bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effect of Pratylenchus zeae infection on the expression of isozyme activities in resistant and susceptible sugarcane clones
Authors: Mehta Usha , Kathiresan Thandavarayan 
Published: December 2005

AbstractThe constitutive levels of both phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL) activities in roots and leaves were found to be greater in sugarcane clones resistant to the lesion nematode Pratylenchus zeae than in susceptible clones. Investigations on the sequential development of PAL and TAL activities were undertaken in resistant (Co 7717) and susceptible (CoC 671) sugarcane clones infected with P. zeae. PAL activity in both roots and leaves of the resistant clone showed a maximum percentage increase, compared with non-infected controls, at 35 and 14 days after infection (DAI), respectively. However, in the susceptible clone the maximum percentage decrease compared with the non-infected clone was observed at 3 and 14 DAI. TAL activity in the resistant clone showed the maximum percentage increase compared with the non-infected control at 28 DAI in roots and 7 DAI in leaves, whereas in the susceptible clone the maximum percentage decrease compared with the non-infected control was at 35 DAI in roots and 28 DAI in leaves. In experiments on the induction of enzyme response to infection by P. zeae, eight resistant and eight susceptible clones were analysed 14 days after P. zeae infection. Among the eight resistant clones six showed increased PAL activity compared with non-infected clones. Four susceptible infected clones showed a decrease as compared with non-infected clones, while the remaining four infected clones showed an increased enzyme activity compared to non-infected clones. Superoxide dismutase (SOD) activity increased quantitatively in both roots and leaves from nematode-infected susceptible clones compared to non-infected clones. The SOD activity decreased in roots and leaves from nematode infected resistant clones, when compared to the non-infected-resistant clones. In native PAGE analysis of SOD and esterase activities the major differences between infected and non-infected clones of resistant and susceptible sugarcane were observed in low and medium electrophoretic mobility ranges.
Culture and High Reliability Organizations: The Case of the Nuclear Submarine
Authors: Bierly Paul E. , Spender J. -C. 
Published: December 2005

Pet-row defined as ‘high risk’ those organizations that combine complexity and tight coupling with the potential for catastrophic failure. He concluded that accidents are ‘normal’ for such organizations because their managers face irreconcilable structural paradoxes. Centralization, the method of dealing with the tight coupling, must be combined with delegation, the method of dealing with the complexity. Weick, researching the complex and tightly coupled systems found in air traffic control and carrier flight-deck operations, saw these problems differently. He argued that strong organizational cultures provide a centralized and focused cognitive system within which delegated and loosely coupled systems can function effectively. High risk organizations thereby become transformed into high reliability organizations (HROs). Drawing on their personal experiences, the paper's authors focus on one type of HRO, the nuclear submarine. We argue for a multi-level model in which culture interacts with and supports formal structure and thereby produces high reliability. In effective organizations culture and formality co-exist. The nuclear submarine service is also the intersection of several different cultures. Rickover created a new culture for the nuclear Navy which is clearly a crucial source of reliability, but it is also in tension with the older naval and submarine traditions.
A transforming growth factor–β–induced protein stimulates endocytosis and is up-regulated in immature dendritic cells
Authors: Cao Weiping , Tan Patrick , Lee Chee How , Zhang Haifeng , Lu Jinhua 
Published: December 2005

AbstractDendritic cells (DCs) exhibit distinct functional properties at immature and mature states. To identify genes preferentially regulated in monocyte-derived immature DCs (imDCs), 13 000-element microarrays were hybridized with RNA isolated from imDCs, mature DCs (mDCs), monocytes, and macrophages and a TGF-β–induced protein (βig-h3) was identified as being most prominently up-regulated in imDCs. By polymerase chain reaction (PCR), little βig-h3 mRNA was detected in monocytes and macrophages, but it was abundant in imDCs. On DC activation with LPS, βig-h3 mRNA became diminished, and in tissues, βig-h3 mRNA was abundantly expressed in lymphoid-rich tissues such as the spleen, bone marrow, small intestines, and colon. βig-h3 was expressed in 293T cells and purified as a 70-kDa protein and, by Western blotting, βig-h3 was predominantly detected in the medium of imDCs. We demonstrate that βig-h3 binds to macrophages and imDCs but not to mDCs and activates the Rac GTPase in macrophages, stimulating macrophage membrane ruffling and enhancing macrophage endocytosis. imDC endocytosis was also inhibited by purified anti–βig-h3 antibodies. Therefore, βig-h3 appears to be selectively up-regulated in imDCs to regulate antigen uptake through endocytosis.
Complete deficiency in ADAMTS13 is prothrombotic, but it alone is not sufficient to cause thrombotic thrombocytopenic purpura
Authors: Banno Fumiaki , Kokame Koichi , Okuda Tomohiko , Honda Shigenori , Miyata Shigeki , Kato Hisashi , Tomiyama Yoshiaki , Miyata Toshiyuki 
Published: December 2005

Abstract
ADAMTS13 is a plasma metalloproteinase that regulates platelet adhesion and aggregation through cleavage of von Willebrand factor (VWF) multimers. In humans, genetic or acquired deficiency in ADAMTS13 causes thrombotic thrombocytopenic purpura (TTP), a condition characterized by thrombocytopenia and hemolytic anemia with microvascular platelet thrombi. In this study, we report characterization of mice bearing a targeted disruption of the Adamts13 gene. ADAMTS13-deficient mice were born in the expected mendelian distribution; homozygous mice were viable and fertile. Hematologic and histologic analyses failed to detect any evidence of thrombocytopenia, hemolytic anemia, or microvascular thrombosis. However, unusually large VWF multimers were observed in plasma of homozygotes. Thrombus formation on immobilized collagen under flow was significantly elevated in homozygotes in comparison with wild-type mice. Thrombocytopenia was more severely induced in homozygotes than in wild-type mice after intravenous injection of a mixture of collagen and epinephrine. Thus, a complete lack of ADAMTS13 in mice was a prothrombotic state, but it alone was not sufficient to cause TTP-like symptoms. The phenotypic differences of ADAMTS13 deficiencies between humans and mice may reflect differences in hemostatic system functioning in these species. Alternatively, factors in addition to ADAMTS13 deficiency may be necessary for development of TTP.
Thrombopoietin regulates IEX-1 gene expression through ERK-induced AML1 phosphorylation
Authors: Hamelin Virginie , Letourneux Claire , Romeo Paul-Henri , Porteu Françoise , Gaudry Murielle 
Published: December 2005

Abstract
The extracellular signal-regulated kinases (ERKs) are required for thrombopoietin (TPO) functions on hematopoietic cells, but the ERKs targets involved remain unknown. Here we show that the regulation of the immediate early gene X-1 (IEX-1), identified as an ERK substrate in response to TPO, was mediated by an ERK-dependent phosphorylation of AML1. The addition of TPO to UT7-Mpl cells and primary megakaryocytes induced gene expression of IEX-1. Neither erythropoietin (EPO) nor granulocyte macrophage-colony stimulating factor (GM-CSF) was able to activate IEX-1 gene expression in UT7-Mpl cells. The induced expression was mediated by a transcriptional activation of the IEX-1 promoter and required an AML1-binding site located at –1068. The direct involvement of AML1 in the regulation of IEX-1 gene expression was shown by both the use of AML1 mutants and by shRNA experiments targeting endogenous AML1. Finally, the ability of TPO to induce the IEX-1 gene expression was inhibited by U0126, a specific inhibitor of the ERKs activator MEK and AML1 transcriptional activity was shown to be modulated by TPO through ERK-dependent phosphorylation. Taken together, these data suggest that AML1 plays a role in modulating the IEX-1 expression and that the ERK-dependent AML1 phosphorylation regulates the TPO-mediated activation of IEX-1.
Extracorporeal photochemotherapy for the treatment of steroid-resistant chronic GVHD
Authors: Couriel Daniel R. , Hosing Chitra , Saliba Rima , Shpall Elizabeth J. , Anderlini Paolo , Rhodes Beverly , Smith Veronica , Khouri Issa , Giralt Sergio , de Lima Marcos , Hsu Yvonne , Ghosh Shubhra , Neumann Joyce , Andersson Borje , Qazilbash Muzzafar , Hymes Sharon , Kim Stella , Champlin Richard , Donato Michele 
Published: December 2005

Abstract
Chronic graft-versus-host disease (GVHD) is a major limitation of successful allogeneic hematopoietic stem cell transplantation (HSCT). Extracorporeal photochemotherapy (ECP) has been tested extensively in small cohorts of patients with chronic GVHD. In this study, we retrospectively evaluated 71 patients with severe chronic GVHD treated with ECP. Response rate was 61% (n = 43), and 14 patients had complete responses (CRs). The best responses were observed in skin, liver, oral mucosa, and eye. Factors affecting outcomes were assessed in the less heavily pretreated subgroup (n = 63). Thrombocytopenia was associated with a lower response rate (P = .04), and there was a trend toward a higher response rate in de novo chronic GVHD. At 6 months, a total of 27 (69%) of 39 patients who were alive continued to have a sustained response (CR 4 [10%] of 39, and partial response [PR] 23 [59%] of 39). The cumulative incidence of steroid discontinuation at 1 year was 22%. The overall survival since initiation of therapy was 53% at 1 year. Response to ECP and platelet count at initiation of therapy were the strongest predictors of nonrelapse mortality (NRM) on univariate analysis. Objective responses were observed in a substantial number of patients with both skin and visceral chronic GVHD failing corticosteroids and other immunosuppression.
Coexistence of multiple mechanisms of PT523 resistance in human leukemia cells harboring 3 reduced folate carrier alleles: transcriptional silencing, inactivating mutations, and allele loss
Authors: Kaufman Yotam , Ifergan Ilan , Rothem Lilah , Jansen Gerrit , Assaraf Yehuda G. 
Published: December 2005

AbstractThe reduced folate carrier (RFC) is the dominant route for the uptake of various antifolates including PT523, a potent dihydrofolate reductase inhibitor (Ki = 0.35 pM) and an excellent transport substrate of the RFC (Kt = 0.7 μM). Here, we describe the multiple mechanisms of RFC inactivation in human leukemia PT523-resistant cells originally harboring 3 RFC alleles. Cellular exposure to gradually increasing PT523 concentrations resulted in sublines displaying up to 3500-fold resistance to various hydrophilic antifolates that rely on RFC for their cellular uptake. Antifolate-resistant cells lost RFC gene expression (65%-99% loss) due to impaired promoter binding of various transcription factors that regulate RFC gene expression. Additionally, DNA sequencing revealed that PT523-resistant cells contained a cluster of 4 nearly consecutive mutations residing on a single RFC allele including L143P, A147V, R148G, and Q150Stop. Southern blot analysis established the loss of an RFC allele in PT523-resistant cells. These alterations resulted in markedly decreased RFC protein levels (∼80%-99% loss) and consequently impaired [3H]methotrexate transport (87%-99% loss). This study provides the first evidence that acquisition of PT523 resistance in human leukemia cells harboring 3 RFC alleles is due to multiple coexisting alterations including transcriptional silencing, inactivating mutations, and RFC allele loss.
Relevance of human metapneumovirus in exacerbations of COPD
Authors: Rohde G , Borg I , Arinir U , Kronsbein J , Rausse R , Bauer TT , Bufe A , Schultze-Werninghaus G 
Published: December 2005

Abstract

Background and methods
Human metapneumovirus (hMPV) is a recently discovered respiratory virus associated with bronchiolitis, pneumonia, croup and exacerbations of asthma. Since respiratory viruses are frequently detected in patients with acute exacerbations of COPD (AE-COPD) it was our aim to investigate the frequency of hMPV detection in a prospective cohort of hospitalized patients with AE-COPD compared to patients with stable COPD and to smokers without by means of quantitative real-time RT-PCR.

Results
We analysed nasal lavage and induced sputum of 130 patients with AE-COPD, 65 patients with stable COPD and 34 smokers without COPD. HMPV was detected in 3/130 (2.3%) AE-COPD patients with a mean of 6.5 × 105 viral copies/ml in nasal lavage and 1.88 × 105 viral copies/ml in induced sputum. It was not found in patients with stable COPD or smokers without COPD.

Conclusion
HMPV is only found in a very small number of patients with AE-COPD. However it should be considered as a further possible viral trigger of AE-COPD because asymptomatic carriage is unlikely.
WebArray: an online platform for microarray data analysis
Authors: Xia Xiaoqin , McClelland Michael , Wang Yipeng 
Published: December 2005

Abstract
Background
Many cutting-edge microarray analysis tools and algorithms, including commonly used limma and affy packages in Bioconductor, need sophisticated knowledge of mathematics, statistics and computer skills for implementation. Commercially available software can provide a user-friendly interface at considerable cost. To facilitate the use of these tools for microarray data analysis on an open platform we developed an online microarray data analysis platform, WebArray, for bench biologists to utilize these tools to explore data from single/dual color microarray experiments.

Results
The currently implemented functions were based on limma and affy package from Bioconductor, the spacings LOESS histogram (SPLOSH) method, PCA-assisted normalization method and genome mapping method. WebArray incorporates these packages and provides a user-friendly interface for accessing a wide range of key functions of limma and others, such as spot quality weight, background correction, graphical plotting, normalization, linear modeling, empirical bayes statistical analysis, false discovery rate (FDR) estimation, chromosomal mapping for genome comparison.

Conclusion
WebArray offers a convenient platform for bench biologists to access several cutting-edge microarray data analysis tools. The website is freely available at http://bioinformatics.skcc.org/webarray/. It runs on a Linux server with Apache and MySQL.
Kinetics of cancer: a method to test hypotheses of genetic causation
Authors: Frank Steven A , Chen Peng-Chieh , Lipkin Steven M 
Published: December 2005

Abstract

Background
Mouse studies have recently compared the age-onset patterns of cancer between different genotypes. Genes associated with earlier onset are tentatively assigned a causal role in carcinogenesis. These standard analyses ignore the great amount of information about kinetics contained in age-onset curves. We present a method for analyzing kinetics that measures quantitatively the causal role of candidate genes in cancer progression. We use our method to demonstrate a clear association between somatic mutation rates of different DNA mismatch repair (MMR) genotypes and the kinetics of cancer progression.

Methods
Most experimental studies report age-onset curves as the fraction diagnosed with tumors at each age for each group. We use such data to estimate smoothed survival curves, then measure incidence rates at each age by the slope of the fitted curve divided by the fraction of mice that remain undiagnosed for tumors at that age. With the estimated incidence curves, we compare between different genotypes the median age of cancer onset and the acceleration of cancer, which is the rate of increase in incidence with age.

Results
The direction of change in somatic mutation rate between MMR genotypes predicts the direction of change in the acceleration of cancer onset in all 7 cases (p ˜ 0.008), with the same result for the association between mutation rate and the median age of onset.

Conclusion
Many animal experiments compare qualitatively the onset curves for different genotypes. If such experiments were designed to analyze kinetics, the research could move to the next stage in which the mechanistic consequences of particular genetic pathways are related to the dynamics of carcinogenesis. The data we analyzed here were not collected to test mechanistic and quantitative hypotheses about kinetics. Even so, a simple reanalysis revealed significant insights about how DNA repair genotypes affect separately the age of onset and the acceleration of cancer. Our method of comparing genotypes provides good statistical tests even with small samples for each genotype.
Integrating complementary and alternative medicine into academic medical centers: Experience and perceptions of nine leading centers in North America
Authors: Vohra Sunita , Feldman Kymm , Johnston Brad , Waters Kellie , Boon Heather 
Published: December 2005

Abstract

Background
Patients across North America are using complementary and alternative medicine (CAM) with increasing frequency as part of their management of many different health conditions. The objective of this study was to develop a guide for academic health sciences centers that may wish to consider starting an integrative medicine program.

Methods
We queried North American leaders in the field of integrative medicine to identify initial sites. Key stakeholders at each of the initial sites visited were then asked to identify additional potential study sites (snowball sampling), until no new sites were identified. We conducted structured interviews to identify critical factors associated with success and failure in each of four domains: research, education, clinical care, and administration. During the interviews, field notes were recorded independently by at least two investigators. Team meetings were held after each visit to reach consensus on the information recorded and to ensure that it was as complete as possible. Content analysis techniques were used to identify key themes that emerged from the field notes.

Results
We identified ten leading North American integrative medical centers, and visited nine during 2002–2003. The centers visited suggested that the initiation of an integrative medicine program requires a significant initial outlay of funding and a motivated "champion". The centers had important information to share regarding credentialing, medico-legal issues and billing for clinical programs; identifying researchers and research projects for a successful research program; and strategies for implementing flexible educational initiatives and establishing a functional administrative structure.

Conclusion
Important lessons can be learned from academic integrative programs already in existence. Such initiatives are timely and feasible in a variety of different ways and in a variety of settings.
Hydrogen production by Cyanobacteria
Authors: Dutta Debajyoti , De Debojyoti , Chaudhuri Surabhi , Bhattacharya Sanjoy K 
Published: December 2005

Abstract
The limited fossil fuel prompts the prospecting of various unconventional energy sources to take over the traditional fossil fuel energy source. In this respect the use of hydrogen gas is an attractive alternate source. Attributed by its numerous advantages including those of environmentally clean, efficiency and renew ability, hydrogen gas is considered to be one of the most desired alternate. Cyanobacteria are highly promising microorganism for hydrogen production. In comparison to the traditional ways of hydrogen production (chemical, photoelectrical), Cyanobacterial hydrogen production is commercially viable. This review highlights the basic biology of cynobacterial hydrogen production, strains involved, large-scale hydrogen production and its future prospects. While integrating the existing knowledge and technology, much future improvement and progress is to be done before hydrogen is accepted as a commercial primary energy source.
Intestinal invasion and disseminated disease associated with Penicillium chrysogenum
Authors: Barcus Adrian L , Burdette Steven D , Herchline Thomas E 
Published: December 2005

Abstract

Background

Penicillium sp., other than P. marneffei, is an unusual cause of invasive disease. These organisms are often identified in immunosuppressed patients, either due to human immunodeficiency virus or from immunosuppressant medications post-transplantation. They are a rarely identified cause of infection in immunocompetent hosts.

Case presentation
A 51 year old African-American female presented with an acute abdomen and underwent an exploratory laparotomy which revealed an incarcerated peristomal hernia. Her postoperative course was complicated by severe sepsis syndrome with respiratory failure, hypotension, leukocytosis, and DIC. On postoperative day 9 she was found to have an anastamotic breakdown. Pathology from the second surgery showed transmural ischemic necrosis with angioinvasion of a fungal organism. Fungal blood cultures were positive for Penicillium chrysogenum and the patient completed a 6 week course of amphotericin B lipid complex, followed by an extended course oral intraconazole. She was discharged to a nursing home without evidence of recurrent infection.

Discussion

Penicillium chrysogenum is a rare cause of infection in immunocompetent patients. Diagnosis can be difficult, but Penicillium sp. grows rapidly on routine fungal cultures. Prognosis remains very poor, but aggressive treatment is essential, including surgical debridement and the removal of foci of infection along with the use of amphotericin B. The clinical utility of newer antifungal agents remains to be determined.
Kinetics of hepatitis C virus RNA load during pegylated interferon alpha-2a and ribavirin treatment in naïve genotype 1 patients
Authors: Ouzan Denis , Khiri Hacène , Pénaranda Guillaume , Joly Hélène , Halfon Philippe 
Published: December 2005

AbstractBackgroundPegylated interferon given for 24 or 48 weeks constitutes the most effective initial therapy for the treatment of chronic hepatitis C. It has been shown that viral load at week 2 appears the best time for predicting response to treatment. The objectives of this study were to assess whether the hepatitis C virus (HCV) RNA viral decline is predictive of sustained virological response (SVR) and to determine the best time for predicting complete response in our cohort of naïve patients treated with pegylated interferon alpha-2a (Peg-IFN alpha-2a) and ribavirin.ResultsTwenty patients treated with Peg-IFN alpha-2a and ribavirin for 48 weeks were studied. Six months after the end of treatment, a SVR (negative HCV RNA measured by PCR six months after the end of therapy) was obtained in 9 patients. Samples were obtained before and at week 2, 4, 8, and 12. At the end of week 2, viral load decreased more than 1.39 log in 8 out of the 9 patients with SVR and in 1 out of the 11 other patients. When we considered the viral load reduction from baseline to each week of treatment, week 2 appeared to be the best point time for predicting SVR, with a sensitivity of 91% (95%CI: 59;99), a specificity of 89% (52;98), a positive predictive value of 91% (59;99) and a negative predictive value of 89% (57;98).ConclusionDuring treatment with Peg-IFN alpha-2a plus ribavirin in genotype 1 patients, when the main objective of the treatment is viral eradication, viral kinetics showed that week 2 appeared to be the best time point for predicting SVR. Our results must be further confirmed on a larger cohort.