bluuebunny/crossref_metadata_2025 huggingface dataset:
Divergence of human and mouse brain transcriptome highlights Alzheimer disease pathways
Authors: Miller Jeremy A. , Horvath Steve , Geschwind Daniel H.
Published: June 2010

Because mouse models play a crucial role in biomedical research related to the human nervous system, understanding the similarities and differences between mouse and human brain is of fundamental importance. Studies comparing transcription in human and mouse have come to varied conclusions, in part because of their relatively small sample sizes or underpowered methodologies. To better characterize gene expression differences between mouse and human, we took a systems-biology approach by using weighted gene coexpression network analysis on more than 1,000 microarrays from brain. We find that global network properties of the brain transcriptome are highly preserved between species. Furthermore, all modules of highly coexpressed genes identified in mouse were identified in human, with those related to conserved cellular functions showing the strongest between-species preservation. Modules corresponding to glial and neuronal cells were sufficiently preserved between mouse and human to permit identification of cross species cell-class marker genes. We also identify several robust human-specific modules, including one strongly correlated with measures of Alzheimer disease progression across multiple data sets, whose hubs are poorly-characterized genes likely involved in Alzheimer disease. We present multiple lines of evidence suggesting links between neurodegenerative disease and glial cell types in human, including human-specific correlation of presenilin-1 with oligodendrocyte markers, and significant enrichment for known neurodegenerative disease genes in microglial modules. Together, this work identifies convergent and divergent pathways in mouse and human, and provides a systematic framework that will be useful for understanding the applicability of mouse models for human brain disorders.
A metagenomic β-glucuronidase uncovers a core adaptive function of the human intestinal microbiome
Authors: Gloux Karine , Berteau Olivier , El oumami Hanane , Béguet Fabienne , Leclerc Marion , Doré Joël
Published: June 2010

In the human gastrointestinal tract, bacterial β-D-glucuronidases (BG; E.C. 3.2.1.31) are involved both in xenobiotic metabolism and in some of the beneficial effects of dietary compounds. Despite their biological significance, investigations are hampered by the fact that only a few BGs have so far been studied. A functional metagenomic approach was therefore performed on intestinal metagenomic libraries using chromogenic glucuronides as probes. Using this strategy, 19 positive metagenomic clones were identified but only one exhibited strong β-D-glucuronidase activity when subcloned into an expression vector. The cloned gene encoded a β-D-glucuronidase (called H11G11-BG) that had distant amino acid sequence homologies and an additional C terminus domain compared with known β-D-glucuronidases. Fifteen homologs were identified in public bacterial genome databases (38–57% identity with H11G11-BG) in the Firmicutes phylum. The genomes identified derived from strains from Ruminococcaceae, Lachnospiraceae, and Clostridiaceae. The genetic context diversity, with closely related symporters and gene duplication, argued for functional diversity and contribution to adaptive mechanisms. In contrast to the previously known β-D-glucuronidases, this previously undescribed type was present in the published microbiome of each healthy adult/child investigated (n= 11) and was specific to the human gut ecosystem. In conclusion, our functional metagenomic approach revealed a class of BGs that may be part of a functional core specifically evolved to adapt to the human gut environment with major health implications. We propose consensus motifs for this unique Firmicutes β-D-glucuronidase subfamily and for the glycosyl hydrolase family 2.
Metabolic fate of polyphenols in the human superorganism
Authors: van Duynhoven John , Vaughan Elaine E. , Jacobs Doris M. , A. Kemperman Robèr , van Velzen Ewoud J. J. , Gross Gabriele , Roger Laure C. , Possemiers Sam , Smilde Age K. , Doré Joël , Westerhuis Johan A. , Van de Wiele Tom
Published: June 2010

Dietary polyphenols are components of many foods such as tea, fruit, and vegetables and are associated with several beneficial health effects although, so far, largely based on epidemiological studies. The intact forms of complex dietary polyphenols have limited bioavailability, with low circulating levels in plasma. A major part of the polyphenols persists in the colon, where the resident microbiota produce metabolites that can undergo further metabolism upon entering systemic circulation. Unraveling the complex metabolic fate of polyphenols in this human superorganism requires joint deployment of in vitro and humanized mouse models and human intervention trials. Within these systems, the variation in diversity and functionality of the colonic microbiota can increasingly be captured by rapidly developing microbiomics and metabolomics technologies. Furthermore, metabolomics is coming to grips with the large biological variation superimposed on relatively subtle effects of dietary interventions. In particular when metabolomics is deployed in conjunction with a longitudinal study design, quantitative nutrikinetic signatures can be obtained. These signatures can be used to define nutritional phenotypes with different kinetic characteristics for the bioconversion capacity for polyphenols. Bottom-up as well as top-down approaches need to be pursued to link gut microbial diversity to functionality in nutritional phenotypes and, ultimately, to bioactivity of polyphenols. This approach will pave the way for personalization of nutrition based on gut microbial functionality of individuals or populations.
Optical activation of lateral amygdala pyramidal cells instructs associative fear learning
Authors: Johansen Joshua P. , Hamanaka Hiroki , Monfils Marie H. , Behnia Rudy , Deisseroth Karl , Blair Hugh T. , LeDoux Joseph E.
Published: June 2010

Humans and animals can learn that specific sensory cues in the environment predict aversive events through a form of associative learning termed fear conditioning. This learning occurs when the sensory cues are paired with an aversive event occuring in close temporal proximity. Activation of lateral amygdala (LA) pyramidal neurons by aversive stimuli is thought to drive the formation of these associative fear memories; yet, there have been no direct tests of this hypothesis. Here we demonstrate that viral-targeted, tissue-specific expression of the light-activated channelrhodopsin (ChR2) in LA pyramidal cells permitted optical control of LA neuronal activity. Using this approach we then paired an auditory sensory cue with optical stimulation of LA pyramidal neurons instead of an aversive stimulus. Subsequently presentation of the tone alone produced behavioral fear responses. These results demonstrate in vivo optogenetic control of LA neurons and provide compelling support for the idea that fear learning is instructed by aversive stimulus-induced activation of LA pyramidal cells.
Phosphorylation of protocadherin proteins by the receptor tyrosine kinase Ret
Authors: Schalm Stefanie S. , Ballif Bryan A. , Buchanan Sean M. , Phillips Greg R. , Maniatis Tom
Published: June 2010

The clustered protocadherins (Pcdhs) are a large family of cadherin-like transmembrane proteins expressed in the nervous system. Stochastic expression of
Pcdh
genes and alternative splicing of their pre-mRNAs have the potential to generate enormous protein diversity at the cell surface of neurons. At present, the regulation and function of Pcdh proteins are largely unknown. Here, we show that Pcdhs form a heteromeric signaling complex(es), consisting of multiple Pcdh isoforms, receptor tyrosine kinases, phosphatases, and cell adhesion molecules. In particular, we find that the receptor tyrosine kinase rearranged during transformation (Ret) binds to Pcdhs in differentiated neuroblastoma cells and is required for stabilization and differentiation-induced phosphorylation of Pcdh proteins. In addition, the Ret ligand glial cell line-derived neurotrophic factor induces phosphorylation of Pcdhγ in motor neurons and phosphorylation of Pcdhα and Pcdhγ in sympathetic neurons. Conversely, Pcdh proteins are also required for the stabilization of activated Ret in neuroblastoma cells and sympathetic ganglia. Thus, Pcdhs and Ret are functional components of a phosphorylation-dependent signaling complex.
War & the Forgotten Continent
Authors: Abrahamsen Rita , Bush Ray
Published: June 2010

As US and UK military forces invade Iraq the death of innocents in the Middle East will be added to those dying from AIDS, famine and preventable illness in Africa. The waging of war at any time, when not sanctioned by international law and the victims pose no threat to neighbours or invaders, is monstrous. It is even more so as US and UK resources are diverted towards the aims of death and destruction when millions in Africa are starving to death. In Iraq itself, the British Overseas Aid Group (Oxfam, Cafod, Christian Aid, Action Aid and Save the Children) warns of the humanitarian consequences of war in a country where more than 16 million are entirely dependent upon food aid. There has been little concern for the lives of those to be affected by military conflict as preparation to relieve the humanitarian disaster has taken second place to the creation of that disaster. The US will spend $12.5 billion a month on the war although it has offered $65 million to provide help with immediate humanitarian assistance. And when it is time for the reconstruction of Iraq, the US will offer only $50 million of a possible $1.5 billion to NGOs and the UN for the process – the rest goes to US companies, including those close to White House officials (The Guardian, 18 March 2003).
Africa: The Next Liberation Struggle?
Authors: Saul John S.
Published: June 2010

This article brings into focus the immediate challenges facing progressives in Africa as they now seek to forge social and political initiatives that can hope to attain power and implement policies able to confront and ultimately to bend the apparent logic of global capitalism – thereby permitting more humane outcomes on the continent. Taking as a starting-point the moment of heightened reflection on such issues that occurred in Dar es Salaam in the 1960s and early 1970s, the article up-dates the insights of that period with reference to the even grimmer circumstances in which Africa currently finds itself. Suggesting that mere ‘reform’ (NEPAD, ‘liberal democratisation’) offers little real promise of meaningful and substantial change of the continent's desperate situation, the article seeks to canvas the range of resistances in Africa that indicate the emergence of a more radical project of transformation. While acknowledging that it is easy to be pessimistic regarding such possibilities, the article identifies sufficient movement on the continent to suggest that Africa, in terms of the emergence of a ‘post-nationalist, post-neo-liberal’ revolutionary politics, now stands at a moment analogous with 1945. At that time few could have anticipated the speed with which African nationalist movements would win independence for their territories from colonial rule. The article concludes with the argument that, despite its current eclipse, the language and vision of socialism will have to become part and parcel of this continuing revival of Africa's revolutionary endeavours and of its ‘next liberation struggle’.
From ‘Growth with Equity’ to ‘Fast-Track’ Reform: Zimbabwe's Land Question
Authors: Sachikonye Lloyd M.
Published: June 2010

This article represents a provisional attempt to explain the changing and competing strands of the debate surrounding the ‘land question’ as it has unfolded in Zimbabwe in the past 23 years. As in most contexts of land reform, the debate is highly political whether packaged in nationalist or technocratic rhetoric. Since independence, three phases of land reform debate can be identified: the early independence years from 1980 to about 1989, the period of structural adjustment and afterwards from 1990–1999, and the current phase which commenced in 2000. The paper concludes by providing an update on the short-term repercussions of the ‘fast-track’ reform programme for the agricultural sector, food security and the wider economy.
Rural Cooperation & the Renewal of Rural Socialism in Africa
Authors: Lawrence Peter
Published: June 2010

This article examines the debates over the role of co-operatives in the building of socialism and more generally their possible role as important organisations for boosting production and creating opportunities for collective decision making in capitalist and transition economies. It does so by putting centre stage the benefits of rural co-operation as well as the historical pitfalls. It stresses the opportunity for cooperatives to boost the democratic imperative for socialist development even at a time of neo-liberal ascendency
Land & Liberation in Eritrea: Reflecting on the work of Lionel Cliffe
Authors: Tesfai Alemseged
Published: June 2010

This article examines the contribution Lionel Cliffe has made to a charcterisation of the war of liberation in Eritrea. It does so by looking at the specificity of the Eritrean case and the dimensions of the struggle for liberation including the military strategy of the EPLF and the strategy for land reform.
Democracy in Southern Africa: Moving Beyond a Difficult Legacy
Authors: Southall Roger
Published: June 2010

The peace dividend in southern Africa may serve to underpin NEPAD's bid for economic growth and development. However, it is by no means so clear that the region is embarked upon an unambiguous progression towards the consolidation of democracy. Indeed, there are deeply worrying indications that the democratic wave which broke upon the region's shores in the 1990s is now moving into reverse. Most particularly, it can be argued that a developing crisis of democracy in southern Africa is characterised by first, an increasingly explicit clash between an authoritarian culture of national liberation and participatory democracy; and second, by a closely related model of state power which, even if obscured under democratic garb, entrenches elites and promotes highly unequal patterns of accumulation and anti-development. It is therefore necessary to move forward to a more advanced conception of democracy which links liberal democratic rights to conditions which combine increased political participation with greater social and economic equality.
Women's Reproductive Health & Population Policy: Tanzania
Authors: Richey Lisa Ann
Published: June 2010

Population policies have rarely been linked to economic policy, although the promoters of economic liberalisation also support the embrace of population policy as important to the economic wellbeing of African states. Using a case study from Tanzania, I argue that population policies with a limited focus on fertility reduction may continue to be successful in the context of post-adjustment African health care systems, but policies that aim for the larger goals of improving women's reproductive health will be severely limited. Tanzania's donors and lenders promoted Neo-Malthusian types of population policies aimed primarily at reducing childbearing as a partial solution to the country's economic crisis. However, in the mid-1990s, the international discourse on population shifted toward a new dependent variable of ‘women's reproductive’ health. The notion of reproductive health reunites population and development issues in the context of basic health care provision. Improvements in the reproductive health of Tanzanian women will require more than simply the effective provision of contraceptives. This article argues that the challenges of improving reproductive health are unlikely to be met without a revitalisation of public health care provision in African countries.
‘The Workers' Struggle’: A South African Text Revisited
Authors: Plaut Martin
Published: June 2010

In April 1982 workers from across South Africa met at the congress of the non-racial trade union movement, the Federation of South African Trade Unions, Fosatu. The federation was just three years old, but in that time it had grown five fold, from around 20,000 workers to over 100,000 (Baskin, 1991:25, 29). What they heard was a speech that must rank as one of the most important statements of principle ever delivered to a South African labour movement. Although the Fosatu general secretary, Joe Foster read it, the speech reflected the work of many people. Its authors have never been revealed, but the hand of Alec Erwin – Fosatu's first general secretary, and currently South Africa's Minister of Trade and Industry – was almost certainly among them.
NON-GAUSSIANITIES IN THE LOCAL CURVATURE OF THE FIVE-YEAR WMAP DATA
Authors: Rudjord Øystein , Groeneboom Nicolaas E. , Hansen Frode K. , Cabella Paolo
Published: June 2010

Using the five-year WMAP data, we re-investigate claims of non-Gaussianities and asymmetries detected in local curvature statistics of the one-year WMAP data. In Hansen et al., it was found that the northern ecliptic hemisphere was non-Gaussian at the ∼1% level testing the densities of hill, lake, and saddle points based on the second derivatives of the cosmic microwave background temperature map. The five-year WMAP data have a much lower noise level and better control of systematics. Using these, we find that the anomalies are still present at a consistent level. Also the direction of maximum non-Gaussianity remains. Due to limited availability of computer resources, Hansen et al. were unable to calculate the full covariance matrix for the χ2-test used. Here, we apply the full covariance matrix instead of the diagonal approximation and find that the non-Gaussianities disappear and there is no preferred non-Gaussian direction. We compare with simulations of weak lensing to see if this may cause the observed non-Gaussianity when using a diagonal covariance matrix. We conclude that weak lensing does not produce non-Gaussianity in the local curvature statistics at the scales investigated in this paper. The cause of the non-Gaussian detection in the case of a diagonal matrix remains unclear.
Pre‐clinical diabetic cardiomyopathy: prevalence, screening, and outcome
Authors: Kiencke Stephanie , Handschin Rolf , von Dahlen Ruth , Muser Jürgen , Brunner‐LaRocca Hans Peter , Schumann Jörg , Felix Barbara , Berneis Kaspar , Rickenbacher Peter
Published: June 2010

Aims

Diabetic cardiomyopathy, characterized by left ventricular (LV) dysfunction and LV hypertrophy independent of myocardial ischaemia and hypertension, could contribute to the increased life‐time risk of congestive heart failure seen in patients with diabetes. We assessed prospectively the prevalence, effectiveness of screening methods [brain natriuretic peptide (BNP) and C‐reactive protein in combination with clinical parameters], and outcome of pre‐clinical diabetic cardiomyopathy.

Methods and results

We studied 100 adults (mean age 57.4 ± 10.2 years, 44% females) with diabetes and no previous evidence of structural heart disease. By echocardiography, diabetic cardiomyopathy was present in 48% of patients. Screening with combinations of clinical parameters (gender, systolic blood pressure, and body mass index), but not BNP, resulted in high negative predictive values for diabetic cardiomyopathy. During a mean follow‐up of 48.5 ± 9.0 months, in the groups with and without diabetic cardiomyopathy, 12.5 vs. 3.9% (P < 0.2) patients died or experienced cardiovascular events and 37.5 vs. 9.6% (P < 0.002) had a deterioration in NYHA functional class. Overall event‐free survival was 54 vs. 87% (P = 0.001) in the groups with and without diabetic cardiomyopathy, respectively. Brain natriuretic peptide was an independent predictor of events [odds ratio 3.5 (1.1–10.9), P = 0.02].

Conclusion

Pre‐clinical diabetic cardiomyopathy is common. Screening with combinations of simple clinical parameters, but not BNP, can be useful to identify those patients needing further evaluation. Patients with pre‐clinical diabetic cardiomyopathy are at increased risk for functional deterioration and possibly cardiovascular events during follow‐up. Brain natriuretic peptide was shown to be an independent predictor of future events.
Feeding habits of some demersal fish on the Charleston Bump off the southeastern United States
Authors: Goldman Sarah F. , Sedberry George R.
Published: June 2010

Goldman, S. F. and Sedberry, G. R. 2011. Feeding habits of some demersal fish on the Charleston Bump off the southeastern United States. – ICES Journal of Marine Science, 68: 390–398. The feeding habits of several demersal fish on the upper continental slope were investigated to determine the trophic relationships of these ecologically dominant and commercially important species, and to determine food sources for slope fish off the southeastern United States. Stomach contents were examined from 534 fish, including wreckfish (Polyprion americanus), barrelfish (Hyperoglyphe perciformis), and red bream (Beryx decadactylus). Fish fed on 46 prey taxa, and there were dietary differences among predators. Wreckfish predominantly consumed teleost fish and squid; barrelfish had a diet dominated by pelagic tunicates and some mesopelagic fish and squid; red bream consumed mainly fish, squid, and crustaceans. Seasonal shifts in diet were observed in all three species. Many of the prey items encountered were vertically migrating organisms, which are a critical link between surface waters and the slope ecosystem.
Sardine potential habitat and environmental forcing off western Portugal
Authors: Zwolinski Juan P. , Oliveira Paulo B. , Quintino Victor , Stratoudakis Yorgos
Published: June 2010

Zwolinski, J. P., Oliveira, P. B., Quintino, V., and Stratoudakis, Y. 2010. Sardine potential habitat and environmental forcing off western Portugal. – ICES Journal of Marine Science, 67: 1553–1564. Relationships between sardine (Sardina pilchardus) distribution and the environment off western Portugal were explored using data from seven acoustic surveys (spring and autumn of 2000, 2001, 2005, and spring 2006). Four environmental variables (salinity, temperature, chlorophyll a, and acoustic epipelagic backscatter other than fish) were related to the acoustic presence and density of sardine. Univariate quotient analysis revealed sardine preferences for waters with high chlorophyll a content, low temperature and salinity, and low acoustic epipelagic backscatter. Generalized additive models depicted significant relationships between the environment and sardine presence but not with sardine density. Maps of sardine potential habitat (SPH) built upon the presence/absence models revealed a clear seasonal effect in the across-bathymetry and alongshelf extension of SPH off western Portugal. During autumn, SPH covered a large part of the northern Portuguese continental shelf but was almost absent from the southern region, whereas in spring SPH extended farther south but was reduced to a narrow band of shallow coastal waters in the north. This seasonal pattern agrees with the spatio-temporal variation of primary production and oceanic circulation described for the western Iberian shelf.
Shifting-balance stock structure in North Pacific walleye pollock (Gadus chalcogrammus)
Authors: Grant W. Stewart , Spies Ingrid , Canino Michael F.
Published: June 2010

Grant, W. S., Spies, I., and Canino, M. F. 2010. Shifting-balance stock structure in North Pacific walleye pollock (Gadus chalcogrammus). – ICES Journal of Marine Science, 67: 1687–1696. High levels of gene flow are expected to produce genetic homogeneity among open-ocean populations of walleye pollock (Gadus chalcogrammus) because of few restrictions on migration. Although most genetic studies confirm this prediction, many surveys of morphology have detected differences among populations. Here, sequences of mitochondrial DNA cytochrome oxidase subunit I in nine samples (n = 433) from Japan to Puget Sound were used to evaluate genetic population structure. Two haplotypes varied clinally across the North Pacific. These clines are likely the result of the isolation of populations in ice-age refugia, secondary post-glacial contact, and restricted long-distance dispersal. Overall, ΦST = 0.030 (p < 0.001), but the greatest partition was attributable to differences between Asian and North American populations (ΦCT = 0.058, p = 0.036). Isolation by distance was detected across the North Pacific, but differentiation among populations within regions was minimal (ΦSC = 0.007, p < 0.092). Climate variability on decadal–centennial scales produces shifts in local abundance, which prevent the appearance of genetically discrete stocks. These cycles of boom and bust, combined with high levels of gene flow, lead to different stock structures, as viewed with morphological, life history, and genetic markers.
“Satisficing” and trade-offs: evaluating rebuilding strategies for Greenland halibut off the east coast of Canada
Authors: Miller David C. M. , Shelton Peter A.
Published: June 2010

Miller, D. C. M., and Shelton, P. A. 2010. “Satisficing” and trade-offs: evaluating rebuilding strategies for Greenland halibut off the east coast of Canada. – ICES Journal of Marine Science, 67: 1896–1902. To be effective, management strategy evaluation (MSE) requires a well-defined procedure for comparing the merits of candidate management strategies. We explore a two-step approach of “satisficing” followed by a trade-off analysis. “Satisficing” (a portmanteau of “satisfy” and “suffice”) is a decision-making procedure that attempts to meet criteria for adequacy, rather than identify an optimal solution. As a case study, we consider the results from a comprehensive MSE for Greenland halibut off the east coast of Canada, carried out under the auspices of the Northwest Atlantic Fisheries Organization. First, we apply satisficing to the results to determine which rebuilding strategies achieve pre-specified thresholds set for imperative performance statistics relating to resource conservation, yield, and stability of the fishery. Next, trade-offs among important, but not necessarily imperative, performance statistics are evaluated for those strategies that pass the satisficing step. For Greenland halibut, a management strategy containing a simple feedback harvest-control rule based on recent trends in survey estimates of abundance satisfices all imperative requirements and provides the best trade-off in other performance statistics. The approach necessitates translating objectives for stock rebuilding and sustainable fisheries into operationally explicit terms and incorporates a priori consideration of stakeholders' concerns.
Understanding Off-the-Books Politics: Conducting Inference on the Determinants of Sensitive Behavior with Randomized Response Surveys
Authors: Gingerich Daniel W.
Published: June 2010

This study presents a survey-based method for conducting inference into the determinants of sensitive political behavior. The approach combines two well-established literatures in statistical methods in the social sciences: the randomized response (RR) methodology utilized to reduce evasive answer bias and the generalized propensity score methodology utilized to draw inferences about causal effects in observational studies. The approach permits one to estimate the causal impact of a multivalued predictor variable of interest on a given sensitive behavior in the face of unknown interaction effects between the predictor and the confounders as well as nonlinearities in the relationship between the confounders and the sensitive behavior. Simulation results point to the superior performance of the RR relative to direct survey questioning using this method for samples of moderate to large size. The utility of the approach is illustrated through an application to corruption in the public bureaucracy in three countries in South America.
Ronin/Hcf-1 binds to a hyperconserved enhancer element and regulates genes involved in the growth of embryonic stem cells
Authors: Dejosez Marion , Levine Stuart S. , Frampton Garrett M. , Whyte Warren A. , Stratton Sabrina A. , Barton Michelle C. , Gunaratne Preethi H. , Young Richard A. , Zwaka Thomas P.
Published: June 2010

Self-renewing embryonic stem (ES) cells have an exceptional need for timely biomass production, yet the transcriptional control mechanisms responsible for meeting this requirement are largely unknown. We report here that Ronin (Thap11), which is essential for the self-renewal of ES cells, binds with its transcriptional coregulator, Hcf-1, to a highly conserved enhancer element that previously lacked a recognized binding factor. The subset of genes bound by Ronin/Hcf-1 function primarily in transcription initiation, mRNA splicing, and cell metabolism; genes involved in cell signaling and cell development are conspicuously underrepresented in this target gene repertoire. Although Ronin/Hcf-1 represses the expression of some target genes, its activity at promoter sites more often leads to the up-regulation of genes essential to protein biosynthesis and energy production. We propose that Ronin/Hcf-1 controls a genetic program that contributes to the unimpeded growth of ES cells.
A brief nap is beneficial for human route-learning: The role of navigation experience and EEG spectral power
Authors: Wamsley Erin J. , Tucker Matthew A. , Payne Jessica D. , Stickgold Robert
Published: June 2010

Here, we examined the effect of a daytime nap on changes in virtual maze performance across a single day. Participants either took a short nap or remained awake following training on a virtual maze task. Post-training sleep provided a clear performance benefit at later retest, but only for those participants with prior experience navigating in a three-dimensional (3D) environment. Performance improvements in experienced players were correlated with delta-rich stage 2 sleep. Complementing observations that learning-related brain activity is reiterated during post-navigation NREM sleep in rodents, the present data demonstrate that NREM sleep confers a performance advantage for spatial memory in humans.
Boron Toxicity Tolerance in Barley through Reduced Expression of the Multifunctional Aquaporin HvNIP2;1
Authors: Schnurbusch Thorsten , Hayes Julie , Hrmova Maria , Baumann Ute , Ramesh Sunita A. , Tyerman Stephen D. , Langridge Peter , Sutton Tim
Published: June 2010

Boron (B) toxicity is a significant limitation to cereal crop production in a number of regions worldwide. Here we describe the cloning of a gene from barley (Hordeum vulgare), underlying the chromosome 6H B toxicity tolerance quantitative trait locus. It is the second B toxicity tolerance gene identified in barley. Previously, we identified the gene Bot1 that functions as an efflux transporter in B toxicity-tolerant barley to move B out of the plant. The gene identified in this work encodes HvNIP2;1, an aquaporin from the nodulin-26-like intrinsic protein (NIP) subfamily that was recently described as a silicon influx transporter in barley and rice (Oryza sativa). Here we show that a rice mutant for this gene also shows reduced B accumulation in leaf blades compared to wild type and that the mutant protein alters growth of yeast (Saccharomyces cerevisiae) under high B. HvNIP2;1 facilitates significant transport of B when expressed in Xenopus oocytes compared to controls and to another NIP (NOD26), and also in yeast plasma membranes that appear to have relatively high B permeability. We propose that tolerance to high soil B is mediated by reduced expression of HvNIP2;1 to limit B uptake, as well as by increased expression of Bot1 to remove B from roots and sensitive tissues. Together with Bot1, the multifunctional aquaporin HvNIP2;1 is an important determinant of B toxicity tolerance in barley.
VERDANDIIs a Direct Target of the MADS Domain Ovule Identity Complex and Affects Embryo Sac Differentiation inArabidopsis
Authors: Matias-Hernandez Luis , Battaglia Raffaella , Galbiati Francesca , Rubes Marco , Eichenberger Christof , Grossniklaus Ueli , Kater Martin M. , Colombo Lucia
Published: June 2010

In Arabidopsis thaliana, the three MADS box genes SEEDSTICK (STK), SHATTERPROOF1 (SHP1), and SHP2 redundantly regulate ovule development. Protein interaction studies have shown that a multimeric complex composed of the ovule identity proteins together with the SEPALLATA MADS domain proteins is necessary to determine ovule identity. Despite the extensive knowledge that has become available about these MADS domain transcription factors, little is known regarding the genes that they regulate. Here, we show that STK, SHP1, and SHP2 redundantly regulate VERDANDI (VDD), a putative transcription factor that belongs to the plant-specific B3 superfamily. The vdd mutant shows defects during the fertilization process resulting in semisterility. Analysis of the vdd mutant female gametophytes indicates that antipodal and synergid cell identity and/or differentiation are affected. Our results provide insights into the pathways regulated by the ovule identity factors and the role of the downstream target gene VDD in female gametophyte development.
Genome-Wide Distribution of TransposedDissociationElements in Maize
Authors: Vollbrecht Erik , Duvick Jon , Schares Justin P. , Ahern Kevin R. , Deewatthanawong Prasit , Xu Ling , Conrad Liza J. , Kikuchi Kazuhiro , Kubinec Tammy A. , Hall Bradford D. , Weeks Rebecca , Unger-Wallace Erica , Muszynski Michael , Brendel Volker P. , Brutnell Thomas P.
Published: June 2010

The maize (Zea mays) transposable element Dissociation (Ds) was mobilized for large-scale genome mutagenesis and to study its endogenous biology. Starting from a single donor locus on chromosome 10, over 1500 elements were distributed throughout the genome and positioned on the maize physical map. Genetic strategies to enrich for both local and unlinked insertions were used to distribute Ds insertions. Global, regional, and local insertion site trends were examined. We show that Ds transposed to both linked and unlinked sites and displayed a nonuniform distribution on the genetic map around the donor r1-sc:m3 locus. Comparison of Ds and Mutator insertions reveals distinct target preferences, which provide functional complementarity of the two elements for gene tagging in maize. In particular, Ds displays a stronger preference for insertions within exons and introns, whereas Mutator insertions are more enriched in promoters and 5′-untranslated regions. Ds has no strong target site consensus sequence, but we identified properties of the DNA molecule inherent to its local structure that may influence Ds target site selection. We discuss the utility of Ds for forward and reverse genetics in maize and provide evidence that genes within a 2- to 3-centimorgan region flanking Ds insertions will serve as optimal targets for regional mutagenesis.
Class XI Myosins Are Required for Development, Cell Expansion, and F-Actin Organization in Arabidopsis
Authors: Peremyslov Valera V. , Prokhnevsky Alexey I. , Dolja Valerian V.
Published: June 2010

The actomyosin system is conserved throughout eukaryotes. Although F-actin is essential for cell growth and plant development, roles of the associated myosins are poorly understood. Using multiple gene knockouts in Arabidopsis thaliana, we investigated functional profiles of five class XI myosins, XI-K, XI-1, XI-2, XI-B, and XI-I. Plants lacking three myosins XI showed stunted growth and delayed flowering, whereas elimination of four myosins further exacerbated these defects. Loss of myosins led to decreased leaf cell expansion, with the most severe defects observed in the larger leaf cells. Root hair length in myosin-deficient plants was reduced ∼10-fold, with quadruple knockouts showing morphological abnormalities. It was also found that trafficking of Golgi and peroxisomes was entirely myosin dependent. Surprisingly, myosins were required for proper organization of F-actin and the associated endoplasmic reticulum networks, revealing a novel, architectural function of the class XI myosins. These results establish critical roles of myosin-driven transport and F-actin organization during polarized and diffuse cell growth and indicate that myosins are key factors in plant growth and development.
Fostering a research culture in UK library practice: barriers and solutions
Authors: McMenemy David
Published: June 2010

Purpose

The purpose of this paper is to discuss how more of a research culture can be fostered within library practice and how universities and library professionals can work together to strengthen this important area.

Design/methodology/approach

The paper provides a reflective viewpoint.

Findings

The dangers of a lack of a research culture present the profession with potential issues that must be addressed if it is to remain vital. The profession and those involved in academic research must work more closely together to foster a research culture, and more emphasis should be placed in ensuring conferences have a research focus.

Practical implication

The paper should be of interest to practitioners who wish to consider the importance of research in their professional practice.

Originality/value

This paper discusses the challenges in creating a research culture in library practice, and as such offers a new debate on what key issues related to research impact on the profession of library and information science.
Public libraries in Croatia and the digitization challenge
Authors: Vrana Radovan
Published: June 2010

Purpose

The purpose of this paper is to present the current state of digitization and digital collection development in public libraries in Croatia.

Design/methodology/approach

This paper is based on an online survey of public libraries in Croatia on digital collection development and digitization. In total, 165 public libraries were invited to participate in the survey, and Web survey was chosen as the most appropriate tool for surveying geographically dispersed libraries.

Findings

The findings indicate that public libraries in Croatia have taken steps towards enlargement of digital content in their holdings by digitizing their existing library collections. Although the number of digital collections in public libraries in Croatia is still rather small, it is expected that it will increase in the near future. It is also encouraging that public libraries started digitization projects on their own, thus gaining the necessary experience and skills that would help them and other libraries in future digitization projects. Still, they need additional education about digital collection development and process of library material digitization.

Originality/value

The paper article contributes to the growing body of knowledge about digital collections development and digitization in public libraries, as well as about benefits digital collections can provide for libraries in general.
The queen of the modern library movement in China: Mary Elizabeth Wood
Authors: Zheng Jing , Deng Chuan‐You , Cheng Shao‐Min , Liu Wen‐Ya , Wang A‐Tao
Published: June 2010

Purpose

The purpose of this paper is to examine the great contributions made by the American library expert, Mary Elizabeth Wood, to Chinese library development.

Design/methodology/approach

As a pioneer of the modern library movement Mary Elizabeth Wood devoted herself to a Chinese library career. It was structured according to the following theme: setting up the Boone Library and introducing the modern American public library into China; establishing Boone Library School and initiating Chinese library science education; raising money and appealing for China's library development; helping forward the foundation of the Library Association of China; as well as promoting Chinese library intercommunion and cooperation with the West.

Findings

With the background of underdeveloped Chinese librarianship, Mary Elizabeth Wood introduced modern American public library spirit into China, opened the gate of Chinese library science, and promoted Chinese library science.

Research limitations/implications

The paper discusses the library history of China and the role of an American librarian in Chinese library history; thus, it should be of wide interest to researchers involved in library history.

Originality/value

Mary Elizabeth Wood devoted herself to a Chinese library career, and promoted Chinese library science greatly, but research on her is limited. This paper considers her contribution to Chinese library science.
The use of information resources by LIS graduate students in Kuwait
Authors: Hamade Samir N. , Al‐Yousef Saud
Published: June 2010

Purpose

The purpose of this paper is to investigate the use of information resources in the research papers of the graduate students in Library and Information Science (LIS) at Kuwait University.

Design/methodology/approach

The methodology chosen for this paper is the bibliometric method by way of citation count of the references found in the literature review papers of LIS graduate students at Kuwait University by identifying the preferred form of publications, retrieval method, time span, subject distribution, and the most cited journals.

Findings

It is shown that the majority of students used journal articles, web pages, and books as the most preferred form of resources. Their preferred method of retrieval was the printed format. Time span of the most used citations is from three to ten years. They mostly used traditional library journals such as Bulletin of MLA, Library Review, The Electronic Library, Library Management, and College and Research Libraries.

Research limitations/implications

The quantity and quality of citations were reviewed and approved by the student advisor, and the sample was drawn from a population of 74 papers based on the availability of original papers.

Originality/value

The findings in this paper provide important insights for the academic library administration to take appropriate measures to achieve a higher level of awareness and skill by the users.
Microrobots and nanorobots: a review of recent developments
Authors: Bogue Robert
Published: June 2010

Purpose

The paper aims to provide a technical review of recent developments in microrobots, together with a less detailed consideration of nanorobotics.

Design/methodology/approach

Following a brief introduction, this paper describes a number of recently reported microrobot development activities. It then briefly considers the emerging field of nanorobotics.

Findings

Microrobots are the topic of a major research effort and many different technological approaches are under study. Critical issues are power and locomotion and magnetic methods are attracting much attention. Nanorobots are at a far earlier stage of development and most are based on DNA‐based molecular technology. Key applications for both classes of device are anticipated in microassembly, healthcare and nanotechnology.

Originality/value

This paper provides a timely review of recent microrobot and nanorobot development activities.
A control method of deceleration assistance system for collision avoidance based on driver's perceptual risk
Authors: Wada Takahiro , Hiraoka Shoji , Doi Shun'ichi
Published: June 2010

Purpose

The purpose of this paper is to realize a smooth and secure brake assistance system to avoid rear‐end collision of automobiles.

Design/methodology/approach

It is important to judge necessity of deceleration assistance as early as possible and initiate the assistance naturally in order to reduce rear‐end crashes. However, it easily results in driver's discomfort. In addition, deceleration profile of the automatic braking is also important to realize smooth collision avoidance. In this paper, a deceleration assistance control for collision avoidance will be proposed based on the formulated braking behavior models of expert drivers to realize smooth, secure brake assistance.

Findings

The proposed brake assistance system can realize smooth deceleration profile and appropriate final status of the two vehicles for various approaching conditions. In addition, experimental results using a driving simulator will show validity of the proposed system based on subjective evaluation. It is also shown that the system realizes smooth deceleration control even under existence of the interaction between human driver and the system.

Research limitations/implications

This paper does not deal with effect of the deceleration method on change of drivers' behavior, including driver's trust on the system. Over‐trust should be eliminated if any.

Originality/value

The originality of the paper is to derive smooth secure collision avoidance system based on the driver's perceptual risk model. This method can realize smooth collision avoidance behavior for the various approaching conditions with a unified simple algorithm.
Two‐step active contour method based on gradient flow
Authors: Zhu Linlin , Fan Baojie , Tang Yandong
Published: June 2010

Purpose

Active contour can describe target's silhouette accurately and has been widely used in image segmentation and target tracking. Its main drawback is huge computation that is still not well resolved. The purpose of this paper is to optimize the evolving path of active contour, to reduce the computation cost and to make the evolution effectively.

Design/methodology/approach

The contour‐evolution process is separated into two steps: global translation and local deformation. The contour global translation and local deformation are realized by average and normal gradient flow of the evolving contour curve, respectively.

Findings

When a contour is far away from the object to be segmented or tracked, the effective way of contour evolution is that it moves to the object without deformation first and then it deforms into the shape of the object when it moves on the object.

Originality/value

The method presented in this paper can optimize the curve evolving path effectively without complicated calculation, such as rebuilding a new inner product, and its computation cost is largely reduced.