bluuebunny/crossref_metadata_2025 huggingface dataset:
The Rise and Fall of the American Artists' Congress
Authors: McCoy Garnett
Published: April 2011

In the fall of 1929, just after the stock market crash but before its effects were widely felt, a group of radical artists and writers in New York established the John Reed Club, named after the already legendary journalist, poet, and revolutionary activist. The founders, some of them members of the Communist Party, some loosely associated with the party's cultural magazine New Masses, were committed but restless young men in search of a focus for their political energies. Soon after the club began, the artist members created an art school, organized exhibitions, and sponsored a lecture series and discussion groups with emphasis on the practice and theory of art and art history from a Marxist point of view. As the Depression deepened, with dire consequences to artists dependent on an art market in a state of collapse, the John Reed Club's approach attracted growing attention.
Schizophrenic City: Souvenirs of Minneapolis
Authors: Levenduski Cristine M.
Published: April 2011

Collecting souvenirs, an impulse nearly as universal as travel it-self, has spawned industries in tourist spots throughout the United States and most other nations of the world. Tourists purchase souvenirs both as commemorative artifacts, that at some future time will call to mind the experiences of the vacation and of the city visited, and as communicative artifacts. T-shirts, coffee mugs and bumper stickers proclaim, “this is where I've been” or “this is where I live” or “this is where my friends vacationed.” Some tourist spots lend themselves to this communicative function more easily than do others. Cities like San Francisco, for example, are highly imageable cities; they have a bridge or building or monument that serves as a symbol of the city consistent with the experience of visitors and residents alike.1 Minneapolis, however, lacks this kind of symbolic artifact. While any Twin Cities' resident, most Minnesotans, and many avid fans of The Mary Tyler Moore Show will recognize the Minneapolis skyline, particularly the prominent IDS building, this same site shown to a New Yorker or Californian who has never visited the area, will fail to serve as an identifiable landmark. Lacking such a symbol, creators of Minneapolis souvenirs have had to find images that represent the city and that are consistent with the sense of the place that tourists and residents experience.
The Long Ordeal of Modernization Theory
Authors: Hoover Dwight
Published: April 2011

The concept of modernization has its roots deep in nineteenth-century German sociology, reaching back to Toennies' distinction between Gemeinschaft and Gesellschaft, to Weber's discussion of the process of increasing rationalization in society, and to Durkheim's contrast between organic and mechanical solidarity in different communities. One of the best descriptions of the two kinds of society envisaged by this idea of modernization has been given by the American anthropologist Robert Redfield:

One may conceive of a society, the Gemeinschaft, characterized by absolute unity derived from the intimate contacts of communal personal association and participation in common values. Here the will of the individual is spontaneous and affective. On the other hand, one may conceive of a society, the Gesellschaft, in which unity is highly individualizing and differentiating.
James Guy: A Surreal Commentator
Authors: Fort Ilene Susan
Published: April 2011

During the decade prior to World War II, James Guy (1910–1983) achieved a substantial reputation in the New York art world. He was one of the earliest American exponents of surrealism, adopting it years before the abstract expressionists responded to the aesthetic. Guy used surrealism as a vehicle for social criticism, creating some of the most pungent attacks on the societal ills of his day. The Depression was a period when many American artists became socially and politically concerned and viewed their art as an instrument of change. Most of these artists have been labeled social realists. While recent literature on socially conscious artists of the 1930s has expanded the term to include artists who do not exactly fit the definition of social realists, no reference to Guy has been given in any of these surveys.
Forms of Self-Representation in Booker T. Washington'sUp from Slavery
Authors: Cain William E.
Published: April 2011

Booker T. Washington'sUp from Slavery(1901) is one of the most famous American autobiographies, yet it is unfortunately also one of the least analyzed. Compared with the American autobiographies that we frequently study and teach, it seems meager and unchallenging. Unlike Whitman and Thoreau, Washington does not propose experiments in form, and he does not undertake a profound inner exploration as his text unfolds. He is not keenly conscious of his competitive relation to the autobiographical writings that have preceded his own and unlike Henry Adams and Henry James, he does not manifest a high degree of selfreflective awareness about the act of telling the story of his life. Nor does Washington's book display the sophisticated rendering of personal and public life that W. E. B. DuBois manages inDusk of Dawn(1940), the subtle and disturbing account of black adolescence and early maturity that Richard Wright crafts inBlack Boy(1945), the stylistic vigor and intelligence that James Baldwin demonstrates inNotes of a Native Son(1955), or the explosive energy that Malcolm X unleashes in his autobiography (1965).
“Away From Home and Amongst Strangers”: Domestic Sphere, Public Arena, and Huckleberry Finn
Authors: Knoper Randall
Published: April 2011

Despite Mark Twain's situating the story “forty to fifty years ago” and in a rural river valley,Adventures of Huckleberry Finnclosely engaged daily dilemmas and concerns of a Northern, urban, middle-class audience. As Carolyn Porter has argued, the familiar comprehension of American fiction as fantasies of escape from society and history, as authorial efforts to light out for the territory, needs to be dislodged by a sensitivity to such writings as acute responses to their immediate context – a developing industrial and capitalist society and culture. Although Huck's world may appear cut off from the landscape and society of bourgeois city dwellers of the 1880s, and although there are not explicit references to industrialization or urbanization, the novel reproduces and addresses new features of daily life, alterations and stresses in private and public behavior and interaction that were being precipitated by the accelerated economic and demographic changes of the late 19th Century.
“Scientia Pro Patria”:Herbert Baxter Adams and Mugwump Academic Reform at Johns Hopkins, 1876–1901
Authors: Cunningham Raymond J.
Published: April 2011

Two days before the 1884 presidential election, Woodrow Wilson, then a graduate student in history and political science at the Johns Hopkins University, confessed somewhat guiltily to his fiancée that he had been scanning the newspapers on the Lord's Day to gauge the chances of the Democratic candidate. “I am exceedingly hopeful,” he wrote, “though so anxious as to be thankful that there is only a day or two more of suspense. Only my profound trust in an over-ruling Providence will keep me from the deepest despondency, my darling, if Cleveland should be defeated.” Wilson's commitment to Grover Cleveland and his aversion to James G. Blaine were characteristic of the feeling at the university. In the department of historical and political science, headed by thirty-fouryear-old Herbert Baxter Adams, such feeling ran high. Adams, a New England Republican who made no secret of his mugwump convictions, took for granted that his students hoped for a Cleveland victory. The Cleveland motto, “Public Office is a Public Trust”, he reminded them, was a truth as old as Aristotle. On election night, Hopkins men scrutinized the returns into the early morning hours, and lectures the next day were heard with slight attention. Cleveland's inauguration was an occasion for celebration, and Adams, with a large contingent of Hopkinsians, went off on a “spree” to the Capital.
Love and Friendship in The Bostonians
Authors: White Robert
Published: April 2011

At the beginning of february, 1884, Henry James was having a typed copy made of his manuscript for “A New England Winter,” a tale written in London, but prompted by his months-long stay the previous winter in Boston–to which he had been recalled by the death of his father.
The Revolt Against Cultural Determinism and the Meaning of Community Action: A View from Cincinnati
Authors: Miller Zane L. , Tucker Bruce
Published: April 2011

Since the 1920s, the discourse about American urban culture has suggested the appropriateness of organizing metropolitan life around territorial subcommunities in two distinctive ways, each of which yielded a distinctive period in the history of professional city and social welfare planning. During the first period, which persisted into the 1950s, the planners focused on the problem of forging a coherent sense of metropolitan community among cultural groups conceived of as separate but equal (or potentially equal). To achieve this goal, they emphasized the role of experts in analyzing the forces controlling urban culture and in devising schemes to segregate, assure the integrity of, and foster mutual understanding and respect among cultural groups whose characteristics stemmed from forces beyond the control of experts or group members. During the second period, which began in the 1950s and persists in our own time, planners abandoned cultural group determinism and the quest for a segregated yet coherent metropolitan community of separate but equal groups in homogeneous neighborhoods. Instead they decided they could control the future of the metropolis by persuading individuals to create heterogeneous neighborhoods through a process of “community action” in which neighborhood residents would define their culture (“lifestyles”) by participating in the design of the social and physical environment of the neighborhood of their choice. This new pattern of thinking about urban culture, which centered on “individualism” and neighborhood rather than groups and metropolitan community, involved a revolt against cultural group determinism, the notion that individuals carry an identity determined by the accident of their membership in the group with characteristics determined by the experience of a group in a social and physical environment created by “outsiders” and or impersonal “forces.”
The Authenticity of American Realism: Samuel Clemens and George Caleb Bingham “On the River”
Authors: Maine Barry
Published: April 2011

In 1846 in Louisville, Kentucky, John Banvard, a self-taught Missouri painter, exhibited hisThree-Mile Painting, a panorama of the Mississippi and Missouri Rivers, painted from hundreds of direct observations and sketches he had executed over a period of many years along the riverbanks. The painting was exhibited by means of a giant pair of rollers upon which the canvas was wound and unwound. Following a successful run in Louisville, the exhibition drew large crowds in Boston and New York City before Banvard capped his triumph with a European tour. In a promotional description of the painting, printed in Boston in 1847 to generate interest in the exhibit, many endorsements testified to the painting's authenticity, including one signed by over one hundred captains and other officers of steamboats who had examined the painting and declared it “correct.” That authenticity and “correctness” were measures of artistic achievement testifies to the premium placed on verisimilitude in art that served as a record of discovery and observation along the American frontier.
Prairie Madonnas and Pioneer Women: Images of Emigrant Women in the Art of the Old West
Authors: Stott Annette
Published: April 2011

In the art of the American West, women have traditionally occupied a minor position. Compared to a surfeit of depictions of cowboys, braves, soldiers, miners, Indian chiefs, scouts, trappers, and traders, there are relatively few images of women; and when considering women who were not native to the plains and prairies, the field narrows still farther. Although literature and popular culture have given us numerous female types of the trans-Mississippi West (saloon and dance-hall girls, frontier mothers, helpless captives, schoolteachers, renegade female outlaws, wild-west-show women), art has virtually ignored all but the emigrant woman who traveled west in a covered wagon to establish a home on the prairie.
The need to implement the Convention on Biological Diversity at the high latitude site, South Georgia
Authors: Barnes D.K.A. , Collins M.A. , Brickle P. , Fretwell P. , Griffiths H.J. , Herbert D. , Hogg O.T. , Sands C.J.
Published: April 2011

The multilateral failure to apply the Convention on Biological Diversity (CBD) by the target year 2010 was headline news as are the accelerating climatic changes which dictate its urgency. Some ecosystems that are vulnerable to anthropogenic change have few species listed as endangered because too little is known about their biota. The highest vulnerability may correspond to where hotspots of species endemism, range limits and physiological sensitivity overlap with areas of most rapid physical change. The old, large and remote archipelago of South Georgia is one such location. Sea-surface temperatures around South Georgia are amongst the most rapidly warming reported. Furthermore oceanographic projections are highlighting the region as extremely vulnerable to ocean acidification. We outline the first polar Darwin Initiative project and the technical advances in generating an interactive and fully integrated georeferenced map of marine biodiversity, seabed topography and physical oceanography at South Georgia. Mapping marine mega and macro-faunal biodiversity onto multiple physical variables has rarely been attempted. This should provide a new tool in assessing the processes driving biological variability, the importance of marine areas in terms of ecosystem services, the threats and vulnerabilities of Polar Regions and should greatly aid implementation of the CBD.
Cognitive Activities During Adulthood Are More Important than Education in Building Reserve
Authors: Reed Bruce R. , Dowling Maritza , Tomaszewski Farias Sarah , Sonnen Joshua , Strauss Milton , Schneider Julie A. , Bennett David A. , Mungas Dan
Published: April 2011

Cognitive reserve is thought to reflect life experiences. Which experiences contribute to reserve and their relative importance is not understood. Subjects were 652 autopsied cases from the Rush Memory and Aging Project and the Religious Orders Study. Reserve was defined as the residual variance of the regressions of cognitive factors on brain pathology and was captured in a latent variable that was regressed on potential determinants of reserve. Neuropathology variables included Alzheimer's disease markers, Lewy bodies, infarcts, microinfarcts, and brain weight. Cognition was measured with six cognitive domain scores. Determinants of reserve were socioeconomic status (SES), education, leisure cognitive activities at age 40 (CA40) and at study enrollment (CAbaseline) in late life. The four exogenous predictors of reserve were weakly to moderately inter-correlated. In a multivariate model, all except SES had statistically significant effects on Reserve, the strongest of which were CA40 (β = .31) and CAbaseline (β = .28). The Education effect was negative in the full model (β = –.25). Results suggest that leisure cognitive activities throughout adulthood are more important than education in determining reserve. Discrepancies between cognitive activity and education may be informative in estimating late life reserve. (JINS, 2011, 17, 615–624)
Relationship between dietary intake and the development of type 2 diabetes in a Chinese population: the Hong Kong Dietary Survey
Authors: Yu Ruby , Woo Jean , Chan Ruth , Sham Aprille , Ho Suzanne , Tso Annette , Cheung Bernard , Lam Tai Hing , Lam Karen
Published: April 2011

Objective

To study the relationship between dietary intake and the development of type 2 diabetes among Chinese adults.

Design

A prospective cohort study. Dietary assessment was carried out using a validated FFQ. Principal component analysis was used to identify dietary patterns. Dietary glycaemic load and variety of snacks were also calculated.

Setting

A hospital-based centre at the Queen Mary Hospital in Hong Kong SAR, China.

Subjects

A total of 1010 Chinese adults aged 25–74 years who participated in a territory-wide dietary and cardiovascular risk factor prevalence survey in 1995–1996 were followed up for 9–14 years for the development of diabetes.

Results

A total of 690 (68·3 %) individuals completed follow-up during 2005–2008 and seventy-four cases of diabetes were identified over the follow-up period. Four dietary patterns were identified (‘more snacks and drinks’, ‘more vegetables, fruits and fish’, ‘more meat and milk products’ and ‘more refined grains’). After adjustment for age, sex, BMI, waist-to-hip ratio, smoking, alcohol intake, participation in exercise/sports and family history of diabetes, the more vegetables, fruits and fish pattern was associated with a 14 % lower risk (OR per 1 sd increase in score = 0·76; 95 % CI 0·58, 0·99), whereas the more meat and milk products pattern was associated with a 39 % greater risk of diabetes (OR per 1 sd increase in score = 1·39; 95 % CI 1·04, 1·84). Dietary glycaemic load, rice intake, snack intake and variety of snacks were not independently associated with diabetes.

Conclusions

The more vegetables, fruits and fish pattern was associated with reduced risk and the more meat and milk products pattern was associated with an increased risk of diabetes.
Eating behaviour and its association with social living conditions and weight status among adolescent girls: results of the cross-sectional Berlin School Children's Cohort study
Authors: Bau Anne-Madeleine , Krull Sarah , Ernert Andrea , Babitsch Birgit
Published: April 2011

Objective

To capture a more holistic picture of eating behaviour by investigating the impact of the social living conditions and weight status of parents and daughters on food consumption frequency, the context of meals and daily portion sizes.

Design

Cross-sectional Berlin School Children's Cohort study.

Setting

A total of sixty-nine schools in Berlin (3 400 000 inhabitants, eastern Germany) participated in the present study.

Subjects

A total of 1519 girls aged 11–14 years were selected. Bi- and multivariate analyses were performed to examine the impact of age, migration background, socio-economic status (SES), parental education, family situation and the weight status of parents and daughters on three different eating behaviour scores according to nutritional recommendations.

Results

For the three dependent eating behaviour variables, different patterns of influencing factors emerged. Multivariate regression (model 1) revealed that low and middle SES, two-parent migration background and older age were significant risk factors. Meal context was also significantly influenced by living with a single parent. Similar results were obtained for the daily portion size scores and maternal overweight status was the most influential. Model 2 succeeded in showing that, within the composite variable of family SES, mothers’ level of education was the dominant component.

Conclusions

SES as a whole, and especially the component of mothers’ level of education and two-parent migration background, was the strongest risk factor for an unfavourable eating pattern among adolescent girls. The results clearly indicated preventive potential. Using three different measures of eating behaviour simultaneously provided an in-depth understanding of general patterns and potential risk factors.
Can Hawaiian carnivorous caterpillars attack invasive ants or vice versa?
Authors: Sugiura Shinji
Published: April 2011

The Hawaiian Islands have allowed insects to evolve unique habits, because the islands are isolated and originally lacked predators, such as ants and wasps. Ambush carnivorous caterpillars (Eupithecia spp.; Lepidoptera: Geometridae) provide a remarkable example of a feeding behaviour unique to the Hawaiian Islands. Their prey includes various arthropods species. Eupithecia larvae even attack predatory arthropods such as parasitoids. However, it is unclear whether Eupithecia can attack ants. Here, I examined whether Eupithecia orichloris can attack the invasive ant Pheidole megacephala under laboratory conditions. Eupithecia orichloris could successfully attack the minor worker of P. megacephala. However, the major worker of P. megacephala counterattacked.
Why plants lose their inhibitions in the Arctic: functional traits, phylogenetics and respiration in the light
Authors: Mirotchnick Nicholas , Atkin Owen , Cadotte Marc , Turnbull Matthew , Griffin Kevin
Published: April 2011

Background/Questions/Methods:

Arctic vegetation represents a significant portion of the world’s global carbon stocks and is particularly sensitive to global climate change. Net plant carbon exchange depends on both photosynthesis and respiration, the latter of which is poorly understood in arctic ecosystems and yet is highly sensitive to global environmental change.Mitochondrial respiration can confound measurements of photosynthesis and thus is often isolated by measuring it in the dark. We also know,however, that respiration can be inhibited by light, which complicates extrapolations from measurements in darkness. Furthermore, the extent of this inhibition may be unique in arctic ecosystems as a result of the constant daylight they receive during growing seasons.We applied the Kok method to a survey of forty of the most common tundra plants found in communities surrounding the Toolik Lake Long Term Ecological Research Site in Alaska’s North Slope. The Kok method segregates rates of respiration in the dark and those in the light by applying incrementally decreasing light levels to leaves. Using this approach, we were able to compare these different rates and determine the extent of light inhibition across a variety of species, functional groups and habitat types.

Results/Conclusions:

Respiration is less inhibited by light in the Arctic than it is expected to be based on observations from lower latitudes. We measured several functional traits in order to identify the mechanisms plants have used to acclimatize to constant daylight. Carbohydrate content,photosynthetic capacity (Amax) and specific leaf area (SLA) were significant predictors of levels of inhibition. There did not appear to be a significant effect of functional group membership on inhibition. We detected considerable intraspecific variation in trait values and levels of inhibition and thus species identity did not explain variation in inhibition. Preliminary tests for effects of evolutionary history on levels of inhibition indicate that inhibition may be lower in plants that have diversified at higher latitudes.These results underline the importance of accounting for respiration in the light in arctic carbon models. Arctic carbon stocks may be significantly lower than previously thought since current estimates don’t include respiration in the light.
Gene diversity among some endogamous population of Amravati District, Maharashtra, India.
Authors: Tekade Rupali , Warghat Nandkishor , Baig M.
Published: April 2011

The present work deals with the distribution of ABO, Rh and sickling alleles as markers to study the genetic structure and micro-demarcation among castes and tribal populations from the Amravati district of Maharashtra. Three loci namely, ABO, Rh and sickling were selected to measure the relative frequency of respective alleles in ten (10) endogamous populations inhabiting the Amravati District. The ABO locus was found to be less polymorphic when compared with other loci. On the other hand, Rh and sickling loci were found to be more polymorphic. Construction of a dendrogram using allele frequency data reveals an interesting relationship among the caste and tribe. An analysis shows three major clades comprising A, B and C. Clade A comprises Islamic Dawoodi Bohra and Hindu Gujrati. Clade B comprises the upper castes, Brahmin, Jain, Kashmiris and Kunbis, while Clade C shows Gonds and Katchhi. This study is a first attempt to provide a genetic landscape of castes and tribes inhabiting the Vidarbha region. The findings are discussed in light of the historical, anthropological and genetic data available for the studied group.
Building conceptual spaces for exploring and linking biomedical resources
Authors: Berlanga Rafael , Nebot Voctoria , Jimenez-Ruiz Ernesto
Published: April 2011

The establishment of links between data (e.g., patient records) and Web resources (e.g., literature) and the proper visualization of such discovered knowledge is still a challenge in most Life Science domains (e.g., biomedicine). In this paper we present our contribution to the community in the form of an infrastructure to annotate information resources, to discover relationships among them, and to represent and visualize the new discovered knowledge. Furthermore, we have also implemented a Web-based prototype tool which integrates the proposed infrastructure.
SPARQL Assist Language Neutral Query Composer
Authors: McCarthy Luke , Vandervalk Ben , Wilkinson Mark
Published: April 2011

SPARQL query composition is difficult for the lay-person or even the experienced bioinformatician in cases where the data model is unfamiliar. Established best-practices and internationalization concerns dictate that semantic web ontologies should use terms with opaque identifiers, further complicating the task. We present SPARQL Assist: a web application that addresses these issues by providing context-sensitive type-ahead completion to existing web forms. Ontological terms are suggested using their labels and descriptions, leveraging existing XML support for internationalization and language-neutrality.
The CALBC RDF Triple store: retrieval over large literature content
Authors: Croset Samuel
Published: April 2011

Integration of the scientific literature into a biomedical research infrastructure requires the processing of the literature, identification of the contained named entities (NEs) and concepts, and to represent the content in a standardised way.The CALBC project partners (PPs) have produced a large-scale annotated biomedical corpus with four different semantic groups through the harmonisation of annotations from automatic text mining solutions (Silver Standard Corpus, SSC). The four semantic groups were chemical entities and drugs (CHED), genes and proteins (PRGE), diseases and disorders (DISO) and species (SPE). The content of the SSC has been fully integrated into RDF Triple Store (4,568,678 triples) and has been aligned with content from the GeneAtlas (182,840 triples), UniProtKb (12,552,239 triples for human) and the lexical resource LexEBI (BioLexicon). RDF Triple Store enables querying the scientific literature and bioinformatics resources at the same time for evidence of genetic causes, such as drug targets and disease involvement.
Systems Biology Graphical Notation: Process Description language Level 1
Authors: Moodie Stuart , Le Novere Nicolas , Demir Emek , Mi Huaiyu , Villeger Alice
Published: April 2011

Standard graphical representations have played a crucial role in science and engineering throughout the last century. Without electrical symbolism, it is very likely that our industrial society would not have evolved at the same pace. Similarly, specialized notations such as the Feynmann notation or the process flow diagrams did a lot for the adoption of concepts in their own fields. With the advent of Systems Biology, and more recently of Synthetic Biology, the need for precise and unambiguous descriptions of biochemical interactions has become more pressing. While some ideas have been advanced over the last decade, with a few detailed proposals, no actual community standard has emerged. The Systems Biology Graphical Notation (SBGN) is a graphical representation crafted over several years by a community of biochemists, modellers and computer scientists. Three orthogonal and complementary languages have been created, the Process Diagrams, the Entity Relationship Diagrams and the Activity Flow Diagrams. Using these three idioms a scientist can represent any network of biochemical interactions, which can then be interpreted in an unambiguous way. The set of symbols used is limited, and the grammar quite simple, to allow its usage in textbooks and its teaching directly in high schools. The first level of the SBGN Process Diagram has been publicly released. Software support for SBGN Process Diagram was developed concurrently with its specification in order to speed-up public adoption. Shared by the communities of biochemists, genomicians, theoreticians and computational biologists, SBGN languages will foster efficient storage, exchange and reuse of information on signalling pathways, metabolic networks and gene regulatory maps.
(Corrected) Speed effects in gliding motility assays due to surface passivation, water isotope, and osmotic stress.
Authors: Maloney Andy , Herskowitz Lawrence , Koch Steven
Published: April 2011

The molecular motor kinesin-1, an ATPase, and the substrate it walks along, microtubules, are vital components of eukaryotic cells. Kinesin converts chemical energy to linear motion as its two motor domains step along microtubules in a process similar to how we walk. Cells create systems of microtubules that direct the motion of kinesin. This directed motion allows kinesin to transport various cargoes inside cells.During the stepping process, the kinesin motor domains bind and unbind from their binding sites on the microtubules. Binding and unbinding rates of biomolecules are highly dependent on hydration and exclusion of water from the binding interface. Osmotic stress will likely strongly affect the binding and unbinding rates for kinesin and thus offers a tool to specifically probe those steps. We will report the effects of different osmolytes on microtubule speed and other observables in the gliding motility assay.Kinesin’s kinetic core cycle hydrolyzes ATP with the help of a water molecule. Any modification to the water molecules the kinesin is in will change how ATP hydrolyzes and will ultimately affect how kinesin moves along microtubules. We will report preliminary results showing how kinesin is affected when the solvent it is in is changed from light water to heavy water.When used in a surface assay or in devices, the kinesin and microtubule system is also dependent on substrate passivation. Kinesin motor domains do not transport microtubules in the gliding motility assay if kinesin is added to a glass microscope slide that has not been functionalized. Functionalization of the glass slides and slips is typically performed with bovine milk proteins called caseins. Bovine casein is a globular protein that can be broken up into four constituents: αs1, αs2, β, and κ. Each casein constituent affects how kinesin adheres to the glass and ultimately the speed at which microtubules are observed to glide at. Building on the work of Verma et.al., we have found that each constituent individually produces different outcomes in gliding assays. We will present these findings and discuss implications they have for the use of gliding assays to study kinesin and the use of the kinesin-microtubule system in microdevices.[1] Chaen, S, N Yamamoto, I Shirakawa, and H Sugi. 2001. Effect of deuterium oxide on actomyosin motility in vitro. Biochimica et biophysica acta 1506, no. 3: 218-23.[2] Vivek Verma, William O Hancock, Jeffrey M Catchmark, "The role of casein in supporting the operation of surface bound kinesin," J. Biol. Eng. 2008; 2: 14.

Acknowledgements:

This work was supported by the DTRA CB Basic Research Program under Grant No. HDTRA1-09-1-008.CORRECTIONS: At the workshop, Erik Schaffer pointed out to us that some of our speed differences (casein data) were surely due to microscope increasing in temperature. I've edited the poster to correct for this. Thanks, Erik!
(Corrected) Osmotic stress and water isotope effects in kinesin-1 gliding motility assays
Authors: Koch Steven , Maloney Andy , Herskowitz Lawrence
Published: April 2011

The osmotic pressure and kinetic properties of water play important roles in biomolecular interactions. As pointed out by Parsegian, Rand, and Rau, these crucial roles are often overlooked[1]. In some fields, osmotic stress and isotope effects have been exploited for probing the role water plays in binding interactions of biomolecules. To our knowledge, there have been no studies of osmotic stress and water isotope effects for kinesin, and only a handful for myosin. We're currently using the gliding motility assay to see whether we can extract new information about kinesin-1 / microtubule interactions by changing osmotic stress and water isotopes. We will describe our open-source, automated analysis platform for extracting microtubule gliding speeds from image series. We will also show our preliminary analyses of the changes seen in gliding assays when done in heavy water (either heavy-hydrogen or heavy-oxygen) or osmolytes (betaine). We will discuss whether osmotic stress and isotopes, particularly heavy-oxygen water, might be an important tool for probing effects of water on binding interactions between kinesin and microtubules. We will also discuss potential applications of deuterium water for stabilizing microtubules and kinesin for lab or device applications.[1] Parsegian, V. A., Rand, R. P., & Rau, D. C. (1995). Macromolecules and water: probing with osmotic stress. Methods in Enzymology, 259.This work was supported by the DTRA CB Basic Research Program under Grant No. HDTRA1-09-1-008 in collaboration with Dr. Susan Atlas lab (UNM).CORRECTIONS: At the workshop, Erik Schaffer pointed out to us that some of our speed differences (casein data) were surely due to microscope increasing in temperature. I’ve edited the poster to correct for this. Thanks, Erik!2011 March Correction: Using temperature stabilization and much-improved technique, Andy has taken higher-quality data for the heavy-hydrogen and heavy-oxygen experiments. See the added slides, 6-7.
Structure and function prediction of human homologue hABH5 of E. coli ALKB5 using in silico approach
Authors: Shankaracharya  , Das Saibal , Vidyarthi Ambarish Sharan
Published: April 2011

Newly discovered human homologues of ALKB protein have shown the activity of DNA damaging drugs, used for cancer therapy. Little is known about the structure and function of hABH5, one of the members of this superfamily. Therefore, in the present study we intend to predict its structure and function using various bioinformatics tools. Modeling was done with modeler 9v7 to predict the 3D structure of the hABH5 protein. 3-D model of hABH5, ALKBH5.B99990005.pdb was predicted and evaluated. Validation results showed 96.8% residues in favor and an additional allowed region of the Ramachandran plot. Ligand binding residues prediction showed four ligand clusters, having 25 ligands in cluster 1. Importantly, conserved pattern of Pro158-X-Asp160-Xn-His266 in the functional domain was detected. DNA and RNA binding sites were also predicted in the model. The predicted and validated model of human homologue hABH5 resulting from this study may unveil the mechanism of DNA damage repair in humans and accelerate research on designing appropriate inhibitors, aiding in chemotherapy and cancer related diseases.
Integrative analysis of large-scale biological data sets
Authors: Glaab Enrico , Garibaldi Jonathan , Krasnogor Natalio
Published: April 2011

We present two novel web-applications for microarray and gene/protein set analysis, ArrayMining.net and TopoGSA. These bioinformatics tools use integrative analysis methods, including ensemble and consensus machine learning techniques, as well as modular combinations of different analysis types, to extract new biological insights from experimental transcriptomics and proteomics data. They enable researchers to combine related algorithms and datasets to increase the robustness and accuracy of statistical analyses and exploit synergies of different computational methods, ranging from statistical learning to optimization and topological network analysis.
The effect of abiotic factors on asymbiotic nitrogen fixation in dead roots from the Pacific Northwest
Authors: Hicks William , Chen Hua
Published: April 2011

High rates of asymbiotic nitrogen fixation have been observed in dead roots. However, little is known about how biotic and abiotic factors influence asymbiotic nitrogen fixation in dead roots. The objective of this study was to examine how nitrogen fixation in dead roots responded to three abiotic factors: temperature, oxygen concentration, and moisture content by measuring acetylene reduction rates in dead roots. For measuring the response to temperature and oxygen, we collected dead roots of Douglas-fir (Pseudotsuga menziesii) from one site in western Oregon, while the effect of moisture content was tested with samples from three species including Douglas-fir, western hemlock (Tsuga heterophylla), and Ponderosa pine (Pinus ponderosa) from three sites in western Oregon. We measured acetylene reduction rates at 5, 13, 20, 30, and 40°C and at oxygen concentrations of 0, 1, 2, 4, 8, and 21% in dead root samples that had been previously wetted. Unaltered root samples with different moisture contents were used to measure the effect of moisture content on acetylene reduction. The optimal temperature for acetylene reduction in roots was 20°C with an acetylene reduction rate of 9.6 nmol/g/d and a standard error of 3.2 nmol/g/d. Asymbiotic nitrogen fixation was greatly reduced above and below this temperature with acetylene reduction rates of 1.2 ± 0.6 nmol/g/d at 5°C and 0.2 ± 0.2 nmol/g/d at 40°C. The highest acetylene reduction rates (13.8 ± 4.2 nmol/g/d) occurred at an oxygen concentration of 2%. Rates dropped sharply under no oxygen condition (3.0 ± 2.8 nmol/g/d) and at an oxygen concentration of 21% (3.0 ± 0.8 nmol/g/d). Optimal acetylene reduction activity occurred above 60% root moisture content and activity was near zero below 60%. These abiotic factors have a similar influence on asymbiotic nitrogen fixation activity in other substrates like dead wood. In the Pacific Northwest, annual nitrogen fixation activity in dead roots tends to be primarily controlled by temperature while above-ground substrates like dead wood can have reduced activity during the dry summer months when lower moisture contents and higher oxygen concentrations can reduce activity.
Getting The Most Out of Your Research
Authors: Erogbogbo Folarin
Published: April 2011

Research is the cornerstone of invention, facilitator of innovation, and mother of discovery. Even though many students are competent in advancing through the class room and getting good grades, excellent research requires a different set of attitudinal and academic skills. This workshop, "Get the most out of your research" is an outstanding program developed from extensive time spent with brilliant scientists and a wide variety of mentored students. Familiarize yourself with the fine points of this workshop and arm yourself for a successful research career.
SNPxGE2: a database for human 3-way SNP-expression associations
Authors: Wang Yupeng , Joseph Sandeep , Liu Xinyu , Kelly Michael , Rekaya Romdhane
Published: April 2011

Recently, gene co-expression relationships have been found to be often conditional and dynamic. Besides, many studies have suggested that single nucleotide polymorphisms (SNPs) have impacts on gene expression variations in human populations. The SNPxGE2 database contains the computationally predicted human 3-way SNP-expression associations, that is, the differential co-expression between 2 genes is associated with a genotype/SNP. This data was generated from a large scale association study that was based on the HapMap data, which covered 269 individuals from 4 human populations, 701,202 SNPs and 15,000 gene expression profiles. Two models of 3-way SNP-expression associations were considered: gap/substitution and on/off. The implementation was carried out using 64 Linux cluster nodes in ~30 days and assessed SNP-expression combinations. The results, including 4,713 on/off associations and 36,170 gap/substitution associations at a p-value cutoff of 0.001, can be queried in the SNPxGE2 database via either gene name or reference SNP ID. For each reported association, a detailed information page is provided. The SNPxGE2 database can be freely accessed at http://tunisia.ads.uga.edu/SNPxGE2/index.php.
DNA Sequence Evolution through Integral Value Transformations
Authors: Hassan Sk Sarif , Pal Choudhury Pabitra , Guha Ranita , Chakraborty Shantanav , Goswami Arunava
Published: April 2011

In deciphering the DNA structures, evolutions and functions, Cellular Automata (CA) do have a significant role. DNA can be thought of as a one-dimensional multi-state CA, more precisely four states of CA namely A, T, C, and G which can be taken as numerals 0, 1, 2 and 3. Earlier, G.Ch. Sirakoulis et al reported the DNA structure, evolution and function through quaternary logic one dimensional CA and the authors have found the simulation results of DNA evolutions with the help of only four linear CA rules. The DNA sequences which are produced through the CA evolutions, however, are seen by our research team not to exist in the established databases of various genomes although the initial seed (initial global state of CA) was taken from the database. This problem motivated us to study the DNA evolutions from a more fundamental point of view. Parallel to the CA paradigm we have devised an enriched set of discrete transformations which have been named as Integral Value Transformations (IVT). Interestingly, on applying the IVT systematically, we have been able to show that each of the DNA sequences at various discrete time instances in IVT evolutions can be directly mapped to a specific DNA sequence existing in the database. This has been possible through our efforts of getting quantitative mathematical parameters of the DNA sequences involving Fractals. Thus we have at our disposal some transformational mechanism between one DNA to another.
Characterization of a pig skeletal muscle microarray to study pork quality: the GenmascqChip 15K
Authors: Damon Marie , Herault Frédéric , Vincent Annie , Le Roy Pascale , Cherel Pierre
Published: April 2011

Pork quality is highly variable and availability of relevant predictors of fresh meat quality at slaughter is critical to optimize carcass use and improve its valuation. High throughput gene expression studies have been widely used to describe biological mechanisms underlying variation of several traits but data are scarce regarding their use as tools for development of biomarkers. The GENMASCQ (GENomics enabled Marker Assisted Selection and Certification of Quality in Pork products ) research program was set up to select, using high-throughput gene expression screening, markers of the biological variation mostly appropriate to describe, and ultimately forecast, the sensory quality of an important meat product, accounting for nearly 40 % of meat protein sources in human food. This report describes the characterization of a porcine skeletal muscle microarray, the GenmascqChip 15K, as a new tool to study pig meat quality. This microarray is annotated at nearly 90 % and permits to explore a list of 9169 unique genes.
Quantitative detection of cereal geminiviruses
Authors: Drechsler Nadine , Habekuß Antje , Thieme Thomas , Schubert Jörg
Published: April 2011

The Geminiviruses _Wheat dwarf virus_ (WDV) and _Barley dwarf virus_ (BDV) cause symptoms such as dwarfing, stunting and yellowing in infected cereals and can lead to reduced yield and even death of the plant. Both viruses are transmitted by the leafhopper _Psammotettix alienus_ Dahlb. in a persistent non propagative manner. WDV is reported in Germany since the early 1990s. In the future an increase of infections is predicted due to global warming which leads to prolonged active periods of the vector in autumn. Furthermore infected plants can hibernate and serve as source of infection in spring.For the first time quantitative PCR assays were developed which allow the sensitive detection and quantification of WDV and BDV both in plants and vectors. Both viruses are detected with primers located in conserved regions of the viral genome. Taqman® Hydrolysis probes were designed for differentiating detection of WDV and BDV. The absolute quantification of viral copies is done by a standard dilution series of cloned viral DNA. The sensitivity of the method was compared to DAS-ELISA. For this purpose, sap of heavily infected plants was diluted with sap of healthy plants. With qPCR, virus was detectable in dilutions of 10-8 whereas the ELISA reaches the limit of detection at dilutions of 10-4.Field plants were analyzed to investigate how many viral copies can be found under natural infection conditions in late spring. ELISA and rating of symptoms were performed in parallel. It could be shown that viral copy number does not correlate with severity of disease symptoms.Winter barley cultivar ‘Rubina’ was inoculated with viruliferous _P. alienus_ under greenhouse conditions to monitor spatial development of infection. Virus titre increased continuously over 4 weeks. The virus was unequally distributed in the plant; the highest amounts were detected in the youngest leaf.Body and head of _P. alienus_ were analyzed separately to quantify virus content. The viruliferous leafhoppers were kept on plants for 7 days to infect them. It became evident that virus content of the vector does not correlate with its ability to infect plants.These highly sensitive and specific PCR assays allow a wide range of applications, e.g. investigations of the development of virus infection in the plant, vector transmission studies and comparisons of virus content of different cultivars for resistance breeding purposes.
Stir Bar Sorptive Extraction – A method for detection of volatiles from potato plants?
Authors: Beyer Katrin , Ziegler Angelika , Ulrich Detlef , Weiß Kirsten , Grünwald René , Wilhelm Ralf
Published: April 2011

The application of Stir Bar Sorptive Extraction (SBSE) as a method for extraction of emitted volatile compounds of potato leaves using GC/MS will be studied. A suitable efficient method shall be developed to describe differences in the spectrum of volatile compounds of potato varieties. It was shown that SBSE yields results similar to other established methods but with less effort. The method will be optimized further. The use of the spectrum of volatile compounds as a parameter for variety assessment (e.g.: plant health, plant protection, biosafety) is planned.
Copper and other heavy metals in specialized crops and their effects on soil coenosis
Authors: Steindl Anna , Strumpf Thomas , Riepert Frank
Published: April 2011

The background of the project are claims of the EU regulation to generate reliable data considering the extent of copper contamination in soils of specialized crops in order to decide about copper restrictions in organic farming.2522 single soil samples were collected on 85 vineyard and 13 hop areas with different management histories. Samples were taken from sites presently under cultivation, formerly cultivated, and sites without anthropogenic copper contamination as control, indicating natural background values. In addition to Aqua Regia extraction for determining total copper contents, available plant copper content was analyzed in NH~4~NO~3~ extraction. Soil parameters such as pH-value, C/N ratio, soil type etc. were also analyzed. The correlation between plant-available and total copper contents is not very high, probably due to the broad range of relevant values e.g. soil parameters or cultivation measurements. An ongoing biological survey about the present status of earthworm populations will give information about possible impairments of soil coenosis.