bluuebunny/crossref_metadata_2025 huggingface dataset:
Dynamic Viscoelastic Effects on Free Vibrations of a Submerged Fluid-filled Thin Cylindrical Shell
Authors: Hasheminejad Seyyed M. , Shahsavarifard A. , Shahsavarifard M.
Published: May 2008

The novel features of the Havriliak-Negami model for dynamic description of viscoelastic material behavior along with the Donnell theory of shell motion are applied to study free vibrational and damping characteristics of an infinitely long viscoelastic thin circular cylindrical shell submerged in and filled with acoustic fluids. The analytical results are illustrated with numerical examples in which two fluid-filled shells of distinctive viscoelastic material properties are undergoing free vibrations in a surrounding ideal fluid medium. The natural frequencies and the associated modal loss factors as a function of the circumferential mode number at selected axial wave lengths and submergence conditions are numerically evaluated and discussed. The numerical results reveal the imperative influence of dynamic viscoelastic properties on the vibrational characteristics of the fluid-coupled system. They demonstrate an interesting correlation between the modal loss factor and the material loss factor in the vicinity of the calculated natural frequency. In particular, the modal loss factor (natural frequency) is found to be highly dependent on (fairly insensitive to) the frequency dependence of the loss factor in the viscoelastic material. A limiting case involving a thin elastic steel shell submerged in water is considered and fair agreement with a well-known solution is established.
Vibration Control of Nonlinear Rotating Beam Using Piezoelectric Actuator and Sliding Mode Approach
Authors: Xue X. , Tang J.
Published: May 2008

In this research, we develop a general methodology for the vibration control of a nonlinear rotating beam. The dynamic model of a rotating Euler-Bernoulli beam integrated with a piezoelectric actuator is formulated. An integral sliding mode approach is proposed for the vibration control of the system with nonlinear coupling effect between the hub rotation and the beam transverse vibration. The vibration control is achieved by using the piezoelectric actuator only, whereas the motor torque is treated as a time-dependent external input. In the sliding mode control design, the sliding manifold is constructed using only the partial states of the system that are associated with the beam vibration. Particularly, utilizing the internal dynamics analysis, the nonlinear coupling effect of the rigid-body rotation and the beam transverse vibration is decoupled, and the robust stability of the system is guaranteed. This integral sliding mode control is continuous in nature, which can alleviate or avoid the chattering problem. A series of simulation studies demonstrate that the proposed control method can effectively suppress the beam vibration induced by the hub rotation and the external disturbance.
The Effects of Race and Insurance on Potentially Avoidable Hospitalizations in Tennessee
Authors: Chang Cyril F. , Mirvis David M. , Waters Teresa M.
Published: May 2008

This study examined effects of race and insurance on the risk of potentially avoidable hospitalizations (PAHs) in Tennessee. Applying the current Agency for Healthcare Research and Quality definitions for ambulatory-care-sensitive conditions to inpatient discharge data, the study found hospitalized Black patients more likely than their White counterparts to have experienced a PAH for chronic conditions. In contrast, Black inpatients' risk was lower than that of White inpatients for acute conditions after controlling for covariates. The results also showed the strong influence of insurance coverage. Finally, an analysis of racial differences in the relative risks for PAHs using data grouped by insurance status showed that hospitalized Blacks within each subset had a greater risk of having a PAH than hospitalized Whites, although the risk varied with insurance type. The variations of PAH risks across racial and insurance categories, together with the extra risks associated with chronic conditions, deserve greater examination.
Messy Problems and Lay Audiences: Teaching Critical Thinking Within the Finance Curriculum
Authors: Carrithers David , Ling Teresa , Bean John C.
Published: May 2008

This article investigates the critical thinking difficulties of finance majors when asked to address ill-structured finance problems. The authors build on previous research in which they asked students to analyze an ill-structured investment problem and recommend a course of action. The results revealed numerous critical thinking weaknesses, including a failure to address the client's problem, use analytical tools systematically, construct rhetorically useful graphics, or translate finance concepts and methodologies into lay language. The present research aims to understand more deeply why students struggle with ill-structured problems. Using think-aloud protocols, audiotaped interviews, and other strategies, the authors explore causes of finance students' difficulties and suggest strategies for addressing them. The results suggest that the homework tasks typically given them, such as quantitative problem sets using algorithmic procedures, do not prepare them to confront ill-structured problems requiring disciplinary arguments aimed at specified audiences. Research further suggests that teaching audience adaptation—especially for nonexpert audiences—is helpful in promoting critical thinking.
Eliciting a Distal Gesture via Dynamic Assessment Among Students With Moderate to Severe Intellectual Disability
Authors: McLaughlin Katherine , Cascella Paul W.
Published: May 2008

This study attempted to elicit distal gestures within dynamic assessment structured sampling events from six children with moderate to severe intellectual disability (ages 8-13). Using four communication temptations and a least-to-most prompting hierarchy across three sessions, three participants who had both pre-symbolic and preintentional communication demonstrated an initial distal gesture, often in response to a choice making temptation. Clinical implications are discussed with regard to the utility of dynamic assessment structured sampling activities.
Spanish Nonword Repetition
Authors: Ebert Kerry Danahy , Kalanek Jocelyne , Cordero Kelly Nett , Kohnert Kathryn
Published: May 2008

Purpose: The current study presents preliminary nonword repetition data from Spanish-speaking preschool children using a new set of stimuli. Method: Twenty nonwords were constructed to be phonotactically possible in Spanish and to conform to published guidelines for nonword repetition stimuli. Fourteen Spanish-speaking typically developing preschool children repeated the nonwords. Results: Both age and word length affected repetition accuracy, and there was an age-by-length interaction. Younger children were less accurate overall and showed steeper decreases in accuracy as length increased. Conclusions: The results provide promising evidence that the stimuli may be developed into a Spanish nonword repetition task for both research and clinical purposes.
Examining the Dependability of Academic Achievement Measures for English Language Learners
Authors: Solano-Flores Guillermo , Li Min
Published: May 2008

The dependability of academic achievement measures for English language learners (ELLs) is influenced by three facts: (a) Each ELL has unique strengths and weaknesses in each language mode (listening, speaking, reading, and writing) both in English and in his or her first language, (b) each test item poses a different set of linguistic demands that do not replicate across languages, and (c) raters may vary in their ability to properly interpret students' responses. Generalizability theory allows examination of the magnitude of score variation due to the language (or dialect) in which tests are administered. The interaction of student, item, and language (and dialect) is the most important source of score variation. The language in which students should be tested and the minimum number of items needed to produce dependable measures of academic achievement for ELLs may be different across communities within a broad group of native speakers of a language.
Ulcer Infection by ESβL-Producing Proteus mirabilis: A Case Report
Authors: Savini Vincenzo , Catavitello Chiara , Talia Marzia , Di Berardino Fabio , Manna Assunta , Balbinot Andrea , Febbo Fabio , Carlino Daniela , Fioritoni Francesca , Di Bonaventura Giovanni , D'Antonio Domenico
Published: May 2008

In this article, a case of decubitus ulcer infection caused by an extended-spectrum β-lactamase-producing Proteus mirabilis strain, successfully treated with oral amoxicillin-clavulanate (1-month therapy) is described. This article focuses on diffusion and clinical effect of extended-spectrum β-lactamases-producing Proteus mirabilis on treatment of gram negative lower extremity infections.
Alternative contingency table measures improve the power and detection of multifactor dimensionality reduction
Authors: Bush William S , Edwards Todd L , Dudek Scott M , McKinney Brett A , Ritchie Marylyn D
Published: May 2008

Background

Multifactor Dimensionality Reduction (MDR) has been introduced previously as a non-parametric statistical method for detecting gene-gene interactions. MDR performs a dimensional reduction by assigning multi-locus genotypes to either high- or low-risk groups and measuring the percentage of cases and controls incorrectly labelled by this classification – the classification error. The combination of variables that produces the lowest classification error is selected as the best or most fit model. The correctly and incorrectly labelled cases and controls can be expressed as a two-way contingency table. We sought to improve the ability of MDR to detect gene-gene interactions by replacing classification error with a different measure to score model quality.

Results

In this study, we compare the detection and power of MDR using a variety of measures for two-way contingency table analysis. We simulated 40 genetic models, varying the number of disease loci in the model (2 – 5), allele frequencies of the disease loci (.2/.8 or .4/.6) and the broad-sense heritability of the model (.05 – .3). Overall, detection using NMI was 65.36% across all models, and specific detection was 59.4% versus detection using classification error at 62% and specific detection was 52.2%.

Conclusion

Of the 10 measures evaluated, the likelihood ratio and normalized mutual information (NMI) are measures that consistently improve the detection and power of MDR in simulated data over using classification error. These measures also reduce the inclusion of spurious variables in a multi-locus model. Thus, MDR, which has already been demonstrated as a powerful tool for detecting gene-gene interactions, can be improved with the use of alternative fitness functions.
FLI-1 Flightless-1 and LET-60 Ras control germ line morphogenesis in C. elegans
Authors: Lu Jiamiao , Dentler William L , Lundquist Erik A
Published: May 2008

Background

In the C. elegans germ line, syncytial germ line nuclei are arranged at the cortex of the germ line as they exit mitosis and enter meiosis, forming a nucleus-free core of germ line cytoplasm called the rachis. Molecular mechanisms of rachis formation and germ line organization are not well understood.

Results

Mutations in the fli-1 gene disrupt rachis organization without affecting meiotic differentiation, a phenotype in C. elegans referred to here as the germ line morphogenesis (Glm) phenotype. In fli-1 mutants, chains of meiotic germ nuclei spanned the rachis and were partially enveloped by invaginations of germ line plasma membrane, similar to nuclei at the cortex. Extensions of the somatic sheath cells that surround the germ line protruded deep inside the rachis and were associated with displaced nuclei in fli-1 mutants. fli-1 encodes a molecule with leucine-rich repeats and gelsolin repeats similar to Drosophila flightless 1 and human Fliih, which have been shown to act as cytoplasmic actin regulators as well as nuclear transcriptional regulators. Mutations in let-60 Ras, previously implicated in germ line development, were found to cause the Glm phenotype. Constitutively-active LET-60 partially rescued the fli-1 Glm phenotype, suggesting that LET-60 Ras and FLI-1 might act together to control germ line morphogenesis.

Conclusion

FLI-1 controls germ line morphogenesis and rachis organization, a process about which little is known at the molecular level. The LET-60 Ras GTPase might act with FLI-1 to control germ line morphogenesis.
Testing a hypothesis of unidirectional hybridization in plants: Observations on Sonneratia, Bruguiera and Ligularia
Authors: Zhou Renchao , Gong Xun , Boufford David , Wu Chung-I , Shi Suhua
Published: May 2008

Background

When natural hybridization occurs at sites where the hybridizing species differ in abundance, the pollen load delivered to the rare species should be predominantly from the common species. Previous authors have therefore proposed a hypothesis on the direction of hybridization: interspecific hybrids are more likely to have the female parent from the rare species and the male parent from the common species. We wish to test this hypothesis using data of plant hybridizations both from our own experimentation and from the literature.

Results

By examining the maternally inherited chloroplast DNA of 6 cases of F1 hybridization from four genera of plants, we infer unidirectional hybridization in most cases. In all 5 cases where the relative abundance of the parental species deviates from parity, however, the direction is predominantly in the direction opposite of the prediction based strictly on numerical abundance.

Conclusion

Our results show that the observed direction of hybridization is almost always opposite of the predicted direction based on the relative abundance of the hybridizing species. Several alternative hypotheses, including unidirectional postmating isolation and reinforcement of premating isolation, were discussed.
Differences in mtDNA haplogroup distribution among 3 Jewish populations alter susceptibility to T2DM complications
Authors: Feder Jeanette , Blech Ilana , Ovadia Ofer , Amar Shirly , Wainstein Julio , Raz Itamar , Dadon Sarah , Arking Dan E , Glaser Benjamin , Mishmar Dan
Published: May 2008

Background

Recent genome-wide association studies searching for candidate susceptibility loci for common complex diseases such as type 2 diabetes mellitus (T2DM) and its common complications have uncovered novel disease-associated genes. Nevertheless these large-scale population screens often overlook the tremendous variation in the mitochondrial genome (mtDNA) and its involvement in complex disorders.

Results

We have analyzed the mitochondrial DNA (mtDNA) genetic variability in Ashkenazi (Ash), Sephardic (Seph) and North African (NAF) Jewish populations (total n = 1179). Our analysis showed significant differences (p < 0.001) in the distribution of mtDNA genetic backgrounds (haplogroups) among the studied populations. To test whether these differences alter the pattern of disease susceptibility, we have screened our three Jewish populations for an association of mtDNA genetic haplogroups with T2DM complications. Our results identified population-specific susceptibility factors of which the best example is the Ashkenazi Jewish specific haplogroup N1b1, having an apparent protective effect against T2DM complications in Ash (p = 0.006), being absent in the NAF population and under-represented in the Seph population. We have generated and analyzed whole mtDNA sequences from the disease associated haplogroups revealing mutations in highly conserved positions that are good candidates to explain the phenotypic effect of these genetic backgrounds.

Conclusion

Our findings support the possibility that recent bottleneck events leading to over-representation of minor mtDNA alleles in specific genetic isolates, could result in population-specific susceptibility loci to complex disorders.
Comparative analysis of transcriptional profiling of CD3+, CD4+ and CD8+ T cells identifies novel immune response players in T-Cell activation
Authors: Wang Min , Windgassen Dirk , Papoutsakis Eleftherios T
Published: May 2008

Background

T-cell activation is an essential step of the immune response and relies on the tightly controlled orchestration of hundreds of genes/proteins, yet the cellular and molecular events underlying this complex process are not fully understood, especially at the genome-scale. Significantly, a comparative genome-scale transcriptional analysis of two T-cell subsets (CD4+ and CD8+) against each other and against the naturally mixed population (CD3+ cells) remains unexplored.

Results

Comparison of the microarray-based gene expression patterns between CD3+ T cells, and the CD4+ and CD8+ subsets revealed largely conserved, but not identical, transcriptional patterns. We employed a Gene-Ontology-driven transcriptional analysis coupled with protein abundance assays in order to identify novel T-cell activation genes and cell-type-specific genes associated with the immune response. We identified potential genes involved in the communication between the two subsets (including IL23A, NR4A2, CD83, PSMB2, -8, MIF, IFI16, TNFAIP1, POU2AF1, and OTUB1) and would-be effector-function-specific genes (XCL2, SLAMF7, TNFSF4, -5, -9, CSF3, CD48 and CD244). Chemokines induced during T-cell activation, but not previously identified in T cells, include CCL20, CXCL9, -10, -11 (in all three populations), and XCL2 (preferentially in CD8+ T cells). Increased expression of other unexpected cytokines (GPI, OSM and MIF) suggests their involvement in T-cell activation with their functions yet to be examined. Differential expression of many receptors, not previously reported in the context of T-cell activation, including CCR5, CCR7, IL1R2, IL1RAP, IL6R, TNFRSF25 and TNFRSF1A, suggests their role in this immune process. Several receptors involved in TCR activation (CD3D, CD3G, TRAT1, ITGAL, ITGB1, ITGB2, CD8A and B (CD8+ T-cell specific) along with LCK, ZAP70 and TYROBP were synchronously downregulated. Members of cell-surface receptors (HLA-Ds and KLRs), none previously identified in the context of T-cell activation, were also downregulated.

Conclusion

This comparative genome-scale, transcriptional analysis of T-cell activation in the CD4+ and CD8+ subsets and the mixed CD3+ populations made possible the identification of many immune-response genes not previously identified in the context of T-cell activation. Significantly, it made possible to identify the temporal patterns of many previously known T-cell activation genes, and also identify genes implicated in effector functions of and communication between CD4+ and CD8+ T cells.
Complete genome sequence of Treponema pallidum ssp. pallidumstrain SS14 determined with oligonucleotide arrays
Authors: Matějková Petra , Strouhal Michal , Šmajs David , Norris Steven J , Palzkill Timothy , Petrosino Joseph F , Sodergren Erica , Norton Jason E , Singh Jaz , Richmond Todd A , Molla Michael N , Albert Thomas J , Weinstock George M
Published: May 2008

Background

Syphilis spirochete Treponema pallidum ssp. pallidum remains the enigmatic pathogen, since no virulence factors have been identified and the pathogenesis of the disease is poorly understood. Increasing rates of new syphilis cases per year have been observed recently.

Results

The genome of the SS14 strain was sequenced to high accuracy by an oligonucleotide array strategy requiring hybridization to only three arrays (Comparative Genome Sequencing, CGS). Gaps in the resulting sequence were filled with targeted dideoxy-terminators (DDT) sequencing and the sequence was confirmed by whole genome fingerprinting (WGF). When compared to the Nichols strain, 327 single nucleotide substitutions (224 transitions, 103 transversions), 14 deletions, and 18 insertions were found. On the proteome level, the highest frequency of amino acid-altering substitution polymorphisms was in novel genes, while the lowest was in housekeeping genes, as expected by their evolutionary conservation. Evidence was also found for hypervariable regions and multiple regions showing intrastrain heterogeneity in the T. pallidum chromosome.

Conclusion

The observed genetic changes do not have influence on the ability of Treponema pallidum to cause syphilitic infection, since both SS14 and Nichols are virulent in rabbit. However, this is the first assessment of the degree of variation between the two syphilis pathogens and paves the way for phylogenetic studies of this fascinating organism.
A novel diffuse gastric cancer susceptibility variant in E-cadherin (CDH1) intron 2: A case control study in an Italian population
Authors: Nasri Soroush , More Helen , Graziano Francesco , Ruzzo Annamaria , Wilson Emily , Dunbier Anita , McKinney Cushla , Merriman Tony , Guilford Parry , Magnani Mauro , Humar Bostjan
Published: May 2008

Background

Inherited genetic factors such as E-cadherin (CDH1) promoter variants are believed to influence the risk towards sporadic diffuse gastric cancer (DGC). Recently, a new regulatory region essential for CDH1 transcription has been identified in CDH1 intron 2.

Methods

We genotyped all known polymorphisms located within conserved sequences of CDH1 intron 2 (rs10673765, rs9932686, rs1125557, rs9282650, rs9931853) in an Italian population consisting of 134 DGC cases and 100 healthy controls (55 patient relatives and 45 unrelated, matched individuals). The influence of individual variants on DGC risk was assessed using χ2-tests and logistic regression. The relative contribution of alleles was estimated by haplotype analysis.

Results

We observed a significant (p < 0.0004) association of the CDH1 163+37235G>A variant (rs1125557) with DGC risk. Odds ratios were 4.55 (95%CI = 2.09–9.93) and 1.38 (95%CI = 0.75–2.55) for AA and GA carriers, respectively. When adjusted for age, sex, smoking status, alcohol intake and H. pylori infection, the risk estimates remained largely significant for AA carriers. Haplotype analysis suggested the 163+37235A-allele contributes to disease risk independently of the other variants studied.

Conclusion

The CDH1 163+37235G>A polymorphism may represent a novel susceptibility variant for sporadic DGC if confirmed in other populations. Considering the broad expression of E-cadherin in epithelia, this exploratory study encourages further evaluation of the 163+37235A-allele as a susceptibility variant in other carcinomas.
Construction of a series of vectors for high throughput cloning and expression screening of membrane proteins from Mycobacterium tuberculosis
Authors: Qin Huajun , Hu Jian , Hua Yuanzhi , Challa Shridhar V , Cross Timothy A , Gao Fei P
Published: May 2008

Background

One of the major challenges for membrane protein structural genomics is establishing high-throughput cloning and expression screening methods to obtain enough purified protein in a homogeneous preparation for structural and functional studies. Here a series of ligation independent cloning based vectors were constructed to address this challenge.

Results

The feasibility of these vectors was tested with 41 putative membrane proteins from Mycobacterium tuberculosis. The efficiency for direct cloning of these target genes from PCR products was 95% (39/41). Over 40% of cloned genes were overexpressed in Escherichia coli BL21 (DE3)-RP codon plus strain in the first round of expression screening. For those proteins which showed no expression, three protein fusion partners were prepared and it was found that each of the target proteins could be overexpressed by at least one of these fusions, resulting in the overexpression of two thirds of the cloned genes.

Conclusion

This expression platform features high throughput cloning, high flexibility for different constructs, and high efficiency for membrane protein overexpression, and is expected to be useful in membrane protein structural and functional studies.
Effects of rosiglitazone on contralateral iliac artery after vascular injury in hypercholesterolemic rabbits
Authors: França Neto Olímpio Ribeiro , Precoma Dalton Bertolim , Alessi Alexandre , Prim Camila , da Silva Ruy FernandoKuenzerCaetano , de Noronha Lucia , Baroncini Liz AndréaVillela
Published: May 2008

Background

The objective was to evaluate the effects of rosiglitazone on iliac arteries of hypercholesterolemic rabbits undergoing balloon catheter injury in the contralateral iliac arteries.

Methods

White male rabbits were fed a hypercholesterolemic diet for 6 weeks and divided into two groups as follows: rosiglitazone group, 14 rabbits treated with rosiglitazone (3 mg/Kg body weight/day) during 6 weeks; and control group, 18 rabbits without rosiglitazone treatment. All animals underwent balloon catheter injury of the right iliac artery on the fourteenth day of the experiment.

Results

There was no significant difference in intima/media layer area ratio between the control group and the rosiglitazone group. Rosiglitazone did not reduce the probability of lesions types I, II, or III (72.73% vs. 92.31%; p = 0.30) and types IV or V (27.27% vs. 7.69%; p = 0.30). There were no differences in the extent of collagen type I and III deposition or in the percentage of animals with macrophages in the intima layer. The percentage of rabbits with smooth muscle cells in the intima layer was higher in rosiglitazone group (p = 0.011).

Conclusion

These findings demonstrate that rosiglitazone given for 6 weeks did not prevent atherogenesis at a vessel distant from the injury site.
Correlation between NK function and response to trastuzumab in metastatic breast cancer patients
Authors: Beano Alessandra , Signorino Elena , Evangelista Andrea , Brusa Davide , Mistrangelo Marinella , Polimeni Maria Antonia , Spadi Rosella , Donadio Michela , Ciuffreda Libero , Matera Lina
Published: May 2008

Background

Trastuzumab is a monoclonal antibody selectively directed against Her2 and approved for the treatment of Her2 overexpressing breast cancer patients. Its proposed mechanisms of action include mediation of antibody-dependent cellular cytotoxicity (ADCC) by triggering FcγRIII on natural killer (NK) cells. This study addresses the correlation between overall NK function and trastuzumab's clinical activity.

Subjects and methods

Clinical and immunological responses were assessed in 26 patients receiving trastuzumab monotherapy as maintenance management after chemotherapy (8 mg/kg load and then standard doses of 6 mg/kg every 3 weeks). Cytotoxic activity against the MHC class I-negative standard NK target K562 cell line and HER2-specific ADCC against a trastuzumab-coated Her2-positive SKBR3 cell line were assessed in peripheral blood mononuclear cells (PBMC) harvested after the first standard dose. After six months, seventeen patients were scored as responders and nine as non-responders according to the RECIST criteria, while Progression-Free Survival (PFS) was calculated during a 12 months follow-up.

Results

The responders had significantly higher levels of both NK and ADCC activities (p < 0.05) that were not different from those of eleven normal controls. The NK activity of the non-responders was significantly (p < 0.05) lower than that of the normal controls. At twelve months, there was a marked correlation between PFS and NK activity only. PFS was significantly longer in patients with high levels of NK activity, whereas its pattern was unrelated to high or low ADCC activity.

Conclusion

One of the mechanisms of action of trastuzumab is NK cell-mediated ADCC lysis of the Her2-positve target cell. We show here that its potency is correlated with the short-term response to treatment, whereas longer protection against tumor expansion seems to be mediated by pure NK activity.
Proteomics with a pinch of salt: A cyanobacterial perspective
Authors: Pandhal Jagroop , Wright Phillip C , Biggs Catherine A
Published: May 2008

Cyanobacteria are ancient life forms and have adapted to a variety of extreme environments, including high salinity. Biochemical, physiological and genetic studies have contributed to uncovering their underlying survival mechanisms, and as recent studies demonstrate, proteomics has the potential to increase our overall understanding further. To date, most salt-related cyanobacterial proteomic studies have utilised gel electrophoresis with the model organismSynechocystissp. PCC6803. Moreover, focus has been on 2–4% w/v NaCl concentrations within different cellular compartments. Under these conditions,Synechocystissp. PCC6803 was found to respond and adapt to salt stress through synthesis of general and specific stress proteins, altering the protein composition of extracellular layers, and re-directing control of complex central intermediary pathways. Post-transcriptional control was also predicted through non-correlating transcript level data and identification of protein isoforms.

In this paper, we also review technical developments with emphasis on improving the quality and quantity of proteomic data and overcoming the detrimental effects of salt on sample preparation and analysis. Developments in gel-free methods include protein and peptide fractionation workflows, which can increase coverage of the proteome (20% inSynechocystissp. PCC6803). Quantitative techniques have also improved in accuracy, resulting in confidence in quantitation approaching or even surpassing that seen in transcriptomic techniques (better than 1.5-fold in differential expression). Furthermore,in vivometabolic labelling andde novoprotein sequencing software have improved the ability to apply proteomics to unsequenced environmental isolates. The example used in this review is a cyanobacterium isolated from a Saharan salt lake.
APRIL facilitates viral-induced erythroleukemia but is dispensable for T cell immunity and lymphomagenesis
Authors: Hardenberg Gijs , Fernandez Leticia , Hendriks Jenny , Chebli Karim , Jacquet Chantal , Sitbon Marc , Hahne Michel , Medema Jan Paul
Published: May 2008

The TNF family member, a proliferation-inducing ligand (APRIL), has been suggested to act as a costimulatory molecule in T cell responses. However, studies addressing this role in vivo are largely lacking. Here, we evaluated the effects of APRIL on physiological T cell responses in vivo. Although receptors for APRIL are expressed on a subset of T cells, neither TCR transgenic (Tg) T cell responses nor endogenous TCR responses were affected by Tg APRIL expression in vivo. Moreover, APRIL did not significantly enhance the induction of T cell lymphomas upon Moloney murine leukemia virus (MLV) infection. This clearly contrasts current belief and indicates that APRIL does not serve a major role in T cell immunity or lymphomagenesis. However, we did observe a strong increase in erythroleukemia formation after MLV inoculation of APRIL Tg mice. Strikingly, this erythroleukemia-facilitating property of APRIL was confirmed using the erythroleukemogenic Friend-MLV. Erythroleukemia in APRIL Tg mice was characterized by low hematocrits and grossly enlarged spleens with an increased percentage of erythroid precursors. Altogether, these results unveil new proerythroleukemogenic properties of APRIL.
Basal-Like Breast Cancer: A Critical Review
Authors: Rakha Emad A. , Reis-Filho Jorge S. , Ellis Ian O.
Published: May 2008

Recent gene expression profiling of breast cancer has identified specific subtypes with clinical, biologic, and therapeutic implications. The basal-like group of tumors is characterized by an expression signature similar to that of the basal/myoepithelial cells of the breast and is reported to have transcriptomic characteristics similar to those of tumors arising in BRCA1 germline mutation carriers. They are associated with aggressive behavior and poor prognosis, and typically do not express hormone receptors or HER-2 (“triple-negative” phenotype). Therefore, patients with basal-like cancers are unlikely to benefit from currently available targeted systemic therapy. Although basal-like tumors are characterized by distinctive morphologic, genetic, immunophenotypic, and clinical features, neither an accepted consensus on routine clinical identification and definition of this aggressive subtype of breast cancer nor a way of systematically classifying this complex group of tumors has been described. Different definitions are, therefore, likely to produce variable and contradictory results that may hamper consistent identification and development of treatment strategies for these tumors. In this review, we discuss definition, heterogeneity, morphologic spectrum, relation to BRCA1, and clinical significance of this important class of breast cancer.
Phase II Study of Palifermin and Concurrent Chemoradiation in Head and Neck Squamous Cell Carcinoma
Authors: Brizel David M. , Murphy Barbara A. , Rosenthal David I. , Pandya Kishan J. , Glück Stefan , Brizel Herbert E. , Meredith Ruby F. , Berger Dietmar , Chen Mon-Gy , Mendenhall William
Published: May 2008

Purpose

Acute mucositis is a dose-limiting toxicity of concurrent chemoradiotherapy regimens for locally advanced head and neck cancer. Palifermin (a recombinant human keratinocyte growth factor; ΔN23-KGF) stimulates the proliferation and differentiation of mucosal epithelium to reduce mucositis in patients receiving intensive therapy for hematologic cancers. This study assessed the efficacy and safety of palifermin in patients receiving concurrent chemoradiotherapy for advanced head and neck squamous cell carcinoma.

Patients and Methods

In a phase II trial, standard radiotherapy was delivered in daily 2-Gy fractions to 70 Gy, or hyperfractionated radiotherapy was delivered in 1.25-Gy fractions twice daily to 72 Gy, over 7 weeks. Chemotherapy included cisplatin 20 mg/m2 for 4 days and continuous-infusion fluorouracil 1,000 mg/m2/d for 4 days on weeks 1 and 5 of irradiation. Patients were randomly assigned 2:1 to palifermin 60 μg/kg or placebo once weekly for 10 doses. A follow-up trial evaluated long-term survival.

Results

Sixty-seven patients received palifermin and 32 received placebo. The median duration of grade ≥ 2 mucositis was 6.5 and 8.1 weeks in the palifermin and placebo groups, respectively (P = .157). Palifermin appeared to reduce mucositis, dysphagia, and xerostomia during hyperfractionated radiotherapy (n = 40) but not standard radiation therapy (n = 59). Adverse events were similar between treatment groups. Palifermin did not alter tumor response or survival.

Conclusion

Ten once-weekly doses of palifermin at 60 μg/kg were well tolerated. Most patients completed treatment, but palifermin did not reduce the morbidity of concurrent chemotherapy and radiotherapy. Future studies should evaluate higher palifermin doses with longer and more standardized assessment of acute mucositis.
Histologic Results of Para-Aortic Lymphadenectomy in Patients Treated for Stage IB2/II Cervical Cancer With Negative [18F]Fluorodeoxyglucose Positron Emission Tomography Scans in the Para-Aortic Area
Authors: Boughanim Mathias , Leboulleux Sophie , Rey Annie , Tuan Pham Chi , Zafrani Yaelle , Duvillard Pierre , Lumbroso Jean , Haie-Meder Christine , Schlumberger Martin , Morice Philippe
Published: May 2008

Purpose

Histologic results of complete para-aortic lymphadenectomy were studied in patients treated for stage IB2/II cervical carcinoma who had no para-aortic uptake on [18F]fluorodeoxyglucose positron emission tomography combined with integrated computed tomography (FDG-PET/CT).

Patients and Methods

Patients were treated between 2004 and 2006 for stage IB2/II cervical cancer. Magnetic resonance imaging of the abdomen and pelvis and FDG-PET/CT were initially performed. Patients with no para-aortic abnormalities were treated with external pelvic radiation therapy and concomitant chemotherapy followed by utero-vaginal brachytherapy. Para-aortic lymphadenectomy was then performed. FDG-PET/CT images were reviewed by two nuclear medicine specialists.

Results

Thirty-eight patients were studied. Three patients had histologically proven para-aortic involvement (metastatic nodes with capsular rupture in the para-aortic area), leading to a negative predictive value of 92% for para-aortic nodal involvement.

Conclusion

In this study, three of 38 patients with no para-aortic uptake on [18F]FDG-PET/CT imaging had histologically proven para-aortic node involvement. PET/CT imaging without histologic examination of the para-aortic area used to determine radiation therapy fields in stage IB2/II cervical cancer would overlook 8% of patients with histologic para-aortic nodal involvement.
The A/B Domain of the Teleost Glucocorticoid Receptors Influences Partial Nuclear Localization in the Absence of Hormone
Authors: Becker Heidi , Sturm Armin , Bron James E. , Schirmer Kristin , Bury Nicolas R.
Published: May 2008

The glucocorticoid (GR) and mineralocorticoid receptor (MR) of extant jawed vertebrates emerged after duplication of an ancestral corticosteroid receptor. The ancestral corticosteroid receptor resembled extant MRs in hormone selectivity, and the different ligand specificity of extant GRs is a secondary derived characteristic. An additional characteristic that distinguishes the mammalian GR from the MR is the cellular distribution pattern in the absence of hormone: the naïve GR resides in the cytoplasm, whereas the naïve MR is found in both the nucleus and cytoplasm. Our results show, by the use of green fluorescent protein-tagged fusion proteins, that the GRs [rainbow trout (rt) GR1 and rtGR2] from a lower vertebrate, the teleost fish, rainbow trout (Oncorhynchus mykiss) resemble mammalian MR rather than GR in their subcellular localization pattern. The addition of cortisol caused the remaining cytoplasmic rtGR1 and rtGR2 to migrate to the nucleus. The speed of nuclear localization was cortisol concentration dependent, with rtGR2 being more sensitive than rtGR1, mimicking the transactivational properties of the receptors in which the cortisol EC50 value is an order of magnitude lower for rtGR2. By the use of chimera constructs between the trout GRs and the rat GR C656G, we show that the E domain of the trout receptors are not involved in the nucleocytoplasmic localization of naïve trout GRs, but the A/B domain, especially if linked to the corresponding trout CD region, plays a pivotal role in the cellular distribution pattern. This is unrelated to the difference in the trout GRs transactivation sensitivity, which is determined by the receptor’s E-domains.
“Communities of Memory” In the Valley of Toluca: The Town of Metepec, 1476–1643
Authors: Megged Amos
Published: May 2008

A close study of Metepec's tale of remembrance brings to light distinct and unique representations of significant episodes and social and political circumstances in its pre-Cortesian past, as well as in the early colonial period. These divergent representations were created by closed circles of factions, neighbors, elders, and kin in this “community of memory” who wished to claim special rights and prerogatives over their shared past. As such, the Códice de Metepec represents a prototype of a dispersed and highly fragmented “canonic tale” that is made up of autochthonous memory plots of various ethnic and splinter groups that tell their own stories of the past in a very different manner though they are within a single community. These distinct and often individualistic memory plots were reworked many times within the primary, local, microcosmic sphere of this community before they shifted to an outside sphere of impact substantially distanced from what united the local people.
Introduction: Narrative Violence: Africa and the Middle East
Authors: Gana Nouri , Härting Heike
Published: May 2008

The essays collected in this issue of Comparative Studies of South Asia, Africa and the Middle East explore the ways in which writers and artists from Africa and the Middle East have deployed diverse genres and modes of narrative or discursive practices in order not only to challenge the entrapments of contemporary violence but also to do so in a self-reflexively anti-redemptory fashion. They conceptualize narrative violence as a modality of cultural and literary analysis, practice and critique; understand violence as a historically situated phenomenon in constant need of social, political, and cultural authorization and reinvention to be effectively implemented at the level of warfare, mobilization, and conscription; and illuminate the ways in which literary and cultural products (literature, film, graphics, etc.) not merely illustrate but actively produce and intervene into the material and palpable workings of violence. As such, the essays in this issue compel us into interrogating the widely circulated discourses about Africa and the Middle East as ahistorical places of violence, death, and disease; question our fatigued notions of the ineluctability and immutability of the contemporary institutionalization of violence; and demonstrate how particular constellations of (corporate) power, (instrumental) knowledge, and (biased) mass media work to foreclose alternative human and humane spaces of survival, agency, resistance, and, above all, narrative departures.
Global Humanitarianism, Race, and the Spectacle of the African Corpse in Current Western Representations of the Rwandan Genocide
Authors: Härting Heike
Published: May 2008

This essay argues that the media-generated spectacle of the dead African body serves as a historically and rhetorically continuous signifier through which the West mounts a revisionary practice of cultural introspection and self-reinvention. Analyzing different representations of the 1994 Rwandan genocide in the West, this essay examines the cultural and narrative logic of the rise of “humanitarianist capital.” Not unlike earlier imperial civilization projects, the cultural production of humanitarianist capital relies on discursive and structural forms of violence that generate patterns of affect and empathy and legitimize the perceived need for economic and institutional aid while reifying the inhabitants of the global South in general and Africa in particular as dependent nonsubjects. Juxtaposing Gil Courtemanche's novel Un dimanche à la piscine à Kigali/A Sunday at the Pool in Kigali (2000/2003) with Marcel Odenbach's video installation In stillen Teichen lauern Krokodile/In Still Ponds Crocodiles May Be Lurking (2002/2004), the essay scrutinizes the ways in which the “necropoeic” narrative strategies of dominant representations of violence in sub-Saharan Africa tend to constitute and perpetuate the social and political death of the African citizen to build Western communities of humanitarianist sentiment. In contrast, Odenbach's installation presents a rare exception to this tendency in that it refuses an immediate access to and consumption of the displayed African body, dismantles the depoliticized economy of humanitarian affect, and stresses the need for and possibility of a politics of proximity and complicity.
Afterword: The Phenomenology of Violence and the Politics of Becoming
Authors: Varadharajan Asha
Published: May 2008

This essay deploys a bricolage of the reflections of Michel Foucault, Jean-Luc Nancy, William E. Connolly, and Achille Mbembe in order to construct a phenomenology of violence. While much of the essay is a response to the collection's trenchant analysis of the historicity of violence and of the conditions of its representability and narration, its effort is to supplement the conversation about the violence of our contemporaneity with philosophical reflections that appear only fleetingly or are differently inflected in the collection. More to the point, the essay shifts the emphasis from the limits, indeed, violence, of representation to a “politics of becoming” grounded in a fragile transcendence of these limits.
From Istanbul to Tabriz: Modernity and Constitutionalism in the Ottoman Empire and Iran
Authors: Zarinebaf Fariba
Published: May 2008

Placing the history of social and intellectual movements in the Middle East in a comparative context, this article examines intellectual interactions between the Young Ottomans and Young Iranians in the late nineteenth and early twentieth centuries. More specifically, it sheds light on the impact of Ottoman reformist and constitutional movements in similar developments in Iran and the role of modernizing bureaucrats, merchants, ulema, and intellectuals in the diffusion of an alternative and indigenous modernist and constitutionalist ideology from Istanbul to Tabriz and the Ottoman Empire to Iran. This article is based on Persian and Turkish newspapers printed in Istanbul, and Ottoman archival as well as Persian and Turkish narrative sources.
Segmented Feminization and the Decline of Neopatriarchy in GCC Countries of the Persian Gulf
Authors: Willoughby John
Published: May 2008

The key argument of this essay is that the increased educational attainment of women who are citizens of Gulf Cooperation Council (GCC) countries is leading to noticeable increases in female labor force participation. As a result of this development, the emergence of new labor market structures characterized by “segmented feminization” is being witnessed in which richer households contain women working in the paid labor force in professional jobs, while poorer households contain mothers, wives, and adult daughters with lower amounts of formal education who do not work outside the home. This development is not taking place without resistance. The struggle to increase employment opportunities for women is noisy and contentious. Complex class politics are interacting with a rentier political culture that supports the extensive use of expatriate workers. Nevertheless, the evidence discussed in this essay suggests that the segmented feminization of GCC labor forces will become a long-term characteristic of these societies. This trend could lead to increasingly differentiated income levels, fertility experiences, and ideological commitments among the national populations of the region. What seems to be a seamless order of extreme male dominance is actually fraught with significant contradictions. Studying these fissures more deeply should be a high priority for scholars concerned with understanding the future of Arabian Peninsula societies.
Mobilizing Muslim Women: Multiple Voices, the Sharia, and the State
Authors: Salime Zakia
Published: May 2008

This article reflects on the challenges faced by Muslim women in Africa in the context of the globalization of women's rights and the politicization of Islam. I argue that the gender hierarchies shaping Muslim women's identity politics are embedded in the broader historical processes of struggles against the colonial regimes, on the one hand, and the different projects of national state building, on the other hand. Central to these processes is a male-interpretation of Islam that has defined the way women would be incorporated into “nationhood” and would become “citizens” in the independent state. I also argue that Islam has been a major site for both the justification of women's oppression by state and nonstate actors and a source for identification and empowerment for women in Africa. In the independent state, women's identity politics were shaped by the institutionalization of gender inequalities in various legislations and by the enforcement of Sharia pressured by the gains of political Islam. My study draws on the substantial body of literature by local activists and scholars to historicize the current political and economic context of struggle for Muslim women in Africa. I use the term Muslim women in this study to refer only to the cultural location of women who may or may not identify with the Islamic faith. I also draw the line between Islamic activists who claim the emergence of Sharia-based states and other groups that inscribe their struggles within the framework of a progressive Islam but do not share the ideology and goals of political Islam. This picture is even more complicated by the location of women at all these levels of cultural framing and political activism in Africa.