bluuebunny/crossref_metadata_2025_split huggingface dataset:
The South and the Black Radical Tradition: Then and Now
Authors: Katz-Fishman Walda , Scott Jerome 
Published: January 2008

From the inception of the emerging American nation, the South is a central battleground in the struggles for freedom, justice, and equality. It is the location of the most intense repression, exploitation, and reaction directed toward Africans Americans, as well as Native Americans and working people generally. At the same time the South is the site of the most heroic resistance to these oppressive conditions of class domination, of white supremacy, and of sexist social relations in the public and private sectors. The institution of chattel slavery thrusts the Black radical tradition into the forefront of these early struggles. Today's globalization in the electronic age and neoliberal policies — the attack on the New Deal and Civil Rights reforms of the past era — again place the Black radical tradition at the center of the struggles for freedom, justice, and equality. We present a historical materialist analysis of the Black radical tradition in the South, from slave resistance and rebellions in the 1500s through the Civil War to the economic and political justice struggles in the current period. Black women — often working class — are always at the core of the Black radical tradition and are frequently in its leadership. Black radicals in each period make revolutionary demands that challenge state policy and/or capitalist property relations. But history reveals that each victory, hard fought and won, merely reforms capitalism and is only temporary. We conclude that the Black radical tradition in America calls for the liberation (i.e., the full economic, political and social equality) of the black masses. Permanent victory means that the Black radical tradition is at the heart of a working class-based movement to bring an end to the global capitalist system and to the class, color, and gender oppression that is its cornerstone.
Models for Unity between Scholarship and Grassroots Activism
Authors: Zerai Assata 
Published: January 2008

Institutional constraints hinder the activist scholar who seeks to create alternative models for scholarship and social transformation. In this paper, I discuss results from a survey administered to Africana scholars on the Association of Black Sociologists listserv and other discussion groups servicing progressive scholars and students on the internet. The primary objective of the survey was to elicit comments on ways that Africana scholars balance activism with scholarship. The survey results indicate that there are many levels on which activists scholars can make a contribution to humanity. These include the intellectual labor of articulating our unique perspectives that we promote within our disciplines, our service as consultants to grassroots organizers, and our progressive applied work in our fi eld. Once we embrace the activist-scholar orientation, our struggle is to strike an appropriate balance among the three different types of contribution.
COPD diagnosis related to different guidelines and spirometry techniques
Authors: Nathell Lennart , Nathell Madelene , Malmberg Per , Larsson Kjell 
Published: January 2008

Abstract
The aim was to compare the diagnosis of COPD among smokers according to different international guidelines and to compare the outcome when using slow (SVC) and forced vital capacity (FVC).
In order to find current smokers a questionnaire was sent to persons who had been on sick leave for more than two weeks. Those who smoked more than 8 cigarettes per day were invited to perform a spirometry.
Totally 3,887 spirometries were performed. In this sample 10.2% fulfilled the NICE COPD-criteria, 14.0% the GOLD COPD-criteria and 21.7% the ERS COPD criteria. The diagnosis according to NICE and GOLD guidelines is based on FVC and in the ERS guidelines the best value of either SVC or FVC is used. Thus, substantially more subjects with COPD were found when the best of either SVC or FVC was used. Forced VC tended to be higher than SVC when lung function was normal and in those with mild obstruction prior to bronchodilatation whereas SVC exceeded FVC after bronchodilatation in those who had severe bronchial obstruction.
The diagnosis of COPD is highly depending on which guidelines are used for defining the disease. If FVC and not the best of SVC and FVC is used when defining COPD the diagnosis will be missed in a substantial number of patients.
Chronic obstructive pulmonary disease and inhaled steroids alter surfactant protein D (SP-D) levels: a cross-sectional study
Authors: Sims Michael W , Tal-Singer Ruth M , Kierstein Sonja , Musani Ali I , Beers Michael F , Panettieri Reynold A , Haczku Angela 
Published: January 2008

AbstractBackgroundSurfactant protein D (SP-D), an innate immune molecule, plays an important protective role during airway inflammation. Deficiency of this molecule induces emphysematous changes in murine lungs, but its significance in human COPD remains unclear.MethodsWe collected bronchoalveolar lavage fluid from 20 subjects with varying degrees of COPD (8 former smokers and 12 current smokers) and 15 asymptomatic healthy control subjects (5 never smokers, 3 remote former smokers, and 7 current smokers). All subjects underwent a complete medical history and pulmonary function testing. SP-D was measured by Enzyme-Linked ImmunoSorbent Assay. Statistical analysis was performed using nonparametric methods and multivariable linear regression for control of confounding. The effect of corticosteroid treatment on SP-D synthesis was studiedin vitrousing an established model of isolated type II alveolar epithelial cell culture.ResultsAmong former smokers, those with COPD had significantly lower SP-D levels than healthy subjects (median 502 and 1067 ng/mL, respectively, p = 0.01). In a multivariable linear regression model controlling for age, sex, race, and pack-years of tobacco, COPD was independently associated with lower SP-D levels (model coefficient -539, p = 0.04) and inhaled corticosteroid use was independently associated with higher SP-D levels (398, p = 0.046). To support the hypothesis that corticosteroids increase SP-D production we used type II alveolar epithelial cells isolated from adult rat lungs. These cells responded to dexamethasone treatment by a significant increase of SP-D mRNA (p = 0.041) and protein (p = 0.037) production after 4 days of culture.ConclusionAmong former smokers, COPD is associated with lower levels of SP-D and inhaled corticosteroid use is associated with higher levels of SP-D in the lung. Dexamethasone induced SP-D mRNA and protein expression in isolated epithelial cellsin vitro. Given the importance of this molecule as a modulator of innate immunity and inflammation in the lung, low levels may play a role in the pathogenesis and/or progression of COPD. Further, we speculate that inhaled steroids may induce SP-D expression and that this mechanism may contribute to their beneficial effects in COPD. Larger, prospective studies are warranted to further elucidate the role of surfactant protein D in modulating pulmonary inflammation and COPD pathogenesis.
Gene function prediction using labeled and unlabeled data
Authors: Zhao Xing-Ming , Wang Yong , Chen Luonan , Aihara Kazuyuki 
Published: January 2008

Abstract

Background
In general, gene function prediction can be formalized as a classification problem based on machine learning technique. Usually, both labeled positive and negative samples are needed to train the classifier. For the problem of gene function prediction, however, the available information is only about positive samples. In other words, we know which genes have the function of interested, while it is generally unclear which genes do not have the function, i.e. the negative samples. If all the genes outside of the target functional family are seen as negative samples, the imbalanced problem will arise because there are only a relatively small number of genes annotated in each family. Furthermore, the classifier may be degraded by the false negatives in the heuristically generated negative samples.

Results
In this paper, we present a new technique, namely Annotating Genes with Positive Samples (AGPS), for defining negative samples in gene function prediction. With the defined negative samples, it is straightforward to predict the functions of unknown genes. In addition, the AGPS algorithm is able to integrate various kinds of data sources to predict gene functions in a reliable and accurate manner. With the one-class and two-class Support Vector Machines as the core learning algorithm, the AGPS algorithm shows good performances for function prediction on yeast genes.

Conclusion
We proposed a new method for defining negative samples in gene function prediction. Experimental results on yeast genes show that AGPS yields good performances on both training and test sets. In addition, the overlapping between prediction results and GO annotations on unknown genes also demonstrates the effectiveness of the proposed method.
Independent Origins of New Sex-Linked Chromosomes in the melanica and robusta Species Groups of Drosophila
Authors: Flores Sergio V , Evans Amy L , McAllister Bryant F 
Published: January 2008

Abstract

Background
Recent translocations of autosomal regions to the sex chromosomes represent important systems for identifying the evolutionary forces affecting convergent patterns of sex-chromosome heteromorphism. Additions to the sex chromosomes have been reported in the melanica and robusta species groups, two sister clades of Drosophila. The close relationship between these two species groups and the similarity of their rearranged karyotypes motivates this test of alternative hypotheses; the rearranged sex chromosomes in both groups are derived through a common origin, or the rearrangements are derived through at least two independent origins. Here we examine chromosomal arrangement in representatives of the melanica and the robusta species groups and test these alternative hypotheses using a phylogenetic approach.

Results
Two mitochondrial and two nuclear gene sequences were used to reconstruct phylogenetic relationships of a set of nine ingroup species having fused and unfused sex chromosomes and representing a broad sample of both species groups. Different methods of phylogenetic inference, coupled with concurrent cytogenetic analysis, indicate that the hypothesis of independent origins of rearranged sex chromosomes within each species group is significantly more likely than the alternative hypothesis of a single common origin. An estimate tightly constrained around 8 My was obtained for the age of the rearranged sex chromosomes in the melanica group; however, a more loosely constrained estimate of 10–15 My was obtained for the age of the rearrangement in the robusta group.

Conclusion
Independent acquisition of new chromosomal arms by the sex chromosomes in the melanica and robusta species groups represents a case of striking convergence at the karyotypic level. Our findings indicate that the parallel divergence experienced by newly sex-linked genomic regions in these groups represents an excellent system for studying the tempo of sex chromosome evolution.
Genome-wide analysis of CCCH zinc finger family in Arabidopsis and rice
Authors: Wang Dong , Guo Yinghui , Wu Changai , Yang Guodong , Li Yingying , Zheng Chengchao 
Published: January 2008

Abstract

Background
Genes in the CCCH family encode zinc finger proteins containing the motif with three cysteines and one histidine residues. They have been known to play important roles in RNA processing as RNA-binding proteins in animals. To date, few plant CCCH proteins have been studied functionally.

Results
In this study, a comprehensive computational analysis identified 68 and 67 CCCH family genes in Arabidopsis and rice, respectively. A complete overview of this gene family in Arabidopsis was presented, including the gene structures, phylogeny, protein motifs, and chromosome locations. In addition, a comparative analysis between these genes in Arabidopsis and rice was performed. These results revealed that the CCCH families in Arabidopsis and rice were divided into 11 and 8 subfamilies, respectively. The gene duplication contributed to the expansion of the CCCH gene family in Arabidopsis genome. Expression studies indicated that CCCH proteins exhibit a variety of expression patterns, suggesting diverse functions. Finally, evolutionary analysis showed that one subfamily is higher plant specific. The expression profile indicated that most members of this subfamily are regulated by abiotic or biotic stresses, suggesting that they could have an effective role in stress tolerance.

Conclusion
Our comparative genomics analysis of CCCH genes and encoded proteins in two model plant species provides the first step towards the functional dissection of this emerging family of potential RNA-binding proteins.
Glioma cells on the run – the migratory transcriptome of 10 human glioma cell lines
Authors: Demuth Tim , Rennert Jessica L , Hoelzinger Dominique B , Reavie Linsey B , Nakada Mitsutoshi , Beaudry Christian , Nakada Satoko , Anderson Eric M , Henrichs Amanda N , McDonough Wendy S , Holz David , Joy Anna , Lin Richard , Pan Kuang H , Lih Chih J , Cohen Stan N , Berens Michael E 
Published: January 2008

Abstract

Background
Glioblastoma multiforme (GBM) is the most common primary intracranial tumor and despite recent advances in treatment regimens, prognosis for affected patients remains poor. Active cell migration and invasion of GBM cells ultimately lead to ubiquitous tumor recurrence and patient death.
To further understand the genetic mechanisms underlying the ability of glioma cells to migrate, we compared the matched transcriptional profiles of migratory and stationary populations of human glioma cells. Using a monolayer radial migration assay, motile and stationary cell populations from seven human long term glioma cell lines and three primary GBM cultures were isolated and prepared for expression analysis.

Results
Gene expression signatures of stationary and migratory populations across all cell lines were identified using a pattern recognition approach that integrates a priori knowledge with expression data. Principal component analysis (PCA) revealed two discriminating patterns between migrating and stationary glioma cells: i) global down-regulation and ii) global up-regulation profiles that were used in a proband-based rule function implemented in GABRIEL to find subsets of genes having similar expression patterns. Genes with up-regulation pattern in migrating glioma cells were found to be overexpressed in 75% of human GBM biopsy specimens compared to normal brain. A 22 gene signature capable of classifying glioma cultures based on their migration rate was developed. Fidelity of this discovery algorithm was assessed by validation of the invasion candidate gene, connective tissue growth factor (CTGF). siRNA mediated knockdown yielded reduced in vitro migration and ex vivo invasion; immunohistochemistry on glioma invasion tissue microarray confirmed up-regulation of CTGF in invasive glioma cells.

Conclusion
Gene expression profiling of migratory glioma cells induced to disperse in vitro affords discovery of genomic signatures; selected candidates were validated clinically at the transcriptional and translational levels as well as through functional assays thereby underscoring the fidelity of the discovery algorithm.
Mutational and transcriptional analyses of an avian pathogenic Escherichia coli ColV plasmid
Authors: Skyberg Jerod A , Johnson Timothy J , Nolan Lisa K 
Published: January 2008

Abstract

Background
Previously we described a 184-kb ColV plasmid, pAPEC-O2-ColV, that contributed to the ability of an E. coli to kill avian embryos, grow in human urine, and colonize the murine kidney. Here, the roles of several genes encoded by this plasmid in virulence were assessed using mutational and transcriptional analyses.

Methods
Genes chosen for deletion were iss, tsh, iutA, iroN, sitA, and cvaB. In addition, a 35-kb region of the plasmid, containing iss, tsh, and the ColV and iro operons, along with a 15-kb region containing both the aerobactin and sit operons, were deleted. Mutants were compared to the wild-type (APEC O2) for lethality to chick embryos and growth in human urine. Expression of the targeted genes was also assessed under these same conditions using RT-PCR

Results
No significant differences between the mutants and the wild-type in these phenotypic traits were detected. However, genes encoding known or predicted iron transport systems were up-regulated during growth in human urine, as compared to growth in LB broth, while iss, hlyF, and iroN were strongly up-regulated in chick embryos.

Conclusion
While no difference was observed between the mutant strains and their wild-type parent in the phenotypic traits assayed, we reasoned that some compensatory virulence mechanism, insensitivity of the virulence assays, or other factor could have obscured changes in the virulence of the mutants. Indeed we found several of these genes to be up-regulated in human urine and/or in the chick embryo, suggesting that certain genes linked to ColV plasmids are involved in the establishment of avian extraintestinal infection.
Using magnetic resonance microscopy to study the growth dynamics of a glioma spheroid in collagen I: A case study
Authors: Huang Shuning , Vader David , Wang Zhihui , Stemmer-Rachamimov Anat , Weitz David A , Dai Guangping , Rosen Bruce R , Deisboeck Thomas S 
Published: January 2008

Abstract

Background
Highly malignant gliomas are characterized by rapid growth, extensive local tissue infiltration and the resulting overall dismal clinical outcome. Gaining any additional insights into the complex interaction between this aggressive brain tumor and its microenvironment is therefore critical. Currently, the standard imaging modalities to investigate the crucial interface between tumor growth and invasion in vitro are light and confocal laser scanning microscopy. While immensely useful in cell culture, integrating these modalities with this cancer's clinical imaging method of choice, i.e. MRI, is a non-trivial endeavour. However, this integration is necessary, should advanced computational modeling be able to utilize these in vitro data to eventually predict growth behaviour in vivo. We therefore argue that employing the same imaging modality for both the experimental setting and the clinical situation it represents should have significant value from a data integration perspective. In this case study, we have investigated the feasibility of using a specific form of MRI, i.e. magnetic resonance microscopy or MRM, to study the expansion dynamics of a multicellular tumor spheroid in a collagen type I gel.

Methods
An U87mEGFR human giloblastoma multicellular spheroid (MTS) containing approximately 4·103 cells was generated and pipetted into a collagen I gel. The sample was then imaged using a T2-weighted 3D spoiled gradient echo pulse sequence on a 14T MRI scanner over a period of 12 hours with a temporal resolution of 3 hours at room temperature. Standard histopathology was performed on the MRM sample, as well as on control samples.

Results
We were able to acquire three-dimensional MR images with a spatial resolution of 24 × 24 × 24 μm3. Our MRM data successfully documented the volumetric growth dynamics of an MTS in a collagen I gel over the 12-hour period. The histopathology results confirmed cell viability in the MRM sample, yet displayed distinct patterns of cell proliferation and invasion as compared to control.

Conclusion
In this study, we demonstrate that a specific form of MRI, i.e. magnetic resonance microscopy or MRM, can be used to study the dynamic growth of a multicellular tumor spheroid (MTS) with a single cell scale spatial resolution that approaches the level of light microscopy. We argue that MRM can be employed as a complementary non-invasive tool to characterize microscopic MTS expansion, and thus, together with integrative computational modeling, may allow bridging of the experimental and clinical scales more readily.
The orthopaedic trauma literature: an evaluation of statistically significant findings in orthopaedic trauma randomized trials
Authors: Sung Jinsil , Siegel Judith , Tornetta Paul , Bhandari Mohit 
Published: January 2008

Abstract

Background
Evidence-based medicine posits that health care research is founded upon clinically important differences in patient centered outcomes. Statistically significant differences between two treatments may not necessarily reflect a clinically important difference. We aimed to quantify the sample sizes and magnitude of treatment effects in a review of orthopaedic randomized trials with statistically significant findings.

Methods
We conducted a comprehensive search (PubMed, Cochrane) for all randomized controlled trials between 1/1/95 to 12/31/04. Eligible studies include those that focused upon orthopaedic trauma. Baseline characteristics and treatment effects were abstracted by two reviewers. Briefly, for continuous outcome measures (ie functional scores), we calculated effect sizes (mean difference/standard deviation). Dichotomous variables (ie infection, nonunion) were summarized as absolute risk differences and relative risk reductions (RRR). Effect sizes >0.80 and RRRs>50% were defined as large effects.
Using regression analysis we examined the association between the total number of outcome events and treatment effect (dichotomous outcomes).

Results
Our search yielded 433 randomized controlled trials (RCTs), of which 76 RCTs with statistically significant findings on 184 outcomes (122 continuous/62 dichotomous outcomes) met study eligibility criteria. The mean effect size across studies with continuous outcome variables was 1.7 (95% confidence interval: 1.43–1.97). For dichotomous outcomes, the mean risk difference was 30% (95%confidence interval:24%–36%) and the mean relative risk reduction was 61% (95% confidence interval: 55%–66%; range: 0%–97%). Fewer numbers of total outcome events in studies was strongly correlated with increasing magnitude of the treatment effect (Pearson's R = -0.70, p < 0.01). When adjusted for sample size, the number of outcome events revealed an independent association with the size of the treatment effect (Odds ratio = 50, 95% confidence interval: 3.0–1000, p = 0.006).

Conclusion
Our review suggests that statistically significant results in orthopaedic trials have the following implications-1) On average large risk reductions are reported 2) Large treatment effects (>50% relative risk reduction) are correlated with few number of total outcome events. Readers should interpret the results of such small trials with these issues in mind.