bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rosemary Sutcliff's The Eagle of the Ninth: A Festival of Britain?
Authors: BURTON PHILIP 
Published: April 2011

Some time about the year A. D. 117, the Ninth Legion…marched north to deal with a rising among the Caledonian tribes, and was never heard of again.During the excavations at Silchester nearly eighteen hundred years later, there was dug up…a wingless Roman Eagle, a cast of which can be seen to this day in Reading Museum. Different people have had different ideas as to how it came to be there, but no one knows, just as no one knows what happened to the Ninth Legion after it marched into the northern mists.It is from these two mysteries, brought together, that I have made the story of ‘The Eagle of the Ninth’.
A comparison of the global status of English and Chinese: towards a new global language?
Authors: Gil Jeffrey 
Published: April 2011

China's rapid development and growing engagement with the rest of the world have prompted much discussion and debate about the Chinese language, especially its prospects for becoming a global language. A report inChina Daily(2004), for example, suggests that:there may even come a day when learning Chinese, like present day English, becomes compulsory for business, politics and cultural exchanges – a trend that has become increasingly plausible as more foreign students enrol in Chinese courses and China as a nation takes a more prominent role on the international stage.
Immunolocalization of BRG1–SWI/SNF protein during folliculogenesis in the porcine ovary
Authors: Lisboa Livia Aires , Bordignon Vilceu , Seneda Marcelo Marcondes 
Published: April 2011

SummaryDynamic changes in chromatin structure and gene expression occur during follicular and oocyte growth. Epigenetic mechanisms regulate these changes through biochemical reactions that modify the nucleosome structure, and consequently affect transcription. Chromatin remodellers that alter DNA–histone interactions can influence transcriptional activity by facilitating or repressing DNA access. The SWItch/Sucrose NonFermentable (SWI/SNF) complex represents an important chromatin remodelling family, which comprises many protein subunits including the BRG1 (brahma-related gene 1). Our aim in this study was to analyse BRG1 expression patterns in different stages of follicular development. Ovaries (n = 10) were collected from prepubertal gilts and then rinsed in phosphate-buffered saline (PBS). Ovarian fragments of 8 × 8 × 8 mm were cut and placed into a 4% paraformaldehyde solution. For immunofluorescence analysis, samples were incubated with primary antibodies: polyclonal rabbit anti-BRG1 (1/200) or control rabbit IgG at the same concentration, overnight at 4°C. Primary antibodies were detected using Alexa Fluor 594-anti-rabbit 1/1000 diluted secondary antibody. Cells were counterstained with 4′,6-diamidino-2-phenylindole (DAPI). Positive fluorescence signal for BRG1 was detected in all analysed samples. In primary follicles, the protein was detected only in the oocyte nucleus. However, in growing follicles, BRG1 was identified in granulosa and theca cells in a well defined pattern, according to the proximity of the cells from the oocyte. These results suggest an important role for BRG1 in the regulation of follicular growth, probably modulating granulosa and theca cell proliferation, as well as oocyte growth and maturation.
Differential gene expression and developmental competence inin vitroproduced bovine embryos
Authors: Ripamonte Paula , Mesquita Lígia Garcia , Cortezzi Sylvia Sanches , de Carvalho Balieiro Júlio César , Fonseca Merighe Giovana Krempel , Watanabe Yeda Fumie , Caetano Alexandre Rodrigues , Meirelles Flávio Vieira 
Published: April 2011

SummaryThe embryonic developmental block occurs at the 8-cell stage in cattle and is characterized by a lengthening of the cell cycle and an increased number of embryos that stop development. The maternal-embryonic transition arises at the same stage resulting in the transcription of many genes. Gene expression studies during this stage may contribute to the understanding of the physiological mechanisms involved in the maternal-embryonic transition. Herein we identified genes differentially expressed between embryos with high or low developmental competence to reach the blastocyst stage using differential display PCR. Embryos were analysed according to developmental kinetics: fast cleavage embryos showing 8 cells at 48 h post insemination (hpi) with high potential of development (F8), and embryos with slow cleavage presenting 4 cells at 48 hpi (S4) and 8 cells at 90 hpi (S8), both with reduced rates of development to blastocyst. The fluorescence DDPCR method was applied and allowed the recovery of 176 differentially expressed bands with similar proportion between high and low development potential groups (52% to F8 and 48% in S4 and S8 groups). A total of 27 isolated fragments were cloned and sequenced, confirming the expected primer sequences and allowing the identification of 27 gene transcripts. PI3KCA and ITM2B were chosen for relative quantification of mRNA using real-time PCR and showed a kinetic and a time-related pattern of expression respectively. The observed results suggest the existence of two different embryonic genome activation mechanisms: fast-developing embryos activate genes related to embryonic development, and slow-developing embryos activate genes related to cellular survival and/or death.
Predicting Behavioral Deficits in Pediatric Traumatic Brain Injury Through Uncinate Fasciculus Integrity
Authors: Johnson Chad P. , Juranek Jenifer , Kramer Larry A. , Prasad Mary R. , Swank Paul R. , Ewing-Cobbs Linda 
Published: April 2011

AbstractBehavioral dysregulation is a common and detrimental consequence of traumatic brain injury (TBI) in children that contributes to poor academic achievement and deficits in social development. Unfortunately, behavioral dysregulation is difficult to predict from either injury severity or early neuropsychological evaluation. The uncinate fasciculus (UF) connects orbitofrontal and anterior temporal lobes, which are commonly implicated in emotional and behavioral regulation. Using probabilistic diffusion tensor tractography (DTT), we examined the relationship between the integrity of the UF 3 months post-injury and ratings of executive functions 12 months post-injury in children with moderate to severe TBI and a comparison group with orthopedic injuries. As expected, fractional anisotropy of the UF was lower in the TBI group relative to the orthopedic injury group. DTT metrics from the UF served as a biomarker and predicted ratings of emotional and behavior regulation, but not metacognition. In contrast, the Glasgow Coma Scale score was not related to either UF integrity or to executive function outcomes. Neuroanatomical biomarkers like the uncinate fasciculus may allow for early identification of behavioral problems and allow for investigation into the relationship of frontotemporal networks to brain-behavior relationships. (JINS, 2011, 17, 663–673)
RACE/ETHNICITY AND U.S. ADULT MORTALITY
Authors: Hummer Robert A. , Chinn Juanita J. 
Published: April 2011

AbstractAlthough there have been significant decreases in U.S. mortality rates, racial/ethnic disparities persist. The goals of this study are to: (1) elucidate a conceptual framework for the study of racial/ethnic differences in U.S. adult mortality, (2) estimate current racial/ethnic differences in adult mortality, (3) examine empirically the extent to which measures of socioeconomic status and other risk factors impact the mortality differences across groups, and (4) utilize findings to inform the policy community with regard to eliminating racial/ethnic disparities in mortality. Relative Black-White differences are modestly narrower when compared to a decade or so ago, but remain very wide. The majority of the Black-White adult mortality gap can be accounted for by measures of socioeconomic resources that reflect the historical and continuing significance of racial socioeconomic stratification. Further, when controlling for socioeconomic resources, Mexican Americans and Mexican immigrants exhibit significantly lower mortality risk than non-Hispanic Whites. Without aggressive efforts to create equality in socioeconomic and social resources, Black-White disparities in mortality will remain wide, and mortality among the Mexican-origin population will remain higher than what would be the case if that population achieved socioeconomic equality with Whites.
RECONSIDERING KENNETH B. CLARK AND THE IDEA OF BLACK PSYCHOLOGICAL DAMAGE, 1931–1945
Authors: Freeman Damon 
Published: April 2011

AbstractOne of the most controversial figures in Black intellectual history is psychologist Kenneth B. Clark. Prominently identified as the main proponent of the idea that racial segregation led to psychological damage in Black children, Clark's work heavily influenced the U.S. Supreme Court in its 1954Brown v. Board of Educationschool desegregation decision. Almost immediately afterwards, his research methods and conclusions were challenged as incomplete and biased. Scholars now argue that Clark and other racial liberals became solely wedded to the idea of racial psychological damage in order to secure victory inBrown. Yet a closer analysis of his thought reveals a more complex picture. During the early 1940s, he developed a new psychological concept which he called the “zoot effect.” He defined the zoot effect as the attempt by a person to gain psychological security in a society which mandated that individual's inferiority. The zoot effect or zoot personality reflected the larger society's pathology, which manifested itself internally in individuals. This concept was heavily shaped by ideas about race, class, and in particular the work of Alfred Adler, which he first learned as a student at Howard University. Using archival and secondary sources, I argue for a reconceptualization of Clark within the broader context of his social thought, suggesting that the zoot-effect concept grounded his research on Black children and set the stage for his later views on desegregation, civil rights, and American society.
MEASURING EVERYDAY RACIAL/ETHNIC DISCRIMINATION IN HEALTH SURVEYS
Authors: Shariff-Marco Salma , Breen Nancy , Landrine Hope , Reeve Bryce B. , Krieger Nancy , Gee Gilbert C. , Williams David R. , Mays Vickie M. , Ponce Ninez A. , Alegría Margarita , Liu Benmei , Willis Gordon , Johnson Timothy P. 
Published: April 2011

AbstractWhile it is clear that self-reported racial/ethnic discrimination is related to illness, there are challenges in measuring self-reported discrimination or unfair treatment. In the present study, we evaluate the psychometric properties of a self-reported instrument across racial/ethnic groups in a population-based sample, and we test and interpret findings from applying two different widely-used approaches to asking about discrimination and unfair treatment. Even though we found that the subset of items we tested tap into a single underlying concept, we also found that different groups are more likely to report on different aspects of discrimination. Whether race is mentioned in the survey question affects both frequency and mean scores of reports of racial/ethnic discrimination. Our findings suggest caution to researchers when comparing studies that have used different approaches to measure racial/ethnic discrimination and allow us to suggest practical empirical guidelines for measuring and analyzing racial/ethnic discrimination. No less important, we have developed a self-reported measure of recent racial/ethnic discrimination that functions well in a range of different racial/ethnic groups and makes it possible to compare how racial/ethnic discrimination is associated with health disparities among multiple racial/ethnic groups.
THE STRANGE DISAPPEARANCE OF HISTORY FROM RACIAL HEALTH DISPARITIES RESEARCH
Authors: Chowkwanyun Merlin 
Published: April 2011

AbstractAlthough thriving in many respects, racial health disparities research suffers from a lack of historical analysis and may be in danger of reaching a saturation point. This article examines how renewed attention to history can enhance the explanatory power of such research. First, it surveys a body of writing on what history can contribute to contemporary social science and policy debates. Next, it compares current racial health disparities research to the analytical impasse encountered by urban poverty researchers of the late 1980s and early 1990s. It contrasts that work with two classic post-Second World War urban histories, and identifies qualities of the latter lacking in conventional social science. The essay then surveys historically oriented works on race and health, pointing out their usefulness to racial health disparities research while discussing promising future research directions. It concludes with a brief reflection on changes in the academic institutional context necessary for fruitful synergy between public health researchers and historians.
TOOTHLESS
Authors: Murakawa Naomi 
Published: April 2011

AbstractFrom “reefer madness” to “crack babies,” American drug scares demonstrate that race shapes the construction of epidemics and diagnoses. This research brief reexamines the racial construction of drug scares in light of the recent methamphetamine (meth) scare, a drug “epidemic” constructed asWhiteand accompanied by a new diagnosis: “meth mouth.” Through examination of survey data and dental research, I challenge the evidence for both the “epidemic” upsurge in meth use and the “meth mouth” diagnosis. Given the weak evidentiary basis for epidemic and diagnosis, I offer a preliminary interpretation that the meth epidemic is constructed as symptom and cause of White status decline, with dental decay the vehicle for anxieties about descent into “White trash” status.
THE SUSTAINING RELEVANCE OF W. E. B. DU BOIS TO HEALTH DISPARITIES RESEARCH
Authors: White Kellee 
Published: April 2011

AbstractWilliam Edward Burghardt Du Bois is considered one of the most prolific and brilliant scholars of our time. While his contributions to civil rights, sociology, history, African American studies, and urban studies are universally recognized, his legacy in the public health and epidemiology discourses is not as widely acknowledged by contemporary health researchers. His seminal workThe Philadelphia Negro: A Social Study(1899) and his report “The Health and Physique of the Negro American” (1906) may be considered early harbingers in general of public health—and more specifically, social epidemiology—research. During the late nineteenth and early twentieth centuries, Black and White differences in mortality and morbidity were largely attributed to notions of biological racial inferiority. Efforts by Du Bois to challenge these predominant notions resulted in the systematic empirical investigation of social factors contributing to Black health risk and health disparities. More than one hundred years after Du Bois's pioneering scholarship, racial/ethnic and social disparities remain a central challenge for public health and medical professionals. Given the persistence of health disparities and the increasing focus on neighborhood social and physical environments as fundamental factors contributing to health inequalities, this paper seeks to historically situate Du Bois's scholarship, describe the methodological and conceptual significance of his seminal studies, and articulate the importance of incorporating Du Bois's legacy to advance the next generation of racial/ethnic health inequality research.
BamTools: a C++ API and toolkit for analyzing and managing BAM files
Authors: Barnett Derek W. , Garrison Erik K. , Quinlan Aaron R. , Strömberg Michael P. , Marth Gabor T. 
Published: April 2011

Abstract
Motivation: Analysis of genomic sequencing data requires efficient, easy-to-use access to alignment results and flexible data management tools (e.g. filtering, merging, sorting, etc.). However, the enormous amount of data produced by current sequencing technologies is typically stored in compressed, binary formats that are not easily handled by the text-based parsers commonly used in bioinformatics research.
Results: We introduce a software suite for programmers and end users that facilitates research analysis and data management using BAM files. BamTools provides both the first C++ API publicly available for BAM file support as well as a command-line toolkit.
Availability: BamTools was written in C++, and is supported on Linux, Mac OSX and MS Windows. Source code and documentation are freely available at http://github.org/pezmaster31/bamtools.
Contact: barnetde@bc.edu
‘Sciencenet’—towards a global search and share engine for all scientific knowledge
Authors: Lütjohann Dominic S. , Shah Asmi H. , Christen Michael P. , Richter Florian , Knese Karsten , Liebel Urban 
Published: April 2011

Abstract
Summary: Modern biological experiments create vast amounts of data which are geographically distributed. These datasets consist of petabytes of raw data and billions of documents. Yet to the best of our knowledge, a search engine technology that searches and cross-links all different data types in life sciences does not exist.
We have developed a prototype distributed scientific search engine technology, ‘Sciencenet’, which facilitates rapid searching over this large data space. By ‘bringing the search engine to the data’, we do not require server farms. This platform also allows users to contribute to the search index and publish their large-scale data to support e-Science. Furthermore, a community-driven method guarantees that only scientific content is crawled and presented. Our peer-to-peer approach is sufficiently scalable for the science web without performance or capacity tradeoff.
Availability and Implementation: The free to use search portal web page and the downloadable client are accessible at: http://sciencenet.kit.edu. The web portal for index administration is implemented in ASP.NET, the ‘AskMe’ experiment publisher is written in Python 2.7, and the backend ‘YaCy’ search engine is based on Java 1.6.
Contact: urban.liebel@kit.edu
Supplementary Material: Detailed instructions and descriptions can be found on the project homepage: http://sciencenet.kit.edu.
SMETHILLIUM: spatial normalization METHod for ILLumina InfinIUM HumanMethylation BeadChip
Authors: Sabbah Camille , Mazo Gildas , Paccard Caroline , Reyal Fabien , Hupé Philippe 
Published: April 2011

Abstract
Summary: DNA methylation is a major epigenetic modification in human cells. Illumina HumanMethylation27 BeadChip makes it possible to quantify the methylation state of 27 578 loci spanning 14 495 genes. We developed a non-parametric normalization method to correct the spatial background noise in order to improve the signal-to-noise ratio. The prediction performance of the proposed method was assessed on three fully methylated samples and three fully unmethylated DNA samples. We demonstrate that the spatial normalization outperforms BeadStudio to predict the methylation state of a given locus.
Availability and Implementation: A R script and the data are available at the following address: http://bioinfo.curie.fr/projects/smethillium.
Contact: smethillium@curie.fr
Supplementary information: Supplementary data are available at Bioinformatics online.
Figure summarizer browser extensions for PubMed Central
Authors: Agarwal Shashank , Yu Hong 
Published: April 2011

Abstract
Summary: Figures in biomedical articles present visual evidence for research facts and help readers understand the article better. However, when figures are taken out of context, it is difficult to understand their content. We developed a summarization algorithm to summarize the content of figures and used it in our figure search engine (http://figuresearch.askhermes.org/). In this article, we report on the development of web browser extensions for Mozilla Firefox, Google Chrome and Apple Safari to display summaries for figures in PubMed Central and NCBI Images.
Availability: The extensions can be downloaded from http://figuresearch.askhermes.org/articlesearch/extensions.php.
Contact: agarwal@uwm.edu
Implications of a warming eastern Bering Sea for Bristol Bay sockeye salmon
Authors: Farley Edward V. , Starovoytov Alexander , Naydenko Svetlana , Heintz Ron , Trudel Marc , Guthrie Charles , Eisner Lisa , Guyon Jeffrey R. 
Published: April 2011

AbstractFarley, E. V., Starovoytov, A., Naydenko, S., Heintz, R., Trudel, M., Guthrie, C., Eisner, L., Guyon, J. R. 2011. Implications of a warming eastern Bering Sea for Bristol Bay sockeye salmon. – ICES Journal of Marine Science, 68: 1138–1146. Overwinter survival of Pacific salmon (Oncorhynchus sp.) is believed to be a function of size and energetic status they gain during their first summer at sea. We test this notion for Bristol Bay sockeye salmon (O. nerka), utilizing data from large-scale fisheries and oceanographic surveys conducted during mid-August to September 2002–2008 and from February to March 2009. The new data presented in this paper demonstrate size-selective mortality for Bristol Bay sockeye salmon between autumn and their first winter at sea. Differences in the seasonal energetic signatures for lipid and protein suggest that these fish are not starving, but instead the larger fish caught during winter apparently are utilizing energy stores to minimize predation. Energetic status of juvenile sockeye salmon was also strongly related to marine survival indices and years with lower energetic status apparently are a function of density-dependent processes associated with high abundance of juvenile sockeye salmon. Based on new information regarding eastern Bering Sea ecosystem productivity under a climate-warming scenario, we hypothesize that sustained increases in spring and summer sea temperatures may negatively affect energetic status of juvenile sockeye salmon, potentially resulting in increased overwinter mortality.