated turning from supine to prone under non invasive ventilation determined a stable improvement of gas exchange and prevented a more invasive approach. Even though NIV in the prone position has not yet entered into clinical practice, it could be an interesting option to achieve a better match between ventilation and perfusion. This technique, which we successfully applied in lung transplantation, can be easily extended to other lung diseases with non‐recruitable dorso‐basal areas.
Is Semen Analysis Useful to Predict the Odds that the Sperm will Meet the Egg?
Authors: Holt WV
Published: July 2009

Content

Any mammalian spermatozoon that achieves successful in vivo fertilization has to perform almost perfectly in many disparate functions and overcome a series of obstacles imposed by the female reproductive tract. This implies that during formation in the testis and epididymis, the spermatozoa did not incur any morphological, metabolic, immunological or genetic abnormalities. Given that the spermatozoa are such highly differentiated cells, this means that every cellular compartment must not only be intact but must also respond appropriately to intracellular and extracellular signals. Assuming that a spermatozoon possesses this level of perfection, and is able to reach and penetrate an oocyte, it can only be regarded as ‘fertile’ if the DNA it carries is intact and able to sustain embryonic development. Although the proportion of inseminated spermatozoa that meet these criteria is vanishingly small, the female reproductive tract applies stringent selection criteria during sperm transport and, as a result, the probability of conception around the time of ovulation is very high. If laboratory tests of semen quality could approach the efficacy of the female reproductive tract, it would be possible to predict the odds of spermatozoa meeting the egg; however, this is not possible at present. In this article, I suggest a simple model to illustrate how a battery of laboratory tests could eventually be used to make these predictions.
Emerging role of tumour necrosis factor‐related apoptosis‐inducing ligand (TRAIL) as a key regulator of inflammatory responses
Authors: Collison Adam , Foster Paul S , Mattes Joerg
Published: July 2009

1. Tumour necrosis factor‐related apoptosis‐inducing ligand (TRAIL) induces apoptosis in tumour cells while leaving most non‐transformed cells unharmed. Binding of TRAIL to its death receptors (DR4 and DR5) activates the extrinsic apoptotic pathway by recruiting procaspase 8 into the death‐inducing silencing complex. Cleavage of the BH‐3 only peptide Bid by caspase 8 links the apoptotic TRAIL signal to the mitochondrial pathway and the subsequent release of cytochromec.

2. In addition, TRAIL binds to neutralizing decoy receptors (DcR1 and DcR2). Signalling through DcR2, DR4 and DR5 can activate pro‐inflammatory intracellular molecules such as mitogen‐activated protein kinase, protein kinase B and nuclear factor‐κB.

3. Recent studies have identified an important role for TRAIL in regulating immune responses to viruses, self‐antigen and allergens. Increased concentrations of TRAIL are found in virus infections of the lung and TRAIL affects the antiviral response and resolution of infection. In addition, TRAIL is upregulated in the airways of asthmatics and inhibition results in reduced inflammation, T helper 2 cytokine and CCL20 release, as well as abolishing the development of airway hyperreactivity in experimental models.

4. Characterization of the specific receptor systems activated and the pro‐inflammatory factors regulated by TRAILin vivomay lead to the development of novel therapeutic strategies for diseases as diverse as infection, autoimmunity and asthma.
Production of a recombinant full‐length collagen type I α‐1 and of a 45‐kDa collagen type I α‐1 fragment in barley seeds
Authors: Eskelin Katri , Ritala Anneli , Suntio Taina , Blumer Susan , Holkeri Heidi , Wahlström Eva H. , Baez Julio , Mäkinen Kristiina , Maria Nuutila Anna
Published: July 2009

Recombinant DNA technology can be used to design and express collagen and gelatin‐related proteins with predetermined composition and structure. Barley seed was chosen as a production host for a recombinant full‐length collagen type I α1 (rCIa1) and a related 45‐kDa rCIa1 fragment. The transgenic barley seeds were shown to accumulate both the rCIa1 and the 45‐kDa rCIa1 fragment. Even when the amount of the rCIa1 was just above the detection threshold, this work using rCIa1 as a model demonstrated for the first time that barley seed can be used as a production system for collagen‐related structural proteins. The 45‐kDa rCI1a fragment expression, targeted to the endoplasmic reticulum, was controlled by three different promoters (a constitutive maize ubiquitin, seed endosperm‐specific rice glutelin and germination‐specific barley α‐amylase fusion) to compare their effects on rCIa1 accumulation. Highest accumulation of the 45‐kDa rCIa1 was obtained with the glutelin promoter (140 mg/kg seed), whereas the lowest accumulation was obtained with the α‐amylase promoter. To induce homozygosity for stable 45‐kDa rCIa1 production in the transgenic lines, doubled haploid (DH) progeny was generated through microspore culture. The 45‐kDa rCIa1 expression levels achieved from the best DH lines were 13 mg/kg dry seeds under the ubiquitin promoter and 45 mg/kg dry seeds under the glutelin promoter. Mass spectroscopy and amino acid composition analysis of the purified 45‐kDa rCIa1 fragment revealed that a small percent of prolines were hydroxylated with no additional detectable post‐translational modifications.
Enhancement of vitamin B6 levels in seeds through metabolic engineering
Authors: Chen Hao , Xiong Liming
Published: July 2009

As a versatile cofactor for many enzymes catalyzing important biochemical reactions, vitamin B6 is required for all cellular organisms. In contrast to bacteria, fungi and plants, which have the ability to synthesize vitamin B6de novo, animals have to take up the vitamin from their diet. Plants are the major source of vitamin B6 for animals. The recent identification of vitamin B6 biosynthetic enzymes PDX1 and PDX2 in plants makes it possible to regulate the biosynthesis of this important vitamin. In this study, we generated Arabidopsis plants overexpressing the PDX1 and/or PDX2 gene and used a liquid chromatography/mass spectrometry/mass spectrometry method to determine the levels of different forms of vitamin B6 in these transgenic plants. It was found that expression of the PDX genes under control of the CaMV 35S promoter caused only a limited increase in pyridoxine contents in dry seeds but not in shoots or roots. When using the Arabidopsis seed‐specific 12S promoter to drive the expression of the PDX genes, the levels of vitamin B6 increased more than twofold in transgenic plants. Our work demonstrates that it is feasible to enhance vitamin B6 content in seeds by metabolic engineering.
Book review
Authors: Kelman Ilan
Published: July 2009

Book reviewed in this issue.

A Billion Lives: An Eyewitness Report from the Frontlines of Humanity
 Jan Egeland
Anthropology at the bottom of the pyramid
Authors: Cross Jamie , Street Alice
Published: July 2009

This article explores what anthropology has to say about contemporary business strategies for market expansion among poor consumers in Africa and Asia. Focusing on the activities of global consumer goods company Unilever in India, we show how anthropology can provide valuable insights into the hidden work and power relations involved in transforming an everyday commodity like soap into a composite object, what we call a ‘social good’, that is capable of simultaneously combating disease, tackling poverty and realizing value for shareholders.
Al‐Qaeda terrorism in the Sahara? Edwin Dyer's murder and the role of intelligence agencies
Authors: Keenan Jeremy
Published: July 2009

In this article, Jeremy Keenan analyses the recent spate of ‘westerners’ taken hostage in the Sahara, reportedly by Al‐Qaeda of the Islamic Maghreb (AQIM). The article, drawing on Keenan's earlier analyses of some three dozen hostage‐takings in the region since the launch of the US ‘War on terror’ in the region in 2003, raises questions about the extent to which AQIM is associated with the Algerian and other regional intelligence services; the extent to which western intelligence services have been compromised by their wider geo‐political and commercial interests and their attempts to manipulate AQIM; and the ethical dilemmas facing anthropologists working in such regions as to how they should position themselves in the interface between anthropology and intelligence.
Bulgarian passports, Macedonian identity: The invention of EU citizenship in the Republic of Macedonia
Authors: Neofotistos Vasiliki P.
Published: July 2009

In this article, I examine some of the social effects that Bulgaria's EU membership has for Macedonia and the meanings that identification documents have for ethnic Macedonians who instrumentalize Bulgarian claims on their Macedonian identity for their own ends. I argue that the case study of Macedonia helps us view identification documents as objects that neither necessarily fix nationality nor are ineluctable guarantees of belonging to the (Bulgarian) nation‐state, and understand state documentation practices as practices that do not always produce determined identities and citizen‐subjects.
A dying art? Archiving photographs in Cameroon
Authors: Zeitlyn David
Published: July 2009

I discuss the practical problems of running an project to archive the contents of a photographers studio in Cameroon with the help of the British Library's Endangered Archives Programme. Reflections on long term fieldwork in a small Cameroonian village end with the current uses of photography which are similar to those in the archive but likely never to receive such attention for reasons which I discuss.

The article is written for a non‐specialist generalist audience.
DocuBurst: Visualizing Document Content using Language Structure
Authors: Collins Christopher , Carpendale Sheelagh , Penn Gerald
Published: July 2009

Textual data is at the forefront of information management problems today. One response has been the development of visualizations of text data. These visualizations, commonly based on simple attributes such as relative word frequency, have become increasingly popular tools. We extend this direction, presenting the first visualization of document content which combines word frequency with the human‐created structure in lexical databases to create a visualization that also reflects semantic content. DocuBurst is a radial, space‐filling layout of hyponymy (the IS‐A relation), overlaid with occurrence counts of words in a document of interest to provide visual summaries at varying levels of granularity. Interactive document analysis is supported with geometric and semantic zoom, selectable focus on individual words, and linked access to source text.
Preconceptions and Individual Differences in Understanding Visual Metaphors
Authors: Ziemkiewicz Caroline , Kosara Robert
Published: July 2009

Understanding information visualization is more than a matter of reading a series of data values; it is also a matter of incorporating a visual structure into one's own thinking about a problem. We have proposed visual metaphors as a framework for understanding high‐level visual structure and its effect on visualization use. Although there is some evidence that visual metaphors can affect visualization use, the nature of this effect is still ambiguous. We propose that a user's preconceived metaphors for data and other individual differences play an important role in her ability to think in a variety of visual metaphors, and subsequently in her ability to use a visualization. We test this hypothesis by conducting a study in which a participant's preconceptions and thinking style were compared with the degree to which she is affected by conflicting metaphors in a visualization and its task questions. The results show that metaphor compatibility has a significant effect on accuracy, but that factors such as spatial ability and personality can lessen this effect. We also find a complex influence of self‐reported metaphor preference on performance. These findings shed light on how people use visual metaphors to understand a visualization.
On Visualization and Reconstruction from Non‐Uniform Point Sets using B‐splines
Authors: Vuçini Erald , Möller Torsten , Gröller M. Eduard
Published: July 2009

In this paper we present a novel framework for the visualization and reconstruction from non‐uniform point sets. We adopt a variational method for the reconstruction of 3D non‐uniform data to a uniform grid of chosen resolution. We will extend this reconstruction to an efficient multi‐resolution uniform representation of the underlying data. Our multi‐resolution representation includes a traditional bottom‐up approach and a novel top‐down hierarchy for adaptive hierarchical reconstruction. Using a hybrid regularization functional we can improve the reconstruction results. Finally, we discuss further application scenarios and show rendering results to emphasize the effectiveness and quality of our proposed framework. By means of qualitative results and error comparisons we demonstrate superiority of our method compared to competing methods.
Scalable, Versatile and Simple Constrained Graph Layout
Authors: Dwyer Tim
Published: July 2009

We describe a new technique for graph layout subject to constraints. Compared to previous techniques the proposed method is much faster and scalable to much larger graphs. For a graph with n nodes, m edges and c constraints it computes incremental layout in time O(n log n+m+c) per iteration. Also, it supports a much more powerful class of constraint: inequalities or equalities over the Euclidean distance between nodes. We demonstrate the power of this technique by application to a number of diagramming conventions which previous constrained graph layout methods could not support. Further, the constraint‐satisfaction method—inspired by recent work in position‐based dynamics—is far simpler to implement than previous methods.
Fully Automatic Visualisation of Overlapping Sets
Authors: Simonetto Paolo , Auber David , Archambault Daniel
Published: July 2009

Visualisation of taxonomies and sets has recently become an active area of research. Many application fields now require more than a strict classification of elements into a hierarchy tree. Euler diagrams, one of the most natural ways of depicting intersecting sets, may provide a solution to these problems.

In this paper, we present an approach for the automatic generation of Euler‐like diagrams. This algorithm differs from previous approaches in that it has no undrawable instances of input, allowing it to be used in systems where the output is always required. We also improve the readability of Euler diagrams through the use of Bézier curves and transparent coloured textures. Our approach has been implemented using the Tulip platform. Both the source and executable program used to generate the results are freely available.
Comparing Parameter Manipulation with Mouse, Pen, and Slider User Interfaces
Authors: Swindells Colin , Tory Melanie , Dreezer Rebecca
Published: July 2009

Visual fixation on one's tool(s) takes much attention away from one's primary task. Following the belief that the best tools ‘disappear’ and become invisible to the user, we present a study comparing visual fixations (eye gaze within locations on a graphical display) and performance for mouse, pen, and physical slider user interfaces. Participants conducted a controlled, yet representative, color matching task that required user interaction representative of many data exploration tasks such as parameter exploration of medical or fuel cell data. We demonstrate that users may spend up to 95% fewer visual fixations on physical sliders versus standard mouse and pen tools without any loss in performance for a generalized visual performance task.
Volume Deformations in Grid‐Less Flow Simulations
Authors: Obermaier Harald , Hering‐Bertram Martin , Kuhnert Jörg , Hagen Hans
Published: July 2009

This paper presents a novel method for the extraction and visualization of volume deformations in grid‐less point based flow simulations. Our primary goals are the segmentation of different paths through a mixing device and the visualization of ellipsoidal particle deformations. The main challenges are the numerically efficient processing of deformation tensors and the robust integration of stream‐ and streaklines at boundaries of the dataset such that closed segments are obtained. Our results show two‐ and three‐dimensional particle deformations as well as the segmentation of volumes in stationary fields and areas in time‐dependent datasets taking consistent paths through a mixing device.
Selecting good views of high‐dimensional data using class consistency
Authors: Sips Mike , Neubert Boris , Lewis John P. , Hanrahan Pat
Published: July 2009

Many visualization techniques involve mapping high‐dimensional data spaces to lower‐dimensional views. Unfortunately, mapping a high‐dimensional data space into a scatterplot involves a loss of information; or, even worse, it can give a misleading picture of valuable structure in higher dimensions. In this paper, we propose class consistency as a measure of the quality of the mapping. Class consistency enforces the constraint that classes of n–D data are shown clearly in 2–D scatterplots. We propose two quantitative measures of class consistency, one based on the distance to the class's center of gravity, and another based on the entropies of the spatial distributions of classes. We performed an experiment where users choose good views, and show that class consistency has good precision and recall. We also evaluate both consistency measures over a range of data sets and show that these measures are efficient and robust.
Semi‐Automatic Time‐Series Transfer Functions via Temporal Clustering and Sequencing
Authors: Woodring Jonathan , Shen Han‐Wei
Published: July 2009

When creating transfer functions for time‐varying data, it is not clear what range of values to use for classification, as data value ranges and distributions change over time. In order to generate time‐varying transfer functions, we search the data for classes that have similar behavior over time, assuming that data points that behave similarly belong to the same feature. We utilize a method we call temporal clustering and sequencing to find dynamic features in value space and create a corresponding transfer function. First, clustering finds groups of data points that have the same value space activity over time. Then, sequencing derives a progression of clusters over time, creating chains that follow value distribution changes. Finally, the cluster sequences are used to create transfer functions, as sequences describe the value range distributions over time in a data set.
Bivariate Transfer Functions on Unstructured Grids
Authors: Song Yuyan , Chen Wei , Maciejewski Ross , Gaither Kelly P. , Ebertt David S.
Published: July 2009

Multi‐dimensional transfer functions are commonly used in rectilinear volume renderings to effectively portray materials, material boundaries and even subtle variations along boundaries. However, most unstructured grid rendering algorithms only employ one‐dimensional transfer functions. This paper proposes a novel pre‐integrated Projected Tetrahedra (PT) rendering technique that applies bivariate transfer functions on unstructured grids. For each type of bivariate transfer function, an analytical form that pre‐integrates the contribution of a ray segment in one tetrahedron is derived, and can be precomputed as a lookup table to compute the color and opacity in a projected tetrahedron on‐the‐fly. Further, we show how to approximate the integral using the pre‐integration method for faster unstructured grid rendering. We demonstrate the advantages of our approach with a variety of examples and comparisons with one‐dimensional transfer functions.
Interactive Visualization of Function Fields by Range‐Space Segmentation
Authors: Anderson John C. , Gosink Luke J. , Duchaineau Mark A. , Joy Kenneth I.
Published: July 2009

We present a dimension reduction and feature extraction method for the visualization and analysis of function field data. Function fields are a class of high‐dimensional, multi‐variate data in which data samples are one‐dimensional scalar functions. Our approach focuses upon the creation of high‐dimensional range‐space segmentations, from which we can generate meaningful visualizations and extract separating surfaces between features. We demonstrate our approach on high‐dimensional spectral imagery, and particulate pollution data from air quality simulations.
TAMING THE ‘AWKWARD STATE’? THE CHANGING FACE OF EUROPEAN POLICY‐MAKING UNDER BLAIR
Authors: JAMES SCOTT
Published: July 2009

This paper analyses the important changes to the European Union (EU) policy‐making process within the UK core executive introduced by the Blair government between 1997 and 2007. Employing a strategic‐relational network framework, it sets out to map the changing face of policy‐making within the Whitehall EU network, and to evaluate and explain the impact of adaptation. The article argues that Labour's reform strategy has been double‐edged: day‐to‐day coordination of EU policy has become increasingly informal, ad hoc and delegated downwards to departmental players while the role of the centre has been greatly strengthened in order to provide more effective strategic direction and political leadership. Despite these seemingly coherent reforms, however, many critical features of the process have been potentially detrimental to the projection of a more constructive European policy.