bluuebunny/crossref_metadata_2025_split huggingface dataset:
Gene Expression Profiling on Lung Cancer Outcome Prediction: Present Clinical Value and Future Premise
Authors: Sun Zhifu , Yang Ping 
Published: November 2006

Abstract
DNA microarray has been widely used in cancer research to better predict clinical outcomes and potentially improve patient management. The new approach provides accurate tumor classification and outcome predictions, such as tumor stage, metastatic status, and patient survival, and offers some hope for individualized medicine. However, growing evidence suggests that gene-based prediction is not stable and little is known about the prediction power of gene expression profiles compared with well-known clinical and pathologic predictors. This review summarized up-to-date publications in microarray-based lung cancer clinical outcome prediction and conducted secondary analyses for those with sufficient sample sizes and associated clinical information. Among the most commonly used analytic approaches, unsupervised clustering mainly recaptures tumor histology and provides variable degrees of prediction for tumor stage, lymph node status, or survival. Overall, most studies lack an independent validation. Supervised learning and testing generally offer a better prediction. Noted is that when conventional predictors of age, gender, stage, cell type, and tumor grade are considered collectively, the predictive advantage of the gene expression profiles diminishes. We conclude that outcome prediction from gene expression signatures selected by current analytic approaches can be mostly explained by well-known conventional predictors, particularly histologic subtype and grade of differentiation. A strategy for establishing independent or more accurate signatures is commented. (Cancer Epidemiol Biomarkers Prev 2006;15(11):2063–8)
The Legal Principles of Muhammad b.Ismāīl al-Bukhārī and their Relationship to Classical Salafi Islam
Authors: Lucas Scott 
Published: November 2006

AbstractThis article analyzes the legal theory of al-Bukhārī as articulated in two books of his famous Sahīh and situates it within the broader framework of Sunni legal theory (usūl al-fiqh). I argue that his legal theory revolves around four themes: (1) The Qurān and the Prophet; (2) agreement and disagreement; (3) valid techniques of ijtihād; and (4) invalid techniques of ijtihād. I devote special attention to the tension between al-B ukhārī's negative attitude towards qiyās (analogical reasoning) and his acceptance of comparison (tashbīh) and indications (dalā'il). Finally, I compare some of his legal principles to those of the 5th/11th-century hadīth-scholars and jurists, al-Bayhaqī, Ibn Hazm, Ibn 'Abd al-Barr, and al-Khatīb al-Baghdādī, and argue that two types of classical Salafi Islam can be discerned in their writings on legal theory.
Anti-Semitism in the Muslim World: A Critical Review
Authors: Krämer Gudrun 
Published: November 2006

AbstractCurrent debates on anti-Semitism in the Muslim world, or as it is often put, 'in Islam' focus on a number of issues: the status of Jews in Islam with regard to both theory and practice; the impact of the Arab-Israeli conflict over Palestine; the adoption and adaptation of anti-Semitic motifs and stereotypes of European origin in nationalist and Islamist discourses; and the politics of memory and commemoration. Here as elsewhere, contextualization is required if we are to understand the meanings and functions of anti-Semitic attitudes and activities among specific audiences. But contextualization must not be used for apologetic purposes.
The Revival of Nyau and Changing Gender Relations in Early Colonial Central Malawi
Authors: Kachapila Hendrina 
Published: November 2006

AbstractThis paper demonstrates how nyau (a male secret society) rede fined relations in Chewa matrilineages in accordance with developments that the Chewa witnessed from the mid-nineteenth century. Thanks to nyau and the relatively hands-off approach the colonial state adopted towards its activities, the Chewa matrilineal system survived the effects of the slave trade, Ngoni and Yao invasions, the spread of Christian missionary teachings, the imposition of colonial rule and the development of capitalism. Nyau accomplished this by ensuring that relations between Chewa men and women remained ambivalent and negotiable. Allowing men to ritually gain increased importance in nyau and indeed in Chewa communities at large not only gave power to men but also ensured their continued involvement in the matrilineages. So, while female prestige declined, as evidenced by the debasement of women by nyau, some important aspects of the matrilineal system, such as matrilocal marriage, were preserved.
Summer Temperature Variations in the European Alps, a.d. 755–2004
Authors: Büntgen Ulf , Frank David C. , Nievergelt Daniel , Esper Jan 
Published: November 2006

Abstract
Annually resolved summer temperatures for the European Alps are described. The reconstruction covers the a.d. 755–2004 period and is based on 180 recent and historic larch [Larix decidua Mill.] density series. The regional curve standardization method was applied to preserve interannual to multicentennial variations in this high-elevation proxy dataset. Instrumental measurements from high- (low-) elevation grid boxes back to 1818 (1760) reveal strongest growth response to current-year June–September mean temperatures. The reconstruction correlates at 0.7 with high-elevation temperatures back to 1818, with a greater signal in the higher-frequency domain (r = 0.8). Low-elevation instrumental data back to 1760 agree with the reconstruction’s interannual variation, although a decoupling between (warmer) instrumental and (cooler) proxy data before ∼1840 is noted. This offset is larger than during any period of overlap with more recent high-elevation instrumental data, even though the proxy time series always contains some unexplained variance. The reconstruction indicates positive temperatures in the tenth and thirteenth century that resemble twentieth-century conditions, and are separated by a prolonged cooling from ∼1350 to 1700. Six of the 10 warmest decades over the 755–2004 period are recorded in the twentieth century. Maximum temperature amplitude over the past 1250 yr is estimated to be 3.1°C between the warmest (1940s) and coldest (1810s) decades. This estimate is, however, affected by the calibration with instrumental temperature data. Warm summers seem to coincide with periods of high solar activity, and cold summers vice versa. The record captures the full range of past European temperature variability, that is, the extreme years 1816 and 2003, warmth during medieval and recent times, and cold in between. Comparison with regional- and large-scale reconstructions reveals similar decadal to longer-term variability.
Retroviral vector insertion sites associated with dominant hematopoietic clones mark “stemness” pathways
Authors: Kustikova Olga S. , Geiger Hartmut , Li Zhixiong , Brugman Martijn H. , Chambers Stuart M. , Shaw Chad A. , Pike-Overzet Karin , Ridder Dick de , Staal Frank J. T. , Keudell Gottfried von , Cornils Kerstin , Nattamai Kalpana Jekumar , Modlich Ute , Wagemaker Gerard , Goodell Margaret A. , Fehse Boris , Baum Christopher 
Published: November 2006

Abstract
Evidence from model organisms and clinical trials reveals that the random insertion of retrovirus-based vectors in the genome of long-term repopulating hematopoietic cells may increase self-renewal or initiate malignant transformation. Clonal dominance of nonmalignant cells is a particularly interesting phenotype as it may be caused by the dysregulation of genes that affect self-renewal and competitive fitness. We have accumulated 280 retrovirus vector insertion sites (RVISs) from murine long-term studies resulting in benign or malignant clonal dominance. RVISs (22.5%) are located in or near (up to 100 kb [kilobase]) to known proto-oncogenes, 49.6% in signaling genes, and 27.9% in other or unknown genes. The resulting insertional dominance database (IDDb) shows substantial overlaps with the transcriptome of hematopoietic stem/progenitor cells and the retrovirus-tagged cancer gene database (RTCGD). RVISs preferentially marked genes with high expression in hematopoietic stem/progenitor cells, and Gene Ontology revealed an overrepresentation of genes associated with cell-cycle control, apoptosis signaling, and transcriptional regulation, including major “stemness” pathways. The IDDb forms a powerful resource for the identification of genes that stimulate or transform hematopoietic stem/progenitor cells and is an important reference for vector biosafety studies in human gene therapy.
Direct and indirect effects of retinoic acid on human Th2 cytokine and chemokine expression by human T lymphocytes
Authors: Dawson Harry D , Collins Gary , Pyle Robert , Key Michael , Weeraratna Ashani , Deep-Dixit Vishwa , Nadal Celeste N , Taub Dennis D 
Published: November 2006

AbstractBackgroundVitamin A (VA) deficiency induces a type 1 cytokine response and exogenously provided retinoids can induce a type 2 cytokine response both invitroandin vivo. The precise mechanism(s) involved in this phenotypic switch are inconsistent and have been poorly characterized in humans. In an effort to determine if retinoids are capable of inducing Th2 cytokine responses in human T cell cultures, we stimulated human PBMCs with immobilized anti-CD3 mAb in the presence or absence of all-transretinoic acid (ATRA) or 9-cis-RA.ResultsStimulation of human PBMCs and purified T cells with ATRA and 9-cis-RA increased mRNA and protein levels of IL-4, IL-5, and IL-13 and decreased levels of IFN-γ, IL-2, IL-12p70 and TNF-α upon activation with anti-CD3 and/or anti-CD28 mAbs. These effects were dose-dependent and evident as early as 12 hr post stimulation. Real time RT-PCR analysis revealed a dampened expression of the Th1-associated gene, T-bet, and a time-dependent increase in the mRNA for the Th2-associated genes, GATA-3, c-MAF and STAT6, upon treatment with ATRA. Besides Th1 and Th2 cytokines, a number of additional proinflammatory and regulatory cytokines including several chemokines were also differentially regulated by ATRA treatment.ConclusionThese data provide strong evidence for multiple inductive roles for retinoids in the development of human type-2 cytokine responses.
High throughput modular chambers for rapid evaluation of anesthetic sensitivity
Authors: Sun Yi , Chen Jingqiu , Pruckmayr Gregory , Baumgardner James E , Eckmann David M , Eckenhoff Roderic G , Kelz Max B 
Published: November 2006

Abstract

Background
Anesthetic sensitivity is determined by the interaction of multiple genes. Hence, a dissection of genetic contributors would be aided by precise and high throughput behavioral screens. Traditionally, anesthetic phenotyping has addressed only induction of anesthesia, evaluated with dose-response curves, while ignoring potentially important data on emergence from anesthesia.

Methods
We designed and built a controlled environment apparatus to permit rapid phenotyping of twenty-four mice simultaneously. We used the loss of righting reflex to indicate anesthetic-induced unconsciousness. After fitting the data to a sigmoidal dose-response curve with variable slope, we calculated the MACLORR (EC50), the Hill coefficient, and the 95% confidence intervals bracketing these values. Upon termination of the anesthetic, Emergence timeRR was determined and expressed as the mean ± standard error for each inhaled anesthetic.

Results
In agreement with several previously published reports we find that the MACLORR of halothane, isoflurane, and sevoflurane in 8–12 week old C57BL/6J mice is 0.79% (95% confidence interval = 0.78 – 0.79%), 0.91% (95% confidence interval = 0.90 – 0.93%), and 1.96% (95% confidence interval = 1.94 – 1.97%), respectively. Hill coefficients for halothane, isoflurane, and sevoflurane are 24.7 (95% confidence interval = 19.8 – 29.7%), 19.2 (95% confidence interval = 14.0 – 24.3%), and 33.1 (95% confidence interval = 27.3 – 38.8%), respectively. After roughly 2.5 MACLORR • hr exposures, mice take 16.00 ± 1.07, 6.19 ± 0.32, and 2.15 ± 0.12 minutes to emerge from halothane, isoflurane, and sevoflurane, respectively.

Conclusion
This system enabled assessment of inhaled anesthetic responsiveness with a higher precision than that previously reported. It is broadly adaptable for delivering an inhaled therapeutic (or toxin) to a population while monitoring its vital signs, motor reflexes, and providing precise control over environmental conditions. This system is also amenable to full automation. Data presented in this manuscript prove the utility of the controlled environment chambers and should allow for subsequent phenotyping of mice with targeted mutations that are expected to alter sensitivity to induction or emergence from anesthesia.
Expressive writing for high-risk drug dependent patients in a primary care clinic: A pilot study
Authors: Baikie Karen A , Wilhelm Kay , Johnson Beverley , Boskovic Mary , Wedgwood Lucinda , Finch Adam , Huon Gail 
Published: November 2006

Abstract

Background
Previous research has shown that expressive writing is beneficial in terms of both physical and emotional health outcomes. This study aimed to investigate the effectiveness and acceptability of a brief expressive writing intervention for high-risk drug dependent patients in a primary care clinic, and to determine the relationship between linguistic features of writing and health outcomes.

Methods
Participants completed four 15-minute expressive writing tasks over a week, in which they described their thoughts and feelings about a recent stressful event. Self-report measures of physical (SF-12) and psychological health (DASS-21) were administered at baseline and at a two-week follow-up. Fifty-three participants were recruited and 14 (26%) completed all measures.

Results
No statistically significant benefits in physical or psychological health were found, although all outcomes changed in the direction of improvement. The intervention was well-received and was rated as beneficial by participants. The use of more positive emotion words in writing was associated with improvements in depression and stress, and flexibility in first person pronoun use was associated with improvements in anxiety. Increasing use of cognitive process words was associated with worsening depressive mood.

Conclusion
Although no significant benefits in physical and psychological health were found, improvements in psychological wellbeing were associated with certain writing styles and expressive writing was deemed acceptable by high-risk drug dependent patients. Given the difficulties in implementing psychosocial interventions in this population, further research using a larger sample is warranted.
Emerging aspects of oesophageal and gastro-oesophageal junction cancer histopathology – an update for the surgical oncologist
Authors: Griffiths Ewen A , Pritchard Susan A , Mapstone Nicholas P , Welch Ian M 
Published: November 2006

Abstract
Adenocarcinoma of the oesophagus and gastro-oesophageal junction are rapidly increasing in incidence and have a well described sequence of carcinogenesis: the Barrett's metaplasia-dysplasia-adenocarcinoma sequence. During recent years there have been changes in the knowledge surrounding disease progression, cancer management and histopathology specimen reporting. Tumours around the gastro-oesophageal junction (GOJ) pose several specific challenges. Numerous difficulties arise when the existing TNM staging systems for gastric and oesophageal cancers are applied to GOJ tumours. The issues facing the current TNM staging and GOJ tumour classification systems are reviewed in this article. Recent evidence regarding the importance of several histopathologically derived prognostic factors, such as circumferential resection margin status and lymph node metastases, have implications for specimen reporting. With the rising use of multimodal treatments for oesophageal cancer it is important that the response of the tumour to this therapy is carefully documented pathologically. In addition, several controversial and novel areas such as endoscopic mucosal resection, lymph node micrometastases and the sentinel node concept are being studied. We aim to review these aspects, with special relevance to oesophageal and gastro-oesophageal cancer specimen reporting, to update the surgical oncologist with an interest in upper gastrointestinal cancer.
xGDB: open-source computational infrastructure for the integrated evaluation and analysis of genome features
Authors: Schlueter Shannon D , Wilkerson Matthew D , Dong Qunfeng , Brendel Volker 
Published: November 2006

AbstractThe eXtensible Genome Data Broker (xGDB) provides a software infrastructure consisting of integrated tools for the storage, display, and analysis of genome features in their genomic context. Common features include gene structure annotations, spliced alignments, mapping of repetitive sequence, and microarray probes, but the software supports inclusion of any property that can be associated with a genomic location. The xGDB distribution and user support utilities are available online at the xGDB project website, http://xgdb.sourceforge.net/.
Immunohistochemical Detection Using the New Rabbit Monoclonal Antibody SP1 of Estrogen Receptor in Breast Cancer Is Superior to Mouse Monoclonal Antibody 1D5 in Predicting Survival
Authors: Cheang Maggie C.U. , Treaba Diana O. , Speers Caroline H. , Olivotto Ivo A. , Bajdik Chris D. , Chia Stephen K. , Goldstein Lynn C. , Gelmon Karen A. , Huntsman David , Gilks C. Blake , Nielsen Torsten O. , Gown Allen M. 
Published: November 2006

Purpose Estrogen receptor (ER) expression predicts improved breast cancer–specific survival and reduced risk of recurrence and is targeted in breast cancer therapy. A high-quality antibody to identify ER-positive patients plays an important role in clinical decision making for women with breast cancer. This study evaluates immunohistochemistry using two anti-ER antibodies, a new rabbit monoclonal antibody (SP1) and the mouse monoclonal antibody (1D5), in relation to biochemical ER assay results and clinical data on survival and adjuvant systemic therapy. Patients and Methods A population-based tissue microarray series of 4,150 invasive breast cancers was constructed. All patients had staging, pathology, treatment, and follow-up information. The median follow-up was 12.4 years and the median age at diagnosis 60 years. Survival analysis and log-rank tests were used to evaluate the prognostic value of ER status and correlations with clinical data. Results Among the 4,105 samples interpretable for both antibodies, SP1 detected ER positivity in 69.5% and 1D5 in 63.1% of cases. Both monoclonal antibodies are demonstrated to be good prognostic indictors for breast cancer–specific and relapse-free survival. In multivariate analysis, including age, tumor size, grade, and lymphovascular and nodal status, SP1 was a better independent prognostic factor than 1D5. Among patients with discrepant ER results, the 8% of patients who were SP1 positive/1D5 negative showed good outcomes, and the 2% SP1-negative/1D5 positive had poor outcomes. Maintaining the same 92% specificity and 98% positive predictive value, SP1 is 8% more sensitive than 1D5 using biochemical assay as gold standard. Conclusion SP1 represents an improved standard for ER immunohistochemistry assessment in breast cancer.
Polymorphisms inXRCC1,XRCC3, andCCND1and Survival After Treatment for Metastatic Breast Cancer
Authors: Bewick Mary A. , Conlon Michael S.C. , Lafrenie Robert M. 
Published: November 2006

PurposeSingle nucleotide polymorphisms (SNPs) in DNA repair and cell cycle control genes may alter protein function and therefore the efficacy of DNA damaging chemotherapy. We retrospectively evaluated the association of SNPs in DNA repair genes, XRCC1-01 (Arg399Gln) and XRCC3-01 (Thr241Met), and a cell cycle control gene, CCND1-02 (A870G), with progression-free survival (PFS) and breast cancer specific survival (BCSS) in patients with metastatic breast cancer (MBC).Patients and MethodsSNPs in 95 patients with MBC enrolled onto one of five prospective clinical trials of high-dose chemotherapy and autologous stem-cell transplantation were evaluated using genotyping assays.ResultsFor XRCC1-01, the hazard ratio (HR) for BCSS was 2.8 (95% CI, 1.60 to 5.00) and the HR for PFS was 2.0 (95%CI, 1.12 to 3.43). For XRCC3-01, the HR for BCSS was 2.0 (95%CI, 1.12 to 3.70) and the HR for PFS was 2.0 (95%CI, 1.09 to 3.59). For CCND1-02, the HR for BCSS was 1.8 (95%CI, 1.12 to 2.78) and the HR for PFS was 1.8 (95%CI, 1.15 to 2.85). Patients carrying one variant genotype (HR, 1.7; 95%CI, 1.07 to 2.82) or combinations of any two variant genotypes (HR, 4.7; 95% CI, 2.41 to 8.94) had significantly poorer BCSS compared with patients carrying zero variants. In multivariable analysis, XRCC1-01, presence of liver metastases, and bone metastases independently predicted BCSS. Combinations of any two variant genotypes were stronger independent predictors of BCSS and PFS than the presence of liver or bone metastases.ConclusionXRCC1-01, XRCC3-01, and CCND1-01 may be predictive of survival outcome in patients with MBC treated with DNA damaging chemotherapy.
Sequential Adjuvant Epirubicin-Based and Docetaxel Chemotherapy for Node-Positive Breast Cancer Patients: The FNCLCC PACS 01 Trial
Authors: Roché Henri , Fumoleau Pierre , Spielmann Marc , Canon Jean-Luc , Delozier Thierry , Serin Daniel , Symann Michel , Kerbrat Pierre , Soulié Patrick , Eichler Françoise , Viens Patrice , Monnier Alain , Vindevoghel Anita , Campone Mario , Goudier Marie-Josèphe , Bonneterre Jacques , Ferrero Jean-Marc , Martin Anne-Laure , Genève Jean , Asselain Bernard 
Published: November 2006

Purpose The PACS 01 trial compared six cycles of fluorouracil, epirubicin, and cyclophosphamide (FEC) with a sequential regimen of three cycles of FEC followed by three cycles of docetaxel (FEC-D) as adjuvant treatment for women with node-positive early breast cancer. Patients and Methods Between June 1997 and March 2000, 1,999 patients with operable node-positive breast cancer were randomly assigned to either FEC every 21 days for six cycles, or three cycles of FEC followed by three cycles of docetaxel, both given every 21 days. Hormone-receptor–positive patients received tamoxifen for 5 years after chemotherapy. The primary end point was 5-year disease-free survival (DFS). Results Median follow-up was 60 months. Five-year DFS rates were 73.2% with FEC and 78.4% with FEC-D (unadjusted P = .011; adjusted P = .012). Multivariate analysis adjusted for prognostic factors showed an 18% reduction in the relative risk of relapse with FEC-D. Five-year overall survival rates were 86.7% with FEC and 90.7% with FEC-D, demonstrating a 27% reduction in the relative risk of death (unadjusted P = .014; adjusted P = .017). The incidence of grade 3 to 4 neutropenia, the need for hematopoietic growth factor, and incidence of nausea/vomiting were higher with FEC. Docetaxel was associated with more febrile neutropenia in the fourth cycle, stomatitis, edema, and nail disorders. Though rare overall, there were fewer cardiac events after FEC-D (P = .03), attributable mainly to the lower anthracycline cumulative dose. Conclusion Sequential adjuvant chemotherapy with FEC followed by docetaxel significantly improves disease-free and overall survival in node-positive breast cancer patients and has a favorable safety profile.