bluuebunny/crossref_metadata_2025 huggingface dataset:
Dietary Phosphorus, Blood Pressure, and Incidence of Hypertension in the Atherosclerosis Risk in Communities Study and the Multi-Ethnic Study of Atherosclerosis
Authors: Alonso Alvaro , Nettleton Jennifer A. , Ix Joachim H. , de Boer Ian H. , Folsom Aaron R. , Bidulescu Aurelian , Kestenbaum Bryan R. , Chambless Lloyd E. , Jacobs David R.
Published: January 2010

Greater phosphorus intake has been associated with lower levels of blood pressure in cross-sectional studies. This association, however, has not been assessed prospectively. We studied 13 444 participants from the Atherosclerosis Risk in Communities cohort and the Multi-Ethnic Study of Atherosclerosis, with diet assessed at baseline using validated food frequency questionnaires. Blood pressure and use of antihypertensive medication were determined at baseline and during follow-up visits. Compared with individuals in the lowest quintile of phosphorus intake at baseline, those in the highest quintile had lower baseline systolic and diastolic blood pressures after adjustment for dietary and nondietary confounders (−2.0 mm Hg [95% CI: −3.6 to −0.5],
P
for trend=0.01; and −0.6 [95% CI: −1.6 to +0.3],
P
for trend=0.20, respectively). During an average 6.2 years of follow-up, 3345 cases of hypertension were identified. Phosphorus intake was associated with the risk of hypertension (hazard ratio: 0.80 [95% CI: 0.80 to 1.00], comparing extreme quintiles;
P
for trend=0.02) after adjustment for nondietary factors but not after additional adjustment for dietary variables (hazard ratio: 1.01 [95% CI: 0.82 to 1.23],
P
for trend=0.88). Phosphorus from dairy products but not from other sources was associated with lower baseline blood pressure and reduced risk of incident hypertension. Hazard ratios (95% CIs) comparing extreme quintiles were 0.86 (0.76 to 0.97;
P
for trend=0.01) for phosphorus from dairy foods and 1.04 (0.93 to 1.17;
P
for trend=0.48) for phosphorus from other foods. These findings could indicate an effect of phosphorus in conjunction with other dairy constituents or of dairy itself without involvement of phosphorus.
Predicting the effect of climate change on aggregation behaviour in four species of terrestrial isopods
Authors: Derhé Mia , Moss Anna , Edwards David , Carmenta Rachel , Hassall Mark
Published: January 2010

Climate warming has changed the spatial distributions and temporal behaviours of several taxa. A key question that remains is how behaviours that alter microclimatic conditions might be used to buffer the effects of climate change. In this study, we focus on the aggregation behaviour of four species of terrestrial isopods, in which groups of individuals clump together to prevent moisture-loss, and use a laboratory protocol to investigate the effects of changes in relative humidity (RH) and temperature on aggregation. We find that three species aggregate more at lower RH and at higher temperatures, and that species that are better adapted to reducing moisture loss aggregate less than do species with fewer such adaptations. These results suggest that behavioural variation can buffer the effects of changes in microclimate. We finish by suggesting that it is critical to determine how such behavioural shifts will affect isopod densities and competitive hierarchies.
Animal tool use: current definitions and an updated comprehensive catalog
Authors: Bentley-Condit Vicki , Smith
Published: January 2010

Despite numerous attempts to define animal tool use over the past four decades, the definition remains elusive and the behaviour classification somewhat subjective. Here, we provide a brief review of the definitions of animal tool use and show how those definitions have been modified over time. While some aspects have remained constant (i.e., the distinction between 'true' and 'borderline' tool use), others have been added (i.e., the distinction between 'dynamic' and 'static' behaviours). We present an updated, comprehensive catalog of documented animal tool use that indicates whether the behaviours observed included any 'true' tool use, whether the observations were limited to captive animals, whether tool manufacture has been observed, and whether the observed tool use was limited to only one individual and, thus, 'anecdotal' (i.e., N = 1). Such a catalog has not been attempted since Beck (1980). In addition to being a useful reference for behaviourists, this catalog demonstrates broad tool use and manufacture trends that may be of interest to phylogenists, evolutionary ecologists, and cognitive evolutionists. Tool use and tool manufacture are shown to be widespread across three phyla and seven classes of the animal kingdom. Moreover, there is complete overlap between the Aves and Mammalia orders in terms of the tool use categories (e.g., food extraction, food capture, agonism) arguing against any special abilities of mammals. The majority of tool users, almost 85% of the entries, use tools in only one of the tool use categories. Only members of the Passeriformes and Primates orders have been observed to use tools in four or more of the ten categories. Thus, observed tool use by some members of these two orders (e.g., Corvus, Papio) is qualitatively different from that of all other animal taxa. Finally, although there are similarities between Aves and Mammalia, and Primates and Passeriformes, primate tool use is qualitatively different. Approximately 35% of the entries for this order demonstrate a breadth of tool use (i.e., three or more categories by any one species) compared to other mammals (0%), Aves (2.4%), and the Passeriformes (3.1%). This greater breadth in tool use by some organisms may involve phylogenetic or cognitive differences — or may simply reflect differences in length and intensity of observations. The impact that tool usage may have had on groups' respective ecological niches and, through niche-construction, on their respective evolutionary trajectories remains a subject for future study.
The delictual origin, penal nature and reipersecutory object of the actio damni iniuriae legis Aquiliae
Authors: Sirks Boudewijn
Published: January 2010

It is commonly assumed that the litis aestimatio of the actio legis Aquiliae was a penalty which, in practice, was set at the loss suffered by the victim of the wrong and therefore functioned as compensation. This assumption is based on the nature of the action as founding in a delict and characterised by the Romans as a penal action. It also shares the elements of penal actions. But this is at odds with other texts which treat the action as directed purely at compensation. It is suggested that in order to understand this we have to distinguish between the origin of the penal actions, which is penal and which carries certain common features such as the fundamental impossibility to sue heirs or descendants of the wrongdoer, and their purpose or object. It is possible to distinguish two groups, one aiming at a penalty, the other aiming at compensation. Only in the latter group the action can be exercised against the heir of the wrongdoer and only restrictedly: it is the compensatory aim which allows for this. Further, the lex Aquilia and its chapters are examined whether a compensatory purpose is distinguishable here as well.
'Augustine' versus Jerome: commentaries on Gratian's Decretum, D. 9, c. 6, from Paucapalea to Juan de Torquemada
Authors: Linde J. Cornelia
Published: January 2010

In his Decretum, D. 9, c. 6, Gratian stated the respective value of Hebrew, Greek and Latin manuscripts of the Bible for the emendation of Latin Scripture. This article deals with the commentaries on this passage from the mid-twelfth to the mid-fifteenth century. Due to the misattribution of a statement to Augustine rather than Jerome in the Decretum, and the later introduction of an out-of-context quotation by Jerome, the two Church Fathers seemed to contradict each other on the matter in question. For three centuries, the decretists sought to explain or even reconcile this contradiction in various ways which are traced in this article.
Antwerp commercial legislation in Amsterdam in the 17th century: legal transplant or jumping board?
Authors: De ruysscher Dave
Published: January 2010

The 1582 Antwerp costuymen influenced Amsterdam law during the seventeenth and eighteenth centuries. Although the Antwerp law has often been considered as an applicable law in the Amstel city, its role was more limited. At the end of the sixteenth century and during the first half of the seventeenth century, it was used as a common and subsidiary applicable law for certain mercantile issues. Later on, as the Amsterdam legislator issued ordinances on these themes, this function declined. Yet, references to the Antwerp law book were still common in the eighteenth century, although they were more a consequence of a cultural attraction than of an actual application of the Brabant law book.
Dutch litigation before the Great Council of Mechlin An additional calendar of the 'Appeals from Holland'
Authors: Wijffels Alain
Published: January 2010

M. Oosterbosch's additional calendar of documents belonging to the series 'Appeals from Holland' (Brussels, General Archives of the Realm, Collection Great Council of Mechlin) refers to hitherto unknown documents which may encourage fresh thematic research and case-studies on conflicts and litigation which originated mostly from Holland and Zeeland (from the 1460s until the 1580s), and to a lesser extent from Utrecht and (also during later periods) from Gelderland.
Influence of the 26°N RAPID–MOCHA Array and Florida Current Cable Observations on the ECCO–GODAE State Estimate
Authors: Baehr Johanna
Published: January 2010

The incorporation of local temperature and salinity observations from the Rapid Climate Change–Meridional Overturning Circulation and Heatflux Array (RAPID–MOCHA), as well as the cable estimates of volume transport in the Florida Current (FC), is tested in the Estimating the Circulation and Climate of the Ocean–Global Ocean Data Assimilation Experiment (ECCO–GODAE) estimation system for their impact on the estimate of the meridional overturning circulation (MOC) and the meridional heat transport in the Atlantic. An experimental setup covering the first deployment period of RAPID–MOCHA from March 2004 to March 2005 is used to test different strategies for incorporating these datasets. Incorporating both monthly means of the FC data and monthly means of the RAPID–MOCHA temperature and salinity measurements at the eastern and western boundaries of the basin as an observational constraint in a 1-yr experiment results in an adjustment to the reference estimate, which does not include these datasets, of approximately 1 Sv (1 Sv ≡ 106 m3 s−1) in the MOC at 26°N and the adjacent latitudes (approximately ±15°), with a larger northward branch of the MOC above 1000 m, compensated by a larger flow in the southward branch of the MOC between approximately 2000 and 3000 m. The meridional heat transport from 26°N to near 40°N is approximately 0.05 PW larger than in the reference experiment.
SST–North American Hydroclimate Links in AMIP Simulations of the Drought Working Group Models: A Proxy for the Idealized Drought Modeling Experiments
Authors: Ruiz-Barradas Alfredo , Nigam Sumant
Published: January 2010

The present study assesses the potential of the U.S. Climate Variability and Predictability (CLIVAR) Drought Working Group (DWG) models in simulating interannual precipitation variability over North America, especially the Great Plains. It also provides targets for the idealized DWG model experiments investigating drought origin. The century-long Atmospheric Model Intercomparison Project (AMIP) simulations produced by version 3.5 of NCAR’s Community Atmosphere Model (CAM3.5), the Lamont-Doherty Earth Observatory’s Community Climate Model (CCM3), and NASA’s Seasonal-to-Interannual Prediction Project (NSIPP-1) atmospheric models are analyzed; CCM3 and NSIPP-1 models have 16- and 14-ensemble simulations, respectively, while CAM3.5 only has 1.

The standard deviation of summer precipitation is different in AMIP simulations. The maximum over the central United States seen in observations is placed farther to the west in simulations. Over the central plains the models exhibit modest skill in simulating low-frequency precipitation variability, a Palmer drought severity index proxy. The presence of a linear trend increases correlations in the period 1950–99 when compared with those for the whole century. The SST links of the Great Plains drought index have features in common with observations over both the Pacific and Atlantic Oceans.

Interestingly, summer-to-fall precipitation regressions of the warm Trend, cold Pacific, and warm Atlantic modes of annual mean SST variability (used in forcing the DWG idealized model experiments) tend to dry the southwestern, midwestern, and southeastern regions of the United States in the observations and, to a lesser extent, in the simulations.

The similarity of the idealized SST-forced droughts in DWG modeling experiments with AMIP precipitation regressions of the corresponding SST principal components, evident especially in the case of the cold Pacific pattern, suggests that the routinely conducted AMIP simulations could have served as an effective proxy for the more elaborated suite of DWG modeling experiments.
The Use of Euclidean Geometric Distance on RGB Color Space for the Classification of Sky and Cloud Patterns
Authors: Mantelli Neto Sylvio Luiz , von Wangenheim Aldo , Pereira Enio Bueno , Comunello Eros
Published: January 2010

The current work describes the use of multidimensional Euclidean geometric distance (EGD) and Bayesian methods to characterize and classify the sky and cloud patterns present in image pixels. From specific images and using visualization tools, it was noticed that sky and cloud patterns occupy a typical locus on the red–green–blue (RGB) color space. These two patterns were linearly distributed parallel to the RGB cube’s main diagonal at distinct distances. A characterization of the cloud and sky patterns EGD was done by supervision to eliminate errors due to outlier patterns in the analysis. The exploratory data analysis of EGD for sky and cloud patterns showed a Gaussian distribution, allowing generalizations based on the central limit theorem. An intensity scale of brightness is proposed from the Euclidean geometric projection (EGP) on the RGB cube’s main diagonal. An EGD-based classification method was adapted to be properly compared with existing ones found in related literature, because they restrict the examined color-space domain. Elimination of this limitation was considered a sufficient criterion for a classification system that has resource restrictions. The EGD-adapted results showed a correlation of 97.9% for clouds and 98.4% for sky when compared to established classification methods. It was also observed that EGD was able to classify cloud and sky patterns invariant to their brightness attributes and with reduced variability because of the sun zenith angle changes. In addition, it was observed that Mie scattering could be noticed and eliminated (together with the reflector’s dust) as an outlier during the analysis. Although Mie scattering could be classified with additional analysis, this is left as a suggestion for future work.
Re-empowering social workers through the online community: The experience of SWForum in Hong Kong
Authors: Leung Zeno C.S. , Lam C.W. , Yau T.Y. , Chu William C.K.
Published: January 2010

This paper focuses on the new form of social participation created by information and communication technologies (ICTs), as experienced by an online professional community, SWForum, in Hong Kong. The group has expressed resistance and contributed to social welfare policy development since 1997, when frontline social workers were disempowered and lost their previously influential status. From this experience, we argue that the online community has created an arena for alternative discourse on social policy and it shows that the technology can be harnessed to create a more equitable participation in policy making in a society.
The role of gender dynamics in decisions on credit and debt in low income families
Authors: Goode Jackie
Published: January 2010

This paper discusses the role of gender dynamics in the experiences of credit and debt in low income families in the UK, drawing on a qualitative longitudinal study funded by the Joseph Rowntree Foundation. It builds on earlier work on: the household economy; the gendered distribution of income specifically within low income families in receipt of benefits; and the extent of credit and debt in the UK currently. Following critiques of traditional sociological and social psychological analyses of the household economy, it takes a more discursive approach, which enables identification of gender dynamics as one of the mechanisms through which decision-making in relation to this area of practice is accomplished.
Cultural Capital and Cross-Border Career Ladders
Authors: Tzeng Rueyling
Published: January 2010

The author argues that cultural capital is an important but neglected aspect of developing cross-border careers, and that it is especially important when social capital is lacking. Most of the supporting information was gathered during in-depth interviews with 40 western professional migrants (36 currently and four previously employed by Taiwanese firms), supplemented by data from interviews with 29 Taiwanese human resource and corporate managers. The data indicate that after using their home cultural capital to find jobs with Taiwanese firms doing business with western companies, the interviewees acquired local cultural and social capital that allowed them to pursue six cross-border career options. Moving to Taiwan is representative of the migration phenomenon from more- to less-developed countries during a period of rapidly expanding economies or economic downturns. The migrants interviewed generally had limited organizational experience (affecting home-country opportunities) and a strong desire for international knowledge and adventure.
Evidence to the UK parliamentary select committee inquiry on preventing violent extremism
Authors:   Institute of Race Relations
Published: January 2010

In recent years, a number of European countries have widened their counter-terrorist policing agendas to include 'counter-radicalisation' policies aimed at preventing people from becoming violent extremists. The most systematic and elaborate of such policies is the UK government s Preventing Violent Extremism programme (known as‘Prevent’), which includes community development work among the general Muslim population of the UK, as well as efforts to identify persons considered to be 'vulnerable to radicalisation' . The Institute of Race Relations (IRR) has carried out research into Prevent and, in October 2009, published its findings in a report entitled Spooked: how not to prevent violent extremism (available at www.irr.org.uk/spooked). Here we republish the IRR s general conclusions which we submitted to the UK parliament's Communities and Local Government Select Committee inquiry into Prevent.
Ankara, a Small Town, Transformed to a Nation’s Capital
Authors: Kacar Duygu
Published: January 2010

Out of the ashes of the Ottoman Empire and at the end of a protracted war of independence that followed close on the heels of the First World War, the Republic of Turkey came into being in 1923. Its founders—a group of career military officers led by Mustafa Kemal Atatürk—set into motion in rapid order a number of societal reforms aimed at building a modernized and Westernized nation-state. Part of the founders’ vision was to build the country’s new capital closer to the center of its landmass. The location of choice was Ankara in the country’s rural interior, and it carried a political message of major proportions. Its implementation, and the visual development of Ankara from the ground up as a major city and cultural center, was another matter. Since the statement needed to be articulated in a modern, or Western, design, Ottoman-Turkish architects were not considered for most of the jobs and, moreover, they were too few for the rapid expansion of Ankara as well as Istanbul. So Turkey assembled a group of top-of-the-line, mostly Austrian and German, talent. While doing this, planning was used as a tool for creating a capital for independence. Using archival documents, this article recounts and illustrates the physical creation of Turkey’s capital city, the emergence of new visions, and the foreign actors of the built environment in the early republican process.
Re-narrations: How pasts change in conversational remembering
Authors: Welzer Harald
Published: January 2010

Research on social memory phenomena is confronted with the problem that social memory has neither a substrate in the sense of a remembering subject nor a central organ of an operating memory in the sense of a human brain. As a consequence, social memory exclusively exists between subjects and not within them, its form of existence consists of communication. In its first part, the article presents examples of family conversations that show that family memory does not serve as storage for memories, but rather serves as a catalyst for the most different elements of the past to be specifically combined by the involved persons. On the basis of a replication of Bartlett’s classical experiment on remembering and re-narrating, the second part of the article demonstrates that the acquisition and transmission of imaginations of the past follows patterns that are specific to the respective generation. This leads to theoretical remarks on the constitutive viscosity of social memory.
‘The good memory of this land’: Reflections on the processes of memory and forgetting
Authors: Ramos Ana Margarita
Published: January 2010

The ‘good memory of this land’ is the way the Mapuche define the processes of remembering and forgetting. From this point of view, memory becomes the means by which the past is acknowledged and advice is transmitted; an instance where people reconfigure their subjectivities and the bonds of belonging that connect them, their ancestors and the physical world. In the specific context of some Mapuche families who decided to recover lands in Argentinean Patagonia that were disputed by the Benetton firm, memory became a central subject of reflection among those involved. This article, based on Mapuche reflections, deals with the theoretical implications of two main demands of collective memory in the local arena: the truth about history and autonomy in the practice of remembering and forgetting in order to create people’s own culture of relatedness.
Film sound and American cultural memory: Resounding trauma in Sophie’s Choice
Authors: Narine Neil
Published: January 2010

One of the most dynamic discussions in memory studies concerns memory’s infusion with phantasy, which Freud also referred to as fantasy. This article examines how memory and fantasy intermingle in ways analogous to the ambivalent human experience of sound: sounds and musical cues can both trigger memories and be active in repressing them by encoding them into fantasmatic ‘counter memories’. Taking Alan J. Pakula’s film Sophie’s Choice (1982) as a case study, I examine how the three principal characters are traumatized by intruding sounds, but use music to repress or reconfigure the memories these sounds trigger. Sophie’s memories of Auschwitz are signalled by Hamlisch’s flute, which provides the soundscape of her fantasy-infused flashbacks; her companion Nathan’s delusional ‘memories’ of the war are safely repressed when the oboe supplies him with his ego’s anthem; and sounds from the narrator Stingo’s childhood rupture the nostalgic soundtrack of violins accompanying his fantasy-inflected narrative. The relevance of Pakula’s melodrama to the social memory of the Holocaust lies in its challenge to the polarized debate between modernist refusals to represent the past ‘directly’ (as in Claude Lanzmann’s 1985 film Shoah) and realist attempts at ‘total representation’ (Steven Spielberg’s 1993 film Schindler’s List). In Sophie’s Choice, acts of individual memory, infused with fantasy soundscapes, are analogous to broader processes of social memory, which are always instilled with our fantasies of what might have been.
Comparative classification of species and the study of pathway evolution based on the alignment of metabolic pathways
Authors: Mano Adi , Tuller Tamir , Béjà Oded , Pinter Ron Y
Published: January 2010

Background

Pathways provide topical descriptions of cellular circuitry. Comparing analogous pathways reveals intricate insights into individual functional differences among species. While previous works in the field performed genomic comparisons and evolutionary studies that were based on specific genes or proteins, whole genomic sequence, or even single pathways, none of them described a genomic system level comparative analysis of metabolic pathways. In order to properly implement such an analysis one should overcome two specific challenges: how to combine the effect of many pathways under a unified framework and how to appropriately analyze co-evolution of pathways.

Here we present a computational approach for solving these two challenges. First, we describe a comprehensive, scalable, information theory based computational pipeline that calculates pathway alignment information and then compiles it in a novel manner that allows further analysis. This approach can be used for building phylogenies and for pointing out specific differences that can then be analyzed in depth. Second, we describe a new approach for comparing the evolution of metabolic pathways. This approach can be used for detecting co-evolutionary relationships between metabolic pathways.

Results

We demonstrate the advantages of our approach by applying our pipeline to data from the MetaCyc repository (which includes a total of 205 organisms and 660 metabolic pathways). Our analysis revealed several surprising biological observations. For example, we show that the different habitats in which Archaea organisms reside are reflected by a pathway based phylogeny. In addition, we discover two striking clusters of metabolic pathways, each cluster includes pathways that have very similar evolution.

Conclusion

We demonstrate that distance measures that are based on the topology and the content of metabolic networks are useful for studying evolution and co-evolution.
Better score function for peptide identification with ETD MS/MS spectra
Authors: Liu Xiaowen , Shan Baozhen , Xin Lei , Ma Bin
Published: January 2010

Background

Tandem mass spectrometry (MS/MS) has become the primary way for protein identification in proteomics. A good score function for measuring the match quality between a peptide and an MS/MS spectrum is instrumental for the protein identification. Traditionally the to-be-measured peptides are fragmented with the collision induced dissociation (CID) method. More recently, the electron transfer dissociation (ETD) method was introduced and has proven to produce better fragment ion ladders for larger and more basic peptides. However, the existing software programs that analyze ETD MS/MS data are not as advanced as they are for CID.

Results

To take full advantage of ETD data, in this paper we develop a new score function to evaluate the match between a peptide and an ETD MS/MS spectrum. Experiments on real data demonstrated that this newly developed score function significantly improved the de novo sequencing accuracy of the PEAKS software on ETD data.

Conclusion

A new and better score function for ETD MS/MS peptide identification was developed. The method used to develop our ETD score function can be easily reused to train new score functions for other types of MS/MS data.
Predicting microRNA precursors with a generalized Gaussian components based density estimation algorithm
Authors: Hsieh Chih-Hung , Chang Darby Tien-Hao , Hsueh Cheng-Hao , Wu Chi-Yeh , Oyang Yen-Jen
Published: January 2010

Background

MicroRNAs (miRNAs) are short non-coding RNA molecules, which play an important role in post-transcriptional regulation of gene expression. There have been many efforts to discover miRNA precursors (pre-miRNAs) over the years. Recently, ab initio approaches have attracted more attention because they do not depend on homology information and provide broader applications than comparative approaches. Kernel based classifiers such as support vector machine (SVM) are extensively adopted in these ab initio approaches due to the prediction performance they achieved. On the other hand, logic based classifiers such as decision tree, of which the constructed model is interpretable, have attracted less attention.

Results

This article reports the design of a predictor of pre-miRNAs with a novel kernel based classifier named the generalized Gaussian density estimator (G2DE) based classifier. The G2DE is a kernel based algorithm designed to provide interpretability by utilizing a few but representative kernels for constructing the classification model. The performance of the proposed predictor has been evaluated with 692 human pre-miRNAs and has been compared with two kernel based and two logic based classifiers. The experimental results show that the proposed predictor is capable of achieving prediction performance comparable to those delivered by the prevailing kernel based classification algorithms, while providing the user with an overall picture of the distribution of the data set.

Conclusion

Software predictors that identify pre-miRNAs in genomic sequences have been exploited by biologists to facilitate molecular biology research in recent years. The G2DE employed in this study can deliver prediction accuracy comparable with the state-of-the-art kernel based machine learning algorithms. Furthermore, biologists can obtain valuable insights about the different characteristics of the sequences of pre-miRNAs with the models generated by the G2DE based predictor.
Annotation of gene promoters by integrative data-mining of ChIP-seq Pol-II enrichment data
Authors: Gupta Ravi , Wikramasinghe Priyankara , Bhattacharyya Anirban , Perez Francisco A , Pal Sharmistha , Davuluri Ramana V
Published: January 2010

Background

Use of alternative gene promoters that drive widespread cell-type, tissue-type or developmental gene regulation in mammalian genomes is a common phenomenon. Chromatin immunoprecipitation methods coupled with DNA microarray (ChIP-chip) or massive parallel sequencing (ChIP-seq) are enabling genome-wide identification of active promoters in different cellular conditions using antibodies against Pol-II. However, these methods produce enrichment not only near the gene promoters but also inside the genes and other genomic regions due to the non-specificity of the antibodies used in ChIP. Further, the use of these methods is limited by their high cost and strong dependence on cellular type and context.

Methods

We trained and tested different state-of-art ensemble and meta classification methods for identification of Pol-II enriched promoter and Pol-II enriched non-promoter sequences, each of length 500 bp. The classification models were trained and tested on a bench-mark dataset, using a set of 39 different feature variables that are based on chromatin modification signatures and various DNA sequence features. The best performing model was applied on seven published ChIP-seq Pol-II datasets to provide genome wide annotation of mouse gene promoters.

Results

We present a novel algorithm based on supervised learning methods to discriminate promoter associated Pol-II enrichment from enrichment elsewhere in the genome in ChIP-chip/seq profiles. We accumulated a dataset of 11,773 promoter and 46,167 non-promoter sequences, each of length 500 bp, generated from RNA Pol-II ChIP-seq data of five tissues (Brain, Kidney, Liver, Lung and Spleen). We evaluated the classification models in building the best predictor and found that Bagging and Random Forest based approaches give the best accuracy. We implemented the algorithm on seven different published ChIP-seq datasets to provide a comprehensive set of promoter annotations for both protein-coding and non-coding genes in the mouse genome. The resulting annotations contain 13,413 (4,747) protein-coding (non-coding) genes with single promoters and 9,929 (1,858) protein-coding (non-coding) genes with two or more alternative promoters, and a significant number of unassigned novel promoters.

Conclusion

Our new algorithm can successfully predict the promoters from the genome wide profile of Pol-II bound regions. In addition, our algorithm performs significantly better than existing promoter prediction methods and can be applied for genome-wide predictions of Pol-II promoters.
Disruption of zebrafish cyclin G-associated kinase (GAK) function impairs the expression of Notch-dependent genes during neurogenesis and causes defects in neuronal development
Authors: Bai Ting , Seebald Jamie L , Kim Kyu-Eui , Ding Hong-Mei , Szeto Daniel P , Chang Henry C
Published: January 2010

Background

The J-domain-containing protein auxilin, a critical regulator in clathrin-mediated transport, has been implicated in Drosophila Notch signaling. To ask if this role of auxilin is conserved and whether auxilin has additional roles in development, we have investigated the functions of auxilin orthologs in zebrafish.

Results

Like mammals, zebrafish has two distinct auxilin-like molecules, auxilin and cyclin G-associated kinase (GAK), differing in their domain structures and expression patterns. Both zebrafish auxilin and GAK can functionally substitute for the Drosophila auxilin, suggesting that they have overlapping molecular functions. Still, they are not completely redundant, as morpholino-mediated knockdown of the ubiquitously expressed GAK alone can increase the specification of neuronal cells, a known Notch-dependent process, and decrease the expression of Her4, a Notch target gene. Furthermore, inhibition of GAK function caused an elevated level of apoptosis in neural tissues, resulting in severe degeneration of neural structures.

Conclusion

In support of the notion that endocytosis plays important roles in Notch signaling, inhibition of zebrafish GAK function affects embryonic neuronal cell specification and Her4 expression. In addition, our analysis suggests that zebrafish GAK has at least two functions during the development of neural tissues: an early Notch-dependent role in neuronal patterning and a late role in maintaining the survival of neural cells.
Novel OBP genes similar to hamster Aphrodisin in the bank vole, Myodes glareolus
Authors: Stopková Romana , Zdráhal Zbyněk , Ryba Štěpán , Šedo Ondřej , Šandera Martin , Stopka Pavel
Published: January 2010

Background

Chemical communication in mammals involves globular lipocalins that protect and transport pheromones during their passage out of the body. Efficient communication via this protein - pheromone complex is essential for triggering multiple responses including aggression, mate choice, copulatory behaviour, and onset and synchronization of oestrus. The roles of lipocalins in communication were studied in many organisms and especially in mice (i.e. Mus musculus domesticus) which excrete Major Urinary Proteins (Mup) in excessive amounts in saliva and urine. Other mammals, however, often lack the genes for Mups or their expression is very low. Therefore, we aimed at characterization of candidate lipocalins in Myodes glareolus which are potentially linked to chemical communication. One of them is Aphrodisin which is a unique lipocalin that was previously described from hamster vaginal discharge and is known to carry pheromones stimulating copulatory behaviour in males.

Results

Here we show that Aphrodisin-like proteins exist in other species, belong to a group of Odorant Binding Proteins (Obp), and contrary to the expression of Aphrodisin only in hamster genital tract and parotid glands of females, we have detected these transcripts in both sexes of M. glareolus with the expression confirmed in various tissues including prostate, prepucial and salivary glands, liver and uterus. On the level of mRNA, we have detected three different gene variants. To assess their relevance for chemical communication we investigated the occurrence of particular proteins in saliva, urine and vaginal discharge. On the protein level we confirmed the presence of Obp2 and Obp3 in both saliva and urine. Appropriate bands in the range of 17-20 kDa from vaginal discharge were, however, beyond the MS detection limits.

Conclusion

Our results demonstrate that three novel Obps (Obp1, Obp2, and Obp3) are predominant lipocalins in Myodes urine and saliva. On the protein level we have detected further variants and thus we assume that similarly as Major Urinary Proteins in mice, these proteins may be important in chemical communication in this Cricetid rodent.
Single nucleotide polymorphisms for assessing genetic diversity in castor bean (Ricinus communis)
Authors: Foster Jeffrey T , Allan Gerard J , Chan Agnes P , Rabinowicz Pablo D , Ravel Jacques , Jackson Paul J , Keim Paul
Published: January 2010

Background

Castor bean (Ricinus communis) is an agricultural crop and garden ornamental that is widely cultivated and has been introduced worldwide. Understanding population structure and the distribution of castor bean cultivars has been challenging because of limited genetic variability. We analyzed the population genetics of R. communis in a worldwide collection of plants from germplasm and from naturalized populations in Florida, U.S. To assess genetic diversity we conducted survey sequencing of the genomes of seven diverse cultivars and compared the data to a reference genome assembly of a widespread cultivar (Hale). We determined the population genetic structure of 676 samples using single nucleotide polymorphisms (SNPs) at 48 loci.

Results

Bayesian clustering indicated five main groups worldwide and a repeated pattern of mixed genotypes in most countries. High levels of population differentiation occurred between most populations but this structure was not geographically based. Most molecular variance occurred within populations (74%) followed by 22% among populations, and 4% among continents. Samples from naturalized populations in Florida indicated significant population structuring consistent with local demes. There was significant population differentiation for 56 of 78 comparisons in Florida (pairwise population ϕPT values, p < 0.01).

Conclusion

Low levels of genetic diversity and mixing of genotypes have led to minimal geographic structuring of castor bean populations worldwide. Relatively few lineages occur and these are widely distributed. Our approach of determining population genetic structure using SNPs from genome-wide comparisons constitutes a framework for high-throughput analyses of genetic diversity in plants, particularly in species with limited genetic diversity.
Evaluation of PermaNet 3.0 a deltamethrin-PBO combination net against Anopheles gambiae and pyrethroid resistant Culex quinquefasciatus mosquitoes: an experimental hut trial in Tanzania
Authors: Tungu Patrick , Magesa Stephen , Maxwell Caroline , Malima Robert , Masue Dennis , Sudi Wema , Myamba Joseph , Pigeon Olivier , Rowland Mark
Published: January 2010

Background

Combination mosquito nets incorporating two unrelated insecticides or insecticide plus synergist are designed to control insecticide resistant mosquitoes. PermaNet 3.0 is a long-lasting combination net incorporating deltamethrin on the side panels and a mixture of deltamethrin and synergist piperonyl butoxide (PBO) on the top panel. PBO is an inhibitor of mixed function oxidases implicated in pyrethroid resistance.

Method

An experimental hut trial comparing PermaNet 3.0, PermaNet 2.0 and a conventional deltamethrin-treated net was conducted in NE Tanzania using standard WHOPES procedures. The PermaNet arms included unwashed nets and nets washed 20 times. PermaNet 2.0 is a long-lasting insecticidal net incorporating deltamethrin as a single active.

Results

Against pyrethroid susceptible Anopheles gambiae the unwashed PermaNet 3.0 showed no difference to unwashed PermaNet 2.0 in terms of mortality (95% killed), but showed differences in blood-feeding rate (3% blood-fed with PermaNet 3.0 versus 10% with PermaNet 2.0). After 20 washes the two products showed no difference in feeding rate (10% with 3.0 and 9% with 2.0) but showed small differences in mortality (95% with 3.0 and 87% with 2.0). Against pyrethroid resistant Culex quinquefasciatus, mediated by elevated oxidase and kdr mechanisms, the unwashed PermaNet 3.0 killed 48% and PermaNet 2.0 killed 32% but after 20 washes there was no significant difference in mortality between the two products (32% killed by 3.0 and 30% by 2.0). For protecting against Culex PermaNet 3.0 showed no difference to PermaNet 2.0 when either unwashed or after 20 washes; both products were highly protective against biting. Laboratory tunnel bioassays confirmed the loss of biological activity of the PBO/deltamethrin-treated panel after washing.

Conclusion

Both PermaNet products were highly effective against susceptible Anopheles gambiae. As a long-lasting net to control or protect against pyrethroid resistant mosquitoes PermaNet 3.0 showed limited improvement over PermaNet 2.0 against Culex quinquefasciatus.
Gait symmetry and regularity in transfemoral amputees assessed by trunk accelerations
Authors: Tura Andrea , Raggi Michele , Rocchi Laura , Cutti Andrea G , Chiari Lorenzo
Published: January 2010

Background

The aim of this study was to evaluate a method based on a single accelerometer for the assessment of gait symmetry and regularity in subjects wearing lower limb prostheses.

Methods

Ten transfemoral amputees and ten healthy control subjects were studied. For the purpose of this study, subjects wore a triaxial accelerometer on their thorax, and foot insoles. Subjects were asked to walk straight ahead for 70 m at their natural speed, and at a lower and faster speed. Indices of step and stride regularity (Ad1 and Ad2, respectively) were obtained by the autocorrelation coefficients computed from the three acceleration components. Step and stride durations were calculated from the plantar pressure data and were used to compute two reference indices (SI1 and SI2) for step and stride regularity.

Results

Regression analysis showed that both Ad1 well correlates with SI1 (R2up to 0.74), and Ad2 well correlates with SI2 (R2up to 0.52). A ROC analysis showed that Ad1 and Ad2 has generally a good sensitivity and specificity in classifying amputee's walking trial, as having a normal or a pathologic step or stride regularity as defined by means of the reference indices SI1 and SI2. In particular, the antero-posterior component of Ad1 and the vertical component of Ad2 had a sensitivity of 90.6% and 87.2%, and a specificity of 92.3% and 81.8%, respectively.

Conclusions

The use of a simple accelerometer, whose components can be analyzed by the autocorrelation function method, is adequate for the assessment of gait symmetry and regularity in transfemoral amputees.
Genetic analysis of chikungunya viruses imported to mainland China in 2008
Authors: Zheng Kui , Li Jiandong , Zhang Quanfu , Liang Mifang , Li Chuan , Lin Miao , Huang Jicheng , Li Hua , Xiang Dapeng , Wang Ninlan , Hong Ye , Huang Li , Li Xiaobo , Pan Deguan , Song Wei , Dai Jun , Guo Boxuan , Li Dexin
Published: January 2010

Background

Chikungunya virus (CHIKV) has caused large outbreaks worldwide in recent years, especially on the islands of the Indian Ocean and India. The virus is transmitted by mosquitoes (Aedes aegypti), which are widespread in China, with an especially high population density in southern China. Analyses of full-length viral sequences revealed the acquisition of a single adaptive mutation providing a selective advantage for the transmission of CHIKV by this species. No outbreaks due to the local transmission of CHIKV have been reported in China, and no cases of importation were detected on mainland China before 2008. We followed the spread of imported CHIKV in southern China and analyzed the genetic character of the detected viruses to evaluate their potential for evolution.

Results

The importation of CHIKV to mainland China was first detected in 2008. The genomic sequences of four of the imported viruses were identified, and phylogenetic analysis demonstrated that the sequences were clustered in the Indian Ocean group; however, seven amino acid changes were detected in the nonstructural protein-coding region, and five amino acid changes were noted in the structural protein-coding regions. In particular, a novel substitution in E2 was detected (K252Q), which may impact the neurovirulence of CHIKV. The adaptive mutation A226V in E1 was observed in two imported cases of chikungunya disease.

Conclusions

Laboratory-confirmed CHIKV infections among travelers visiting China in 2008 were presented, new mutations in the viral nucleic acids and proteins may represent adaptive mutations for human or mosquito hosts.
SiO2 nanoparticles induce cytotoxicity and protein expression alteration in HaCaT cells
Authors: Yang Xifei , Liu Jianjun , He Haowei , Zhou Li , Gong Chunmei , Wang Xiaomei , Yang Lingqing , Yuan Jianhui , Huang Haiyan , He Lianhua , Zhang Bing , Zhuang Zhixiong
Published: January 2010

Background

Nanometer silicon dioxide (nano-SiO2) has a wide variety of applications in material sciences, engineering and medicine; however, the potential cell biological and proteomic effects of nano-SiO2 exposure and the toxic mechanisms remain far from clear.

Results

Here, we evaluated the effects of amorphous nano-SiO2 (15-nm, 30-nm SiO2). on cellular viability, cell cycle, apoptosis and protein expression in HaCaT cells by using biochemical and morphological analysis, two-dimensional differential gel electrophoresis (2D-DIGE) as well as mass spectrometry (MS). We found that the cellular viability of HaCaT cells was significantly decreased in a dose-dependent manner after the treatment of nano-SiO2 and micro-sized SiO2 particles. The IC50 value (50% concentration of inhibition) was associated with the size of SiO2 particles. Exposure to nano-SiO2 and micro-sized SiO2 particles also induced apoptosis in HaCaT cells in a dose-dependent manner. Furthermore, the smaller SiO2 particle size was, the higher apoptotic rate the cells underwent. The proteomic analysis revealed that 16 differentially expressed proteins were induced by SiO2 exposure, and that the expression levels of the differentially expressed proteins were associated with the particle size. The 16 proteins were identified by MALDI-TOF-TOF-MS analysis and could be classified into 5 categories according to their functions. They include oxidative stress-associated proteins; cytoskeleton-associated proteins; molecular chaperones; energy metabolism-associated proteins; apoptosis and tumor-associated proteins.

Conclusions

These results showed that nano-SiO2 exposure exerted toxic effects and altered protein expression in HaCaT cells. The data indicated the alterations of the proteins, such as the proteins associated with oxidative stress and apoptosis, could be involved in the toxic mechanisms of nano-SiO2 exposure.