bluuebunny/crossref_metadata_2025_split huggingface dataset:
Vaccine site inflammation potentiates idiotype DNA vaccine-induced therapeutic T cell–, and not B cell–, dependent antilymphoma immunity
Authors: Qin Hong , Cha Soung-chul , Neelapu Sattva S. , Lou Yanyan , Wei Jinsong , Liu Yong-Jun , Kwak Larry W. 
Published: September 2009

AbstractLymphoma idiotype protein vaccines have shown therapeutic potential in previous clinical studies, and results from a completed pivotal, phase 3 controlled trial are promising. However, streamlined production of these patient-specific vaccines is required for eventual clinical application. Here, we show that second-generation, chemokine-fused idiotype DNA vaccines, when combined with myotoxins that induced sterile inflammation with recruitment of antigen-presenting cells at vaccination sites, were exceptional in their ability to provoke memory antitumor immunity in mice, compared with several TLR agonists. The combined vaccination strategy elicited both antigen-specific T-cell responses and humoral immunity. Unexpectedly, vaccine-induced tumor protection was intact in B cell–deficient mice but was abrogated completely by T-cell depletion in vivo, suggesting T-cell dependence. Furthermore, the optimal effect of myotoxins was observed with fusion vaccines that specifically targeted antigen delivery to antigen-presenting cells and not with vaccines lacking a targeting moiety, suggesting that the rational vaccine design will require combination strategies with novel, proinflammatory agents and highly optimized molecular vaccine constructs. These studies also challenge the paradigm that antibody responses are the primary of idiotype-specific antitumor effects and support the optimization of idiotype vaccines designed to induce primarily T-cell immunity.
Uptake of CCR7 and acquisition of migratory properties by human KIR+ NK cells interacting with monocyte-derived DC or EBV cell lines: regulation by KIR/HLA-class I interaction
Authors: Marcenaro Emanuela , Cantoni Claudia , Pesce Silvia , Prato Carola , Pende Daniela , Agaugué Sophie , Moretta Lorenzo , Moretta Alessandro 
Published: September 2009

AbstractC-C chemokine receptor type 7 (CCR7) is a chemokine receptor playing a pivotal role in the induction of human natural killer (NK)–cell migration to lymph nodes. We show that “licensed” peripheral blood killer immunoglobulin-like receptor–positive (KIR+) NK-cell populations, as well as KIR+ NK-cell clones, de novo express CCR7 upon coculture with mature dendritic cells (mDCs) or Epstein-Barr virus (EBV)–transformed lymphoblastoid cell lines. As a consequence, they become capable of migrating in response to the CCR7-specific chemokines C-C chemokine ligand (CCL)–19 and/or CCL21. The acquisition of CCR7 by NK cells requires direct cell-to-cell contact, is detectable within a few minutes, and is due to receptor uptake from CCR7+ cells. This mechanism is tightly regulated by KIR-mediated recognition of human leukocyte antigen (HLA) class I as well as by adhesion molecules including leukocyte function-associated antigen 1 (LFA-1) and CD2. Analysis of NK-cell clones revealed that alloreactive (KIR-ligand mismatched) but not autologous NK cells acquire CCR7. These data have important implications in haploidentical hematopoietic stem cell transplantation (HSCT), in which alloreactive NK cells may acquire the ability to migrate to secondary lymphoid compartments (SLCs), where they can kill recipient antigen-presenting cells (APCs) and T cells thus preventing graft-versus-host (and host-versus-graft) reactions.
Characterization of membranous and cytoplasmic EGFR expression in human normal renal cortex and renal cell carcinoma
Authors: Pu Yeong-Shiau , Huang Chao-Yuan , Kuo Yi-Zih , Kang Wang-Yi , Liu Guang-Yaw , Huang A-Mei , Yu Hong-Jeng , Lai Ming-Kuen , Huang Shu-Pin , Wu Wen-Jeng , Chiou Shean-Jaw , Hour Tzyh-Chyuan 
Published: September 2009

Abstract
Metastatic renal cell carcinoma (RCC) is highly resistant to conventional systemic treatments, including chemotherapy, radiotherapy and hormonal therapies. Previous studies have shown over-expression of EGFR is associated with high grade tumors and a worse prognosis. Recent studies suggest anticancer therapies targeting the EGFR pathway have shown promising results in clinical trials of RCC patients. Therefore, characterization of the level and localization of EGFR expression in RCC is important for target-dependent therapy. In this study, we investigated the clinical significance of cellular localization of EGFR in human normal renal cortex and RCC. RCC and adjacent normal kidney tissues of 63 patients were obtained for characterization of EGFR expression. EGFR protein expression was assessed by immunohistochemistry on a scale from 0 to 300 (percentage of positive cells × staining intensity) and Western blotting. EGFR membranous staining was significantly stronger in RCC tumors than in normal tissues (P < 0.001). In contrast, EGFR cytoplasmic staining was significantly higher in normal than in tumor tissues (P < 0.001). The levels of membranous or cytoplasmic EGFR expression in RCC tissues were not correlated with sex, tumor grade, TNM stage or overall survival (P > 0.05). These results showed abundant expression of membranous EGFR in RCC, and abundant expression of cytoplasmic EGFR in normal tissues. EGFR expression in RCC was mostly located in the cell membrane, whereas the EGFR expression in normal renal tissues was chiefly seen in cytoplasm. Our results suggest different locations of EGFR expression may be associated with human renal tumorigenesis.
Improving power in genetic-association studies via wavelet transformation
Authors: Jiang Renfang , Dong Jianping , Dai Yilin 
Published: September 2009

Abstract

Background
A key to increasing the power of multilocus association tests is to reduce the number of degrees of freedom by suppressing noise from data. One of the difficulties is to decide how much noise to suppress. An often overlooked problem is that commonly used association tests based on genotype data cannot utilize the genetic information contained in spatial ordering of SNPs (see proof in the Appendix), which may prevent them from achieving higher power.

Results
We develop a score test based on wavelet transform with empirical Bayesian thresholding. Extensive simulation studies are carried out under various LD structures as well as using HapMap data from many different chromosomes for both qualitative and quantitative traits. Simulation results show that the proposed test automatically adjusts the level of noise suppression according to LD structures, and it is able to consistently achieve higher or similar powers than many commonly used association tests including the principle component regression method (PCReg).

Conclusion
The wavelet-based score test automatically suppresses the right amount of noise and uses the information contained in spatial ordering of SNPs to achieve higher power.
Gene-based microsatellites for cassava (Manihot esculentaCrantz): prevalence, polymorphisms, and cross-taxa utility
Authors: Raji Adebola AJ , Anderson James V , Kolade Olufisayo A , Ugwu Chike D , Dixon Alfred GO , Ingelbrecht Ivan L 
Published: September 2009

AbstractBackgroundCassava (Manihot esculentaCrantz), a starchy root crop grown in tropical and subtropical climates, is the sixth most important crop in the world after wheat, rice, maize, potato and barley. The repertoire of simple sequence repeat (SSR) markers for cassava is limited and warrants a need for a larger number of polymorphic SSRs for germplasm characterization and breeding applications.ResultsA total of 846 putative microsatellites were identifiedin silicofrom an 8,577 cassava unigene set with an average density of one SSR every 7 kb. One hundred and ninety-two candidate SSRs were screened for polymorphism among a panel of cassava cultivars from Africa, Latin America and Asia, four wildManihotspecies as well as two other important taxa in the Euphorbiaceae, leafy spurge (Euphorbia esula) and castor bean (Ricinus communis). Of 168 markers with clean amplification products, 124 (73.8%) displayed polymorphism based on high resolution agarose gels. Of 85 EST-SSR markers screened, 80 (94.1%) amplified alleles from one or more wild species (M epruinosa, M glaziovii,M brachyandra,M tripartita) whereas 13 (15.3%) amplified alleles from castor bean and 9 (10.6%) amplified alleles from leafy spurge; hence nearly all markers were transferable to wild relatives ofM esculentawhile only a fraction was transferable to the more distantly related taxa. In a subset of 20 EST-SSRs assessed by fluorescence-based genotyping the number of alleles per locus ranged from 2 to 10 with an average of 4.55 per locus. These markers had a polymorphism information content (PIC) from 0.19 to 0.75 with an average value of 0.55 and showed genetic relationships consistent with existing information on these genotypes.ConclusionA set of 124 new, unique polymorphic EST-SSRs was developed and characterized which extends the repertoire of SSR markers for cultivated cassava and its wild relatives. The markers show high PIC values and therefore will be useful for cultivar identification, taxonomic studies, and genetic mapping. The study further shows that mining ESTs is a highly efficient strategy for polymorphism detection within the cultivated cassava gene pool.
Gene expression meta-analysis supports existence of molecular apocrine breast cancer with a role for androgen receptor and implies interactions with ErbB family
Authors: Sanga Sandeep , Broom Bradley M , Cristini Vittorio , Edgerton Mary E 
Published: September 2009

Abstract

Background
Pathway discovery from gene expression data can provide important insight into the relationship between signaling networks and cancer biology. Oncogenic signaling pathways are commonly inferred by comparison with signatures derived from cell lines. We use the Molecular Apocrine subtype of breast cancer to demonstrate our ability to infer pathways directly from patients' gene expression data with pattern analysis algorithms.

Methods
We combine data from two studies that propose the existence of the Molecular Apocrine phenotype. We use quantile normalization and XPN to minimize institutional bias in the data. We use hierarchical clustering, principal components analysis, and comparison of gene signatures derived from Significance Analysis of Microarrays to establish the existence of the Molecular Apocrine subtype and the equivalence of its molecular phenotype across both institutions. Statistical significance was computed using the Fasano & Franceschini test for separation of principal components and the hypergeometric probability formula for significance of overlap in gene signatures. We perform pathway analysis using LeFEminer and Backward Chaining Rule Induction to identify a signaling network that differentiates the subset. We identify a larger cohort of samples in the public domain, and use Gene Shaving and Robust Bayesian Network Analysis to detect pathways that interact with the defining signal.

Results
We demonstrate that the two separately introduced ER- breast cancer subsets represent the same tumor type, called Molecular Apocrine breast cancer. LeFEminer and Backward Chaining Rule Induction support a role for AR signaling as a pathway that differentiates this subset from others. Gene Shaving and Robust Bayesian Network Analysis detect interactions between the AR pathway, EGFR trafficking signals, and ErbB2.

Conclusion
We propose criteria for meta-analysis that are able to demonstrate statistical significance in establishing molecular equivalence of subsets across institutions. Data mining strategies used here provide an alternative method to comparison with cell lines for discovering seminal pathways and interactions between signaling networks. Analysis of Molecular Apocrine breast cancer implies that therapies targeting AR might be hampered if interactions with ErbB family members are not addressed.
Decreased PPARγ Expression Compromises Perigonadal-Specific Fat Deposition and Insulin Sensitivity
Authors: Tsai Yau-Sheng , Tsai Pei-Jane , Jiang Man-Jin , Chou Ting-Yu , Pendse Avani , Kim Hyung-Suk , Maeda Nobuyo 
Published: September 2009

AbstractMutations and polymorphisms in PPARG have been linked to adiposity and partial lipodystrophy in humans. However, how disturbances in PPARG lead to depot-specific effects on adipose tissue, as shown by the characteristic aberrant fat distribution in patients, remains unclear. By manipulating the 3′-untranslated region of the Pparg gene, we have generated mice with peroxisome proliferator-activated receptor γ (PPARγ) gene expression ranging from 25% to 100% normal. Basal levels of PPARγ transcripts between 50% and approximately 100% had no significant effect on body weight, fat mass, and insulin sensitivity. In contrast, mice with 25% normal PPARγ expression exhibited reduced body weight and total fat mass, insulin resistance, and dyslipidemia. Interestingly, fat mass was selectively reduced in perigonadal depot without significant changes in inguinal and other depots. Expression of adipogenic factor CCAAT enhancer binding protein-α and some other metabolic genes containing peroxisome proliferator response element were reduced in a perigonadal depot-specific fashion. This was further associated with depot-specific reduction in the expression of adipokines, increased expression of TNFα, and increased ectopic lipid deposition in muscles. Together, these results underscore the differential sensitivity of the individual fat depots on PPARγ availability as an underlying mechanism of partial lipodystrophy.
Effects of physical interference on life history shifts in Daphnia pulex
Authors: Ban Syuhei , Tenma Hideaki , Mori Tsukasa , Nishimura Kinya 
Published: September 2009

SUMMARY
Daphnia pulex were reared in 50 ml flasks, each containing 1, 20 or 40 individuals, which were serially connected with a 20-μm mesh screens between, in order to examine the effect of physical interference due to crowding on shifts of life history traits throughout two consecutive generations. A flow-through system, designed to maintain a sufficient food supply and minimize the accumulation of metabolites, was used. To eliminate the effect of infochemicals from crowded animals, a single-individual treatment flask was connected to two crowded flasks. In the first generation, D. pulex reared under crowded conditions grew more slowly after day 4 when oogenesis normally starts, and produced less offspring after day 9,compared with an animal reared alone, even when supplied with sufficient food. Although second generation daphniids of each treatment matured faster than in the first generation, crowded females grew more slowly even after day 2 and produced less offspring than single females. Age to maturity was no different between treatments in both generations. Crowded females, therefore, matured to smaller sizes but produced larger neonates compared with single females. Weight-specific reproduction rates of the first clutch were not significantly different between the treatments. These results suggest that physical interference between neighboring individuals due to crowding negatively affects growth and reproduction in daphniids. Crowded daphniids may allocate more energy to reproduction in order to produce larger and more starvation-tolerant offspring in preparation for severe food shortages. Crowding also triggered ephippial egg production and reduced survival compared with the single-individual treatment.
Othello at the Market Theatre
Authors: Seeff Adele 
Published: September 2009

This article discusses the cultural work performed by Janet Suzman's 1987 production of Othello at the Market Theatre in Johannesburg: the first production to breach South Africa's colour-bar in casting black South African actor John Kani in the title role. Through an incorporation of reviews, a close reading of the playtexts, performance and reception history, literary criticism, and an awareness of the South African political and cultural context, the study situates Suzman's production in its specific historical moment, as well as considering its broader history in order to determine what it is about the production that merits the labels of 'radical' and 'ground-breaking' affixed to it by critics. In doing so, it shifts the focus from the production's multiracial casting and onto its treatment of women within the context of racial politics, positioning the white Desdemona's desire for the black Othello - arguably also present in Shakespeare's text - as the truly radical aspect of Suzman's production, in which racial difference is presented as the source of sexual power: a concept which finds parallels in the exchanges between Iago and Emilia and Roderigo and Bianca. The discussion of this neglected aspect of Suzman's radical production emphasizes the impact of social change on any production as well as on the reception of a black actor performing Othello: a performance which, in the case of Suzman's production, invites audiences to recognise the patriarchal societal forces which construct racism and oppression.
Cold War in the Countryside: Conflict in Guerrero, Mexico
Authors: Blacker O'Neill 
Published: September 2009

“Our struggle has its inspirational roots in [our] national history and reality: our flag . . . is the same raised by Hidalgo, Morelos and Guerrero, Juarez, Zapata and Villa.”Genaro Vazquez Rojas, La Asociacion Civica Nacional Revolucionaria, 1968
The mammalian aryl hydrocarbon (Ah) receptor: from mediator of dioxin toxicity toward physiological functions in skin and liver
Authors: Bock Karl Walter , Köhle Christoph 
Published: September 2009

AbstractThe mammalian Ah receptor (AhR) is a ligand-activated transcription factor with multiple functions in adaptive metabolism, development and dioxin toxicity in a variety of organs and cell systems. Phenotypes observed following sustained activation by dioxin or in AhR-null mice suggest organ-dependent physiological functions. These functions are probably deregulated following exposure to dioxin. We focus on skin and liver to facilitate discussion of mechanisms linking phenotypes and AhR-modulated genotypes. After a brief summary of currently discussed AhR ligand candidates, two groups of direct AhR target genes/proteins and associated functions are highlighted: (i) xenobiotic-metabolizing enzymes which are also involved in homeostasis of endogenous ligands and (ii) proteins controlling cell proliferation/apoptosis, differentiation and inflammation. Homeostatic feedback loops might not only include CYP1A1 but also Phase II enzymes such as UGT1A1 which controls the antioxidant AhR ligand bilirubin. The AhR is involved in extensive crosstalk with other transcription factors and multiple signaling pathways. Efforts elucidating the pathway toward identification of physiological functions of the AhR remain challenging and promising.
Safety aspects of 36 months of administration of long-acting intramuscular testosterone undecanoate for treatment of female-to-male transgender individuals
Authors: Jacobeit J W , Gooren L J , Schulte H M 
Published: September 2009

DesignTestosterone treatment is essential for the induction and maintenance of virilization of female-to-male (FTM) transsexuals.AimTo test the safety of a novel testosterone preparation for this purpose.MethodsParenteral long-acting testosterone undecanoate (TU) was administered to 17 FTM transsexuals over 36 months. Observations were made while subjects received treatment.ResultsSerum testosterone rose from 0.50±0.25 to 6.2±1.3 ng/ml at 6 months and remained stable thereafter. The testosterone profiles were largely identical with those in hypogonadal receiving TU. There were no side effects. Over the 36 months of the study, there was a small but significant decrease in plasma cholesterol (from 218±47 to 188±42 mg/dl) and low-density lipoprotein-cholesterol (from 139±48 to 139±48 mg/dl), while plasma levels of high-density lipoprotein-cholesterol and triglycerides did not change significantly. Liver enzymes did not change during treatment. There was an increase of both levels in hemoglobin (from 13.6±1.2 to 16.0±1.5 g/dl) and hematocrit (from 41±4 to 46±4) upon administration but they remained almost without exception within the physiological range. No special measures were needed. Breast and gonads/internal genitalia did not show pathological changes over the observation period.ConclusionThis study reports that TU is suited for induction of virilization in FTM transsexuals without significant side effects over a longer term.
Where Should we Submit our Manuscript? An Analysis of Journal Submission Strategies
Authors: Heintzelman Martin , Nocetti Diego 
Published: September 2009

Abstract
In this paper, we analyze the problem faced by impatient researchers attempting to balance the considerations of journal quality, submission lags, and acceptance probabilities in choosing appropriate outlets for their work. We first study the case in which probabilities of submission outcomes are exogenous parameters and show that authors can find the optimal submission path through the use of journal 'scores' based only on the journals' characteristics and the author's degree of impatience. Then, we analyze a more realistic framework in which acceptance probability is determined by the quality of the manuscript, in which the reviewing process may be imperfect, and in which authors may not be certain of the manuscript's quality. Throughout, we illustrate our analysis with data on actual economics journals. We also consider the problem of journals facing a large number of submissions, limited space, and limited resources to review papers and, in particular, we examine the relative effectiveness of using submission fees and reviewing lags to ration article submissions.
Implication of 5-aminolevulinic acid fluorescence of the ventricular wall for postoperative communicating hydrocephalus associated with cerebrospinal fluid dissemination in patients with glioblastoma multiforme: a report of 7 cases
Authors: Hayashi Yutaka , Nakada Mitsutoshi , Tanaka Shingo , Uchiyama Naoyuki , Hayashi Yasuhiko , Kita Daisuke , Hamada Jun-ichiro 
Published: September 2009

Object
Fluorescence-guided surgery using 5-aminolevulinic acid (5-ALA) has been broadly recognized as a beneficial tool for the resection of glioblastoma multiforme (GBM). Fluorescence in the ventricular walls, which were apparently free of macroscopic tumor or MR imaging enhancement indicative of CSF dissemination, was detected during surgery for GBM. To evaluate the clinical significance of the 5-ALA fluorescence, the authors resected ventricle wall tissue together with the adjacent tumors for pathological examination and then followed up the clinical courses of the patients.

Methods
Seven consecutive GBMs located near the lateral ventricle were surgically treated using a fluorescence-guided technique with 5-ALA at the authors' hospital since acquiring instrumentation for the detection of 5-ALA fluorescence in 2007. All of the procedures were performed using a ventricular entry, and 5-ALA fluorescence of the ventricular wall was detected despite the absence of macroscopic tumor invasion of the wall.

Results
A pathological examination of the resected ventricular wall tissues revealed tumor cells in 6 of the 7 cases and disruption of the ependymal cell layer in all 7 cases. Delayed communicating hydrocephalus followed surgery in all 7 patients, and ventricular wall enhancements on MR imaging were demonstrated after hydrocephalus in 2 of the patients.

Conclusions
Data in this study suggest that 5-ALA fluorescence of the ventricular wall may be predictive of postoperative hydrocephalus associated with CSF dissemination even in cases without evidence of CSF dissemination on MR imaging studies before surgery. The authors also speculate that postoperative radiotherapy covering the whole ventricular system may be a better therapeutic option for these patients.