bluuebunny/crossref_metadata_2025 huggingface dataset:
7,8‐Diaminoperlargonic acid aminotransferase from Mycobacterium tuberculosis, a potential therapeutic target
Authors: Mann Stéphane , Ploux Olivier
Published: September 2006

Diaminopelargonic acid aminotransferase (DAPA AT), which is involved in biotin biosynthesis, catalyzes the transamination of 8‐amino‐7‐oxononanoic acid (KAPA) using S‐adenosyl‐l‐methionine (AdoMet) as amino donor. Mycobacterium tuberculosis DAPA AT, a potential therapeutic target, has been overproduced in Escherichia coli and purified to homogeneity using a single efficient step on a nickel‐affinity column. The enzyme shows an electronic absorption spectrum typical of pyridoxal 5′‐phosphate‐dependent enzymes and behaves as a homotetramer in solution. The pH profile of the activity at saturation shows a single ionization group with a pKa of 8.0, which was attributed to the active‐site lysine residue. The enzyme shows a Ping Pong Bi Bi kinetic mechanism with strong substrate inhibition with the following parameters: KmAdoMet = 0.78 ± 0.20 mm, KmKAPA = 3.8 ± 1.0 µm, kcat = 1.0 ± 0.2 min−1, KiKAPA = 14 ± 2 µm. Amiclenomycin and a new analogue, 4‐(4c‐aminocyclohexa‐2,5‐dien‐1r‐yl)propanol (referred to as compound 1), were shown to be suicide substrates of this enzyme, with the following inactivation parameters: Ki = 12 ± 2 µm, kinact = 0.35 ± 0.05 min−1, and Ki = 20 ± 2 µm, kinact = 0.56 ± 0.05 min−1, for amiclenomycin and compound 1, respectively. The inactivation was irreversible, and the partition ratios were 1.0 and 1.1 for amiclenomycin and compound 1, respectively, which make these inactivators particularly efficient. compound 1 (100 µg·mL−1) completely inhibited the growth of an E. coli C268bioA mutant strain transformed with a plasmid expressing the M. tuberculosis bioA gene, coding for DAPA AT. Reversal of the antibiotic effect was observed on the addition of biotin or DAPA. Thus, compound 1 specifically targets DAPA AT in vivo.
Are blood flow and lipolysis in subcutaneous adipose tissue influenced by contractions in adjacent muscles in humans?
Authors: Stallknecht Bente , Dela Flemming , Helge Jørn Wulff
Published: September 2006

Aerobic exercise increases whole body adipose tissue lipolysis, but is lipolysis higher in subcutaneous adipose tissue (SCAT) adjacent to contracting muscles than in SCAT adjacent to resting muscles? Ten healthy, overnight-fasted males performed one-legged knee extension exercise at 25% of maximal workload (Wmax) for 30 min followed by exercise at 55% Wmax for 120 min with the other leg and finally exercised at 85% Wmax for 30 min with the first leg. Subjects rested for 30 min between exercise periods. Femoral SCAT blood flow was estimated from washout of 133Xe, and lipolysis was calculated from femoral SCAT interstitial and arterial glycerol concentrations and blood flow. In general, blood flow and lipolysis were higher in femoral SCAT adjacent to contracting than adjacent to resting muscle (time 15–30 min; blood flow: 25% Wmax 6.6 ± 1.0 vs. 3.9 ± 0.8 ml·100 g−1·min−1, P < 0.05; 55% Wmax 7.3 ± 0.6 vs. 5.0 ± 0.6 ml·100 g−1·min−1, P < 0.05; 85% Wmax 6.6 ± 1.3 vs. 5.9 ± 0.7 ml·100 g−1·min−1, P > 0.05; lipolysis: 25% Wmax 102 ± 19 vs. 55 ± 14 nmol·100 g−1·min−1, P = 0.06; 55% Wmax 86 ± 11 vs. 50 ± 20 nmol·100 g−1·min−1, P > 0.05; 85% Wmax 88 ± 31 vs. −9 ± 25 nmol·100 g−1·min−1, P < 0.05). In conclusion, blood flow and lipolysis are generally higher in SCAT adjacent to contracting than adjacent to resting muscle irrespective of exercise intensity. Thus specific exercises can induce “spot lipolysis” in adipose tissue.
Evaluation of Apolipoprotein A1 and Posttranslationally Modified Forms of Transthyretin as Biomarkers for Ovarian Cancer Detection in an Independent Study Population
Authors: Moore Lee E. , Fung Eric T. , McGuire Marielena , Rabkin Charles C. , Molinaro Annette , Wang Zheng , Zhang Fujun , Wang Jing , Yip Christine , Meng Xiao-Ying , Pfeiffer Ruth M.
Published: September 2006

Background: Although overall 5-year survival rates for ovarian cancer are poor (10-30%), stage I/IIa patients have a 95% 5-year survival. New biomarkers that improve the diagnostic performance of existing tumor markers are critically needed. A previous study by Zhang et al. reported identification and validation of three biomarkers using proteomic profiling that together improved early-stage ovarian cancer detection.

Methods: To evaluate these markers in an independent study population, postdiagnostic/pretreatment serum samples were collected from women hospitalized at the Mayo Clinic from 1980 to 1989 as part of the National Cancer Institute Immunodiagnostic Serum Bank. Sera from 42 women with ovarian cancer, 65 with benign tumors, and 76 with digestive diseases were included in this study. Levels of various posttranslationally forms of transthyretin and apolipoprotein A1 were measured in addition to CA125.

Results: Mean levels of five of the six forms of transthyretin were significantly lower in cases than in controls. The specificity of a model including transthyretin and apolipoprotein A1 alone was high [96.5%; 95% confidence interval (95% CI), 91.9-98.8%] but sensitivity was low (52.4%; 95% CI, 36.4-68.0%). A class prediction algorithm using all seven markers, CA125, and age maintained high specificity (94.3%; 95% CI, 89.1-97.5%) but had higher sensitivity (78.6%; 95% CI, 63.2-89.7%).

Conclusions: We were able to replicate the findings reported by Zhang et al. in an independently conducted blinded study. These results provide some evidence that including age of patient and these markers in a model may improve specificity, especially when CA125 levels are ≥35 units/mL. Influences of sample handling, subject characteristics, and other covariates on biomarker levels require further consideration in discovery and replication or validation studies. (Cancer Epidemiol Biomarkers Prev 2006;15(9):1641–6)
Personal Permanent Hair Dye Use Is Not Associated with Bladder Cancer Risk: Evidence from a Case-Control Study
Authors: Lin Jie , Dinney Colin P. , Grossman H. Barton , Wu Xifeng
Published: September 2006

Whether personal hair dye use is associated with an increased bladder cancer risk has been controversial and there are limited available data addressing this issue. We used a large case-control study of 712 incident bladder cancer cases and 712 age-, gender-, and ethnicity-matched controls to evaluate this association. After adjusting for confounding variables, the use of permanent hair dye was not associated with bladder cancer risk in all subjects [odds ratio (OR), 0.81; 95% confidence interval (95% CI), 0.50-1.30], in women (OR, 0.90; 95% CI, 0.41-1.96), or in men (OR, 0.68; 95% CI, 0.36-1.29). The lack of association was not modified by duration of use, frequency of use, lifetime use, age at first use, or color of use in subsequent stratified analyses. Our data do not support personal hair dye use as an important risk factor for bladder cancer. (Cancer Epidemiol Biomarkers Prev 2006;15(9):1746–9)
Proteomic Profiling Identifies Cyclooxygenase-2-Independent Global Proteomic Changes by Celecoxib in Colorectal Cancer Cells
Authors: Lou Jianrong , Fatima Naheed , Xiao Zhen , Stauffer Stacy , Smythers Gary , Greenwald Peter , Ali Iqbal Unnisa
Published: September 2006

Celecoxib, a selective inhibitor of the enzyme cyclooxygenase-2 (COX-2), has been shown to be a promising chemoprevention agent. The chemopreventive efficacy of celecoxib is believed to be a consequence of its COX-2-dependent and COX-2-independent effects on a variety of cellular processes including proliferation, apoptosis, angiogenesis, and immunosurveillance. In an attempt to identify proteomic markers modulated by celecoxib that are independent of its inhibitory effect on COX-2, the colorectal cancer cell line HCT-116, a nonexpresser of COX-2, was treated with celecoxib. We used the powerful, state-of-the-art two-dimensional difference gel electrophoresis technology coupled with mass spectrometric sequencing to compare global proteomic profiles of HCT-116 cells before and after treatment with celecoxib. Among the differentially expressed proteins identified following celecoxib treatment were proteins involved in diverse cellular functions including glycolysis, protein biosynthesis, DNA synthesis, mRNA processing, protein folding, phosphorylation, redox regulation, and molecular chaperon activities. Our study presents a comprehensive analysis of large-scale celecoxib-modulated proteomic alterations, at least some of which may be mechanistically related to the COX-2-independent chemopreventive effect of celecoxib. (Cancer Epidemiol Biomarkers Prev 2006;15(9):1598–606)
Association of Polymorphisms in AhR, CYP1A1, GSTM1, and GSTT1 Genes with Levels of DNA Damage in Peripheral Blood Lymphocytes among Coke-Oven Workers
Authors: Chen Yongwen , Bai Yun , Yuan Jing , Chen Weihong , Sun Jianya , Wang Hong , Liang Huashan , Guo Liang , Yang Xiaobo , Tan Hao , Su Yougong , Wei Qingyi , Wu Tangchun
Published: September 2006

Accumulating evidence has shown that both DNA damage caused by the metabolites of polycyclic aromatic hydrocarbons (PAH) and genetic polymorphisms in PAH-metabolic genes contribute to individual susceptibility to PAH-induced carcinogenesis. However, the functional relevance of genetic polymorphisms in PAH-metabolic genes in exposed individuals is still unclear. In this study of 240 coke-oven workers (the exposed group) and 123 non–coke-oven workers (the control group), we genotyped for polymorphisms in the AhR, CYP1A1, GSTM1, and GSTT1 genes by PCR methods, and determined the levels of DNA damage in peripheral blood lymphocytes using the alkaline comet assay. We found that the ln-transformed Olive tail moment (Olive TM) values in the exposed group were significantly higher than those in the control group (P < 0.001). Furthermore, in the exposed group, the Olive TM values in subjects with the AhR Lys554 variant genotype were higher than those with the AhR Arg554/Arg554 genotype (P = 0.021). Similarly, the Olive TM values in the non–coke-oven workers with the CYP1A1 MspI CC + CT genotype were lower than the values of those with the CYP1A1 MspI TT genotype (P = 0.005). However, these differences were not evident for GSTM1 and GSTT1. These results suggested that the polymorphism of AhR might modulate the effects of PAHs in the exposed group; however, the underlying molecular mechanisms by which this polymorphism may have affected the levels of PAH-induced DNA damage warrant further investigation. (Cancer Epidemiol Biomarkers Prev 2006;15(9):1703–7)
Approaches to DNA/RNA Extraction and Whole Genome Amplification
Authors: Santella Regina M.
Published: September 2006

Analysis of DNA and/or RNA is an important component of most epidemiologic studies. The methods used for their preparation vary depending on the number of samples in the study as well as the amount of tissue or cells available, the specific downstream assay, and the resources available. They range from classic phenol/chloroform extractions to robotic methods suitable for large-scale studies. Several methods are also available for the quantitation of DNA/RNA, including UV or fluorescence measurements and PCR. For DNA samples of limited quantity, it is also now possible to use whole genome amplification to increase the amount of DNA suitable for genotyping. Finally, a major issue in quality control is the careful labeling and handling of samples. (Cancer Epidemiol Biomarkers Prev 2006;15(9):1585–7)
Cyclin D3 is down-regulated by rapamycin in HER-2-overexpressing breast cancer cells
Authors: García-Morales Pilar , Hernando Eva , Carrasco-García Estefanía , Menéndez-Gutierrez María Piedad , Saceda Miguel , Martínez-Lacaci Isabel
Published: September 2006

Rapamycin and its analogues are being tested as new antitumor agents. Rapamycin binds to FKBP-12 and this complex inhibits the activity of FRAP/mammalian target of rapamycin, which leads to dephosphorylation of 4EBP1 and p70 S6 kinase, resulting in blockade of translation initiation. We have found that RAP inhibits the growth of HER-2-overexpressing breast cancer cells. The phosphorylation of mammalian target of rapamycin, p70 S6 kinase, and 4EBP1 is inhibited by rapamycin and cells are arrested in the G1 phase, as determined by growth assays, fluorescence-activated cell sorting analysis, and bromodeoxyuridine incorporation studies. Rapamycin causes down-regulation of cyclin D3 protein, retinoblastoma hypophosphorylation, loss of cyclin-dependent kinase (cdk) 4, cdk6, and cdk2 activity. The half-life of cyclin D3 protein decreases after rapamycin treatment, but not its synthesis, whereas the synthesis or half-life of cyclin D1 protein is not affected by the drug. Additionally, rapamycin caused accumulation of ubiquitinated forms of cyclin D3 protein, proteasome inhibitors blocked the effect of rapamycin on cyclin D3, and rapamycin stimulated the activity of the proteasome, showing that the effect of rapamycin on cyclin D3 is proteasome proteolysis dependent. This effect depends on the activity of HER-2 because Herceptin, a neutralizing antibody against HER-2, is able to block both the induction of proteasome activity and the cyclin D3 down-regulation due to rapamycin. Furthermore, inhibition of HER-2 gene expression by using small interfering RNA blocked the rapamycin effects on cyclin D3. These data indicate that rapamycin causes a G1 arrest in HER-2-overexpressing breast cancer cells that is associated with a differential destabilization and subsequent down-regulation of cyclin D3 protein. [Mol Cancer Ther 2006;5(9):2172–81]
Genetic alterations associated with acquired temozolomide resistance in SNB-19, a human glioma cell line
Authors: Auger Nathalie , Thillet Joëlle , Wanherdrick Krystell , Idbaih Ahmed , Legrier Marie-Emmanuelle , Dutrillaux Bernard , Sanson Marc , Poupon Marie-France
Published: September 2006

Gliomas are highly lethal neoplasms that cannot be cured by currently available therapies. Temozolomide is a recently introduced alkylating agent that has yielded a significant benefit in the treatment of high-grade gliomas. However, either de novo or acquired chemoresistance occurs frequently and has been attributed to increased levels of O6-methylguanine-DNA methyltransferase or to the loss of mismatch repair capacity. However, very few gliomas overexpress O6-methylguanine-DNA methyltransferase or are mismatch repair–deficient, suggesting that other mechanisms may be involved in the resistance to temozolomide. The purpose of the present study was to generate temozolomide-resistant variants from a human glioma cell line (SNB-19) and to use large-scale genomic and transcriptional analyses to study the molecular basis of acquired temozolomide resistance. Two independently obtained temozolomide-resistant variants exhibited no cross-resistance to other alkylating agents [1,3-bis(2-chloroethyl)-1-nitrosourea and carboplatin] and shared genetic alterations, such as loss of a 2p region and loss of amplification of chromosome 4 and 16q regions. The karyotypic alterations were compatible with clonal selection of preexistent resistant cells in the parental SNB-19 cell line. Microarray analysis showed that 78 out of 17,000 genes were differentially expressed between parental cells and both temozolomide-resistant variants. None are implicated in known resistance mechanisms, such as DNA repair, whereas interestingly, several genes involved in differentiation were down-regulated. The data suggest that the acquisition of resistance to temozolomide in this model resulted from the selection of less differentiated preexistent resistant cells in the parental tumor. [Mol Cancer Ther 2006;5(9):2182–92]
Nuclear factor-κB maintains TRAIL resistance in human pancreatic cancer cells
Authors: Khanbolooki Sanaz , Nawrocki Steffan T. , Arumugam Thiruvengadam , Andtbacka Robert , Pino Maria S. , Kurzrock Razelle , Logsdon Craig D. , Abbruzzese James L. , McConkey David J.
Published: September 2006

Although it displays promising activity in other tumor models, the effects of tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) on human pancreatic cancer cells have not been comprehensively explored. We report that a majority of human pancreatic cancer cell lines (seven of nine) underwent apoptosis when they were exposed to recombinant human TRAIL in vitro. Characterization of surface TRAIL receptors by fluorescence-activated cell sorting showed that TRAIL-resistant cells (Panc-1 and HS766T) expressed lower levels of DR4 and DR5 than did TRAIL-sensitive cells. The proteasome inhibitor bortezomib (PS-341, Velcade) further increased TRAIL responsiveness in the TRAIL-sensitive cells and synergized with TRAIL to reverse resistance in Panc-1 and HS776T cells. The effects of bortezomib were mimicked by transfection with a small interfering RNA construct specific for the p65 subunit of nuclear factor-κB (NF-κB) or exposure to a selective chemical inhibitor of IKK (PS-1145). Silencing IκBα prevented TRAIL sensitization by PS-1145, confirming that IκBα mediated the effects of PS-1145. NF-κB inhibition resulted in down-regulation of BCL-XL and XIAP, and silencing either restored TRAIL sensitivity in TRAIL-resistant cells. Finally, therapy with TRAIL plus PS-1145 reversed TRAIL resistance in vivo to produce synergistic growth inhibition in orthotopic Panc-1 tumors. Together, our results show that NF-κB inhibits TRAIL-induced apoptosis in human pancreatic cancer cells and suggest that combination therapy with TRAIL and NF-κB inhibitors, such as bortezomib, PS-1145, or curcumin, should be considered as a possible treatment strategy in patients with pancreatic cancer. [Mol Cancer Ther 2006;5(9):2251–60]
Changes in Antihypertensive Prescribing During US Outpatient Visits for Uncomplicated Hypertension Between 1993 and 2004
Authors: Ma Jun , Lee Ky-Van , Stafford Randall S.
Published: September 2006

Monitoring national patterns of antihypertensive drug therapy is essential to assessing adherence to treatment guidelines and the impact of major scientific publications on physician prescribing. We analyzed data from 2 US National Ambulatory Care Surveys to examine trends between 1993 and 2004 in the prescription of antihypertensive drug classes for uncomplicated hypertension and the association between thiazide and β-blocker prescribing and physician and patient characteristics. Diuretic prescriptions remained level through 2001 (39%; 95% CI: 34% to 44%) but increased to 53% (48% to 58%) in 2003, largely because of a 72% increase in thiazide prescriptions in the first quarter of 2003 (50%; 95% CI: 40% to 59%). However, these increases did not sustain in 2004. β-Blocker prescriptions increased modestly from 1993 (24%; 95% CI: 19% to 29%) to 2004 (33%; 95% CI: 28% to 39%). Prescription of calcium channel blockers and angiotensin-converting enzyme inhibitors declined significantly following the sixth Joint National Committee report, but both subsequently rebounded to prereport levels. Prescription of angiotensin II receptor blockers increased continuously from 1% in 1995 to 23% by 2004. Polytherapy prescriptions, particularly those involving ≥3 drug classes, became increasingly prevalent, accounting for 60% of antihypertensive drug visits by 2004. Prescriptions of thiazides and β-blockers were both more likely in 1998–2004 (versus 1993–1997). Blacks, women, and hospital outpatients were more likely to receive thiazides. Also, cardiologists were more likely to prescribe β-blockers. Evidence-based guidelines for antihypertensive drug therapy do impact physician prescribing, but the impact seems to be short lived. Future interventions are imperative for promoting long-term adherence to published guidelines.
Exercise and Respiratory Training Improve Exercise Capacity and Quality of Life in Patients With Severe Chronic Pulmonary Hypertension
Authors: Mereles Derliz , Ehlken Nicola , Kreuscher Sandra , Ghofrani Stefanie , Hoeper Marius M. , Halank Michael , Meyer F. Joachim , Karger Gabriele , Buss Jan , Juenger Jana , Holzapfel Nicole , Opitz Christian , Winkler Jörg , Herth Felix F.J. , Wilkens Heinrike , Katus Hugo A. , Olschewski Horst , Grünig Ekkehard
Published: September 2006

Background—

Pulmonary hypertension (PH) is associated with restricted physical capacity, limited quality of life, and a poor prognosis because of right heart failure. The present study is the first prospective randomized study to evaluate the effects of exercise and respiratory training in patients with severe symptomatic PH.

Methods and Results—

Thirty patients with PH (21 women; mean age, 50±13 years; mean pulmonary artery pressure, 50±15 mm Hg; mean World Health Organization [WHO] class, 2.9±0.5; pulmonary arterial hypertension, n=23; chronic thromboembolic PH, n=7) on stable disease-targeted medication were randomly assigned to a control (n=15) and a primary training (n=15) group. Medication remained unchanged during the study period. Primary end points were the changes from baseline to week 15 in the distance walked in 6 minutes and in scores of the Short Form Health Survey quality-of-life questionnaire. Changes in WHO functional class, Borg scale, and parameters of echocardiography and gas exchange also were assessed. At week 15, patients in the primary and secondary training groups had an improved 6-minute walking distance; the mean difference between the control and the primary training group was 111 m (95% confidence interval, 65 to 139 m;
P
<0.001). Exercise training was well tolerated and improved scores of quality of life, WHO functional class, peak oxygen consumption, oxygen consumption at the anaerobic threshold, and achieved workload. Systolic pulmonary artery pressure values at rest did not change significantly after 15 weeks of exercise and respiratory training (from 61±18 to 54±18 mm Hg) within the training group.

Conclusions—

This study indicates that respiratory and physical training could be a promising adjunct to medical treatment in severe PH. The effects add to the beneficial results of modern medical treatment.
Role of Store-Operated Calcium Channels and Calcium Sensitization in Normoxic Contraction of the Ductus Arteriosus
Authors: Hong Zhigang , Hong Fangxiao , Olschewski Andrea , Cabrera Jesus A. , Varghese Anthony , Nelson Daniel P. , Weir E. Kenneth
Published: September 2006

Background—At birth, the increase in oxygen causes contraction of the ductus arteriosus, thus diverting blood flow to the lungs. Although this contraction is modulated by substances such as endothelin and dilator prostaglandins, normoxic contraction is an intrinsic property of ductus smooth muscle. Normoxic inhibition of potassium channels causes membrane depolarization and calcium entry through L-type calcium channels. However, the studies reported here show that after inhibition of this pathway there is still substantial normoxic contraction, indicating the involvement of additional mechanisms.

Methods and Results—Using ductus ring experiments, calcium imaging, reverse-transcription polymerase chain reaction, Western blot, and cellular electrophysiology, we find that this depolarization-independent contraction is caused by release of calcium from the IP3-sensitive store in the sarcoplasmic reticulum, by subsequent calcium entry through store-operated channels, and by increased calcium sensitization of actin-myosin filaments, involving Rho-kinase.

Conclusions—Much of the normoxic contraction of the ductus arteriosus at birth is related to calcium entry through store-operated channels, encoded by the transient receptor potential superfamily of genes, and to increased calcium sensitization. A clearer understanding of the mechanisms involved in normoxic contraction of the ductus will permit the development of better therapy to close the patent ductus arteriosus, which constitutes ≈10% of all congenital heart disease and is especially common in premature infants.
VWF protects FVIII from endocytosis by dendritic cells and subsequent presentation to immune effectors
Authors: Dasgupta Suryasarathi , Repessé Yohann , Bayry Jagadeesh , Navarrete Ana-Maria , Wootla Bharath , Delignat Sandrine , Irinopoulou Theano , Kamaté Caroline , Saint-Remy Jean-Marie , Jacquemin Marc , Lenting Peter J. , Borel-Derlon Annie , Kaveri Srinivas V. , Lacroix-Desmazes Sébastien
Published: September 2006

Von Willebrand factor (VWF) is a chaperone molecule for procoagulant factor VIII (FVIII). Its role in the reduction of the immunogenicity of therapeutic FVIII in patients with hemophilia A has been evoked but lacks clear cellular and molecular rationale. Here, we demonstrate that VWF protects FVIII from being endocytosed by human dendritic cells (DCs) and subsequently presented to FVIII-specific T cells. The immunoprotective effect of VWF requires a physical interaction with FVIII because the endocytosis of FVIII was significantly restored on hindering the formation of the VWF-FVIII complex. Interestingly, VWF had no direct inhibitory effect either on the ability of DCs to present antigenic peptides or on the activation potency of CD4+ T cells. We thus propose that VWF may reduce the immunogenicity of FVIII by preventing, upstream from the activation of immune effectors, the entry of FVIII in professional antigen-presenting cells.
Thiolated chitosan nanoparticles enhance anti-inflammatory effects of intranasally delivered theophylline
Authors: Lee Dong-Won , Shirley Shawna A , Lockey Richard F , Mohapatra Shyam S
Published: September 2006

Background

Chitosan, a polymer derived from chitin, has been used for nasal drug delivery because of its biocompatibility, biodegradability and bioadhesiveness. Theophylline is a drug that reduces the inflammatory effects of allergic asthma but is difficult to administer at an appropriate dosage without causing adverse side effects. It was hypothesized that adsorption of theophylline to chitosan nanoparticles modified by the addition of thiol groups would improve theophylline absorption by the bronchial epithelium and enhance its anti-inflammatory effects.

Objectives

We sought to develop an improved drug-delivery matrix for theophylline based on thiolated chitosan, and to investigate whether thiolated chitosan nanoparticles (TCNs) can enhance theophylline's capacity to alleviate allergic asthma.

Methods

A mouse model of allergic asthma was used to test the effects of theophylline in vivo. BALB/c mice were sensitized to ovalbumin (OVA) and OVA-challenged to produce an inflammatory allergic condition. They were then treated intranasally with theophylline alone, chitosan nanoparticles alone or theophylline adsorbed to TCNs. The effects of theophylline on cellular infiltration in bronchoalveolar lavage (BAL) fluid, histopathology of lung sections, and apoptosis of lung cells were investigated to determine the effectiveness of TCNs as a drug-delivery vehicle for theophylline.

Results

Theophylline alone exerts a moderate anti-inflammatory effect, as evidenced by the decrease in eosinophils in BAL fluid, the reduction of bronchial damage, inhibition of mucus hypersecretion and increased apoptosis of lung cells. The effects of theophylline were significantly enhanced when the drug was delivered by TCNs.

Conclusion

Intranasal delivery of theophylline complexed with TCNs augmented the anti-inflammatory effects of the drug compared to theophylline administered alone in a mouse model of allergic asthma. The beneficial effects of theophylline in treating asthma may be enhanced through the use of this novel drug delivery system.
Tuberculosis chemotherapy: current drug delivery approaches
Authors: du Toit Lisa Claire , Pillay Viness , Danckwerts Michael Paul
Published: September 2006

Tuberculosis is a leading killer of young adults worldwide and the global scourge of multi-drug resistant tuberculosis is reaching epidemic proportions. It is endemic in most developing countries and resurgent in developed and developing countries with high rates of human immunodeficiency virus infection. This article reviews the current situation in terms of drug delivery approaches for tuberculosis chemotherapy. A number of novel implant-, microparticulate-, and various other carrier-based drug delivery systems incorporating the principal anti-tuberculosis agents have been fabricated that either target the site of tuberculosis infection or reduce the dosing frequency with the aim of improving patient outcomes. These developments in drug delivery represent attractive options with significant merit, however, there is a requisite to manufacture an oral system, which directly addresses issues of unacceptable rifampicin bioavailability in fixed-dose combinations. This is fostered by the need to deliver medications to patients more efficiently and with fewer side effects, especially in developing countries. The fabrication of a polymeric once-daily oral multiparticulate fixed-dose combination of the principal anti-tuberculosis drugs, which attains segregated delivery of rifampicin and isoniazid for improved rifampicin bioavailability, could be a step in the right direction in addressing issues of treatment failure due to patient non-compliance.
Searching for interpretable rules for disease mutations: a simulated annealing bump hunting strategy
Authors: Jiang Rui , Yang Hua , Sun Fengzhu , Chen Ting
Published: September 2006

Background

Understanding how amino acid substitutions affect protein functions is critical for the study of proteins and their implications in diseases. Although methods have been developed for predicting potential effects of amino acid substitutions using sequence, three-dimensional structural, and evolutionary properties of proteins, the applications are limited by the complication of the features and the availability of protein structural information. Another limitation is that the prediction results are hard to be interpreted with physicochemical principles and biological knowledge.

Results

To overcome these limitations, we proposed a novel feature set using physicochemical properties of amino acids, evolutionary profiles of proteins, and protein sequence information. We applied the support vector machine and the random forest with the feature set to experimental amino acid substitutions occurring in theE. colilac repressor and the bacteriophage T4 lysozyme, as well as to annotated amino acid substitutions occurring in a wide range of human proteins. The results showed that the proposed feature set was superior to the existing ones. To explore physicochemical principles behind amino acid substitutions, we designed a simulated annealing bump hunting strategy to automatically extract interpretable rules for amino acid substitutions. We applied the strategy to annotated human amino acid substitutions and successfully extracted several rules which were either consistent with current biological knowledge or providing new insights for the understanding of amino acid substitutions. When applied to unclassified data, these rules could cover a large portion of samples, and most of the covered samples showed good agreement with predictions made by either the support vector machine or the random forest.

Conclusion

The prediction methods using the proposed feature set can achieve larger AUC (the area under the ROC curve), smaller BER (the balanced error rate), and larger MCC (the Matthews' correlation coefficient) than those using the published feature sets, suggesting that our feature set is superior to the existing ones. The rules extracted by the simulated annealing bump hunting strategy have comparable coverage and accuracy but much better interpretability as those extracted by the patient rule induction method (PRIM), revealing that the strategy is more effective in inducing interpretable rules.
Sex-specific expression of alternative transcripts in Drosophila
Authors: McIntyre Lauren M , Bono Lisa M , Genissel Anne , Westerman Rick , Junk Damion , Telonis-Scott Marina , Harshman Larry , Wayne Marta L , Kopp Artyom , Nuzhdin Sergey V
Published: September 2006

Background

Many genes produce multiple transcripts due to alternative splicing or utilization of alternative transcription initiation/termination sites. This 'transcriptome expansion' is thought to increase phenotypic complexity by allowing a single locus to produce several functionally distinct proteins. However, sex, genetic and developmental variation in the representation of alternative transcripts has never been examined systematically. Here, we describe a genome-wide analysis of sex-specific expression of alternative transcripts in Drosophila melanogaster.

Results

We compared transcript profiles in males and females from eight Drosophila lines (OregonR and 2b, and 6 RIL) using a newly designed 60-mer oligonucleotide microarray that allows us to distinguish a large proportion of alternative transcripts. The new microarray incorporates 7,207 oligonucleotides, satisfying stringent binding and specificity criteria that target both the common and the unique regions of 2,768 multi-transcript genes, as well as 12,912 oligonucleotides that target genes with a single known transcript. We estimate that up to 22% of genes that produce multiple transcripts show a sex-specific bias in the representation of alternative transcripts. Sexual dimorphism in overall transcript abundance was evident for 53% of genes. The X chromosome contains a significantly higher proportion of genes with female-biased transcription than the autosomes. However, genes on the X chromosome are no more likely to have a sexual bias in alternative transcript representation than autosomal genes.

Conclusion

Widespread sex-specific expression of alternative transcripts in Drosophila suggests that a new level of sexual dimorphism at the molecular level exists.
NONSTANDARD VERBAL PARADIGMS IN EARLIER WHITE SOUTHERN AMERICAN ENGLISH
Authors: Trüb Regina
Published: September 2006

This article presents an analysis of subject-verb concord in earlier white Southern American Vernacular English (SAVE). The data were taken from the Southern Plantation Overseers Corpus (SPOC), a collection of vernacular letters dating from the late eighteenth to mid-nineteenth century. Part one focuses on the effect of two internal linguistic constraints that govern the occurrence of present-tense verbal -s: The first constraint affects the auxiliaries have and be and predicts higher rates of -s when compared to lexical verbs. A second, functional constraint, which to the author's knowledge has not been investigated in other studies to date, operates on be, depending on its function as copula or other auxiliary verb. Part two investigates was/were variation in the early SAVE past-tense be paradigm. Separate analyses of all idiolects that combine to make up the community grammar of the overseers demonstrate that idiolects need to be considered in a sound interpretation and explanation of the results of group analysis.
THE CASE OF APPALACHIAN EXPLETIVETHEY
Authors: Tortora Christina
Published: September 2006

This article examines Appalachian English existentials, which employ they as the so-called “expletive” (e.g., They is a big creek yet). Given the morphological identity of expletive they with the third-person plural pronoun (e.g., They are happy), the question arises as to why the verb appears in the singular form in the existential despite the expletive's apparent plurality; this question arises in light of Cardinaletti (1997), who observes that cross-linguistically, Nominative Case-marked expletives trigger agreement. To explain the Appalachian contradiction, this work pursues the proposal that Appalachian expletive they is “weak,” lacking a value for its number feature. This allows us to maintain the idea that the Appalachian expletive does trigger agreement, despite appearances to the contrary. The article also explores (rarer) cases of Appalachian existentials with an apparently plural verb (e.g., They are another one down the street), and discusses three possible analyses of such grammars, where (1) the expletive might have a [+ plural] number feature, (2) the verb might actually be singular (despite appearances to the contrary), or (3) in the case of a plural postverbal subject (They have been some fellows...), the “associate” might raise at LF to agree with the verb.
Perfusion with cGMP analogue adapts the action potential response of pheromone-sensitive sensilla trichoidea of the hawkmoth Manduca sextain a daytime-dependent manner
Authors: Flecke Christian , Dolzer Jan , Krannich Steffi , Stengl Monika
Published: September 2006

Pheromone-dependent mate search is under strict circadian control in different moth species. But it remains unknown whether daytime-dependent changes in pheromone sensitivity already occur at the periphery in male moths. Because adapting pheromone stimuli cause rises of cyclic guanosine monophosphate (cGMP) in pheromone-sensitive trichoid sensilla of the night-active hawkmoth Manduca sexta, we wanted to determine whether cGMP decreases pheromone-sensitivity of olfactory receptor neurons in a daytime-dependent manner. Long-term tip recordings from trichoid sensilla were performed at the early day (ZT 1-4), when many moths are still active, and at the middle of the day (ZT 8-11), when moths are resting. A non-adapting pheromone-stimulation protocol combined with perfusion of the sensillum lymph with the membrane-permeable cGMP analogue 8bcGMP adapted the action potential response but not the sensillar potential. Perfusion with 8bcGMP decreased the initial action potential frequency, decreased the numbers of action potentials elicited in the first 100 ms of the pheromone response and attenuated the reduction of action potential amplitude. Furthermore, the decrease in 8bcGMP-dependent action potential frequency was stronger in recordings made at ZT 8-11 than at ZT 1-4. In the control recordings during the course of the day the pheromone responses became increasingly tonic and less phasic. At ZT 8-11 only, this daytime-dependent effect was further enhanced by 8bcGMP application. Thus we hypothesize that during the moths' resting phase,elevated cGMP levels underlie a daytime-dependent decrease in pheromone sensitivity and a decline in the temporal resolution of pheromone pulses.
Modified Ring Shear Apparatus for Unsaturated Soils Testing
Authors: Sedano JAI , Vanapalli SK , Garga VK
Published: September 2006

This paper presents the design details of an automated modified ring shear apparatus for the testing of unsaturated soils using the axis-translation technique. The components of this automated system are described, as well as the types of tests that it can be used for. The key cell components include a flushing system and a precise volume gage system. The paper presents typical test results including the continuous monitoring of water as the test proceeds. A methodology to correct the water content measurements for the effect of air infiltration and evaporation or condensation of water is included.
Evaluation of the Chinese Accelerated Test for Alkali-Carbonate Reaction
Authors: Lu D , Fournier B , Grattan-Bellew P , Xu Z , Tang M
Published: September 2006

As part of an multi-laboratory study on accelerated concrete microbar test for alkali-carbonate reaction, the effect of a number of variables on expansion were evaluated, including the effect of alkali content of the cement, the type and source of alkali, the aggregate particle size, and the bar size. The expansivities of various dolomitic limestones from different origins were evaluated in the concrete prism test and in the accelerated concrete microbar test. The effect of replacement of a portion of the portland cement with fly ash on the expansion of microbars containing selected dolomitic limestones and a typical alkalisilica reactive aggregate were also evaluated. The paper presents the obtained results and the correlation between expansions in the concrete prism test and the accelerated test.
Antifungal Prophylaxis to Prevent Neonatal Candidiasis: A Survey of Perinatal Physician Practices
Authors: Burwell Lauren A. , Kaufman David , Blakely Jennifer , Stoll Barbara J. , Fridkin Scott K.
Published: September 2006

BACKGROUND. Bloodstream infections with Candida species have a high mortality rate in very low birth weight infants. Preliminary data suggest that prophylaxis with fluconazole reduces the incidence of colonization and invasive Candida infections in high-risk, very low birth weight neonates. The extent of antifungal prophylaxis use to prevent neonatal candidemia is unknown.

METHODS. We surveyed a 20% random sample of the members of the American Academy of Pediatrics Section on Perinatal Pediatrics. We collected information on prophylactic agents used, indications for use, and rationale for reported practices.

RESULTS. A total of 219 (47%) of 469 members sampled responded; 3 clinicians who did not provide care to very low birth weight infants were excluded. Antifungal prophylaxis use was reported by 73 (34%) respondents. Agents used included intravenous fluconazole (66%), oral nystatin (59%), and intravenous amphotericin B (21%). Decreased birth weight or early gestational age was the most frequent indication to start prophylaxis (57 [78%]). Respondents who did not use antifungal prophylaxis compared with respondents who used fluconazole prophylaxis were significantly more likely to have concerns about (1) the emergence of antifungal resistance, (2) unclear criteria on which to base the decision to start prophylaxis, and (3) the need for clarification of the role of surveillance cultures.

CONCLUSIONS. Although preliminary data suggest that fluconazole is efficacious to prevent candidemia in a subset of neonates, this practice is not used widely by clinicians who care for very low birth weight infants. Additional efficacy studies should address the emergence of antifungal resistance or clarification of criteria to initiate prophylaxis, including the role of surveillance cultures.
Octyl-2-cyanoacrylate Tissue Glue (Dermabond) versus Monocryl 6 × 0 Sutures in Lip Closure
Authors: Spauwen Paul H. M. , de Laat Wendy A. A. , Hartman Ed H. M.
Published: September 2006

Objective:

To assess the value of octyl-2-cyanoacrylate tissue glue in lip closure versus Monocryl stitches.

Design:

Closure of a cleft lip can be done using transcutaneous Monocryl 6 × 0 sutures or using octyl-2-cyanoacrylate tissue glue (Dermabond). In 15 consecutive patients, the cleft lip was closed with Monocryl 6 × 0 and in another 15 consecutive patients, Dermabond was applied. Outcome parameters were complications, satisfaction of the parents with the cosmetic result, and the cosmetic result as judged by professionals. Satisfaction of the parents was assessed using a questionnaire and a visual analog scale. The cosmetic result as judged by professionals was measured by rating standardized pictures according to a visual analog scale.

Setting:

A tertiary referral center for children with craniofacial anomalies.

Results:

Complications were equal in both patient groups (p = .273). Satisfaction of the parents, as well as the professionals, with the cosmetic result did not show significant differences between the Monocryl 6 × 0 and the Dermabond groups (p = .922 and .983, respectively). However, parents were significantly more positive about the cosmetic result than the professionals were (p = .000).

Conclusion:

The results of lip closure using Dermabond tissue glue equal the cosmetic results of lip closure using transcutaneous Monocryl 6 × 0 sutures.
Monte Carlo Techniques Applied to Well Forecasting: Some Pitfalls
Authors: Williamson H. S. , Sawaryn S. J. , Morrison J. W.
Published: September 2006

Monte Carlo simulation is rapidly superceding deterministic methods as the preferred technique for many well-forecasting applications. This paper contrasts the two techniques and highlights the potential benefits of the former. The main part of the paper is a discussion of the application of Monte Carlo simulation to time and cost estimation of single wells and, in particular, of some common errors that the authors have observed practitioners to make (or have themselves made) within this context. This discussion, together with sections covering multiwell programs, scheduling, and production issues, demonstrates that although Monte Carlo simulation has the potential to enhance the reliability of well forecasts, this potential can be realized only if the technique is applied with great care.
Sequentially Adapted Flow-Based PEBI Grids for Reservoir Simulation
Authors: Mlacnik M. J. , Durlofsky L. J. , Heinemann Z. E.
Published: September 2006

A technique for the sequential generation of perpendicularbisectional (PEBI) grids adapted to flow information is presented and applied. The procedure includes a fine-scale flow solution, the generation of an initial streamline–isopotential grid, grid optimization, and upscaling. The grid optimization is accomplished through application of a hybrid procedure with gradient and Laplacian smoothing steps, while the upscaling is based on a global-local procedure that makes use of the global solution used in the grid-determination step. The overall procedure is successfully applied to a complex channelized reservoir model involving changing well conditions. The gridding and upscaling procedures presented here may also be suitable for use with other types of structured or unstructured grid systems.
Compositional Modeling of Discrete-Fractured Media Without Transfer Functions by the Discontinuous Galerkin and Mixed Methods
Authors: Hoteit H. , Firoozabadi A.
Published: September 2006

In a recent work, we introduced a numerical approach that combines the mixed-finite-element (MFE) and the discontinuous Galerkin (DG) methods for compositional modeling in homogeneous and heterogeneous porous media. In this work, we extend our numerical approach to 2D fractured media. We use the discrete-fracture model (crossflow equilibrium) to approximate the two-phase flow with mass transfer in fractured media. The discrete-fracture model is numerically superior to the single-porosity model and overcomes limitations of the dual-porosity model including the use of a shape factor. The MFE method is used to solve the pressure equation where the concept of total velocity is invoked. The DG method associated with a slope limiter is used to approximate the species-balance equations. The cell-based finite-volume schemes that are adapted to a discrete-fracture model have deficiency in computing the fracture/fracture fluxes across three and higher intersecting-fracture branches. In our work, the problem is solved definitively because of the MFE formulation. Several numerical examples in fractured media are presented to demonstrate the superiority of our approach to the classical finite-difference method.
Top-Drive Casing-Running Process Improves Safety and Capability
Authors: Warren Tommy , Johns Roger , Zipse Dean
Published: September 2006

The conventional casing-running process is personnel-intensive and requires considerable human contact with the casing. A new casing-running system facilitates mechanizing the casing-running process. This technology eliminates potential safety hazards, provides assurance that the casing can be run to the intended casing point, offers the ability to ream casing to bottom, reduces personnel requirements for running casing, and eliminates the need for a stabber in the derrick.

A portable casing-drive tool is used to pick up joints of casing from the "V-door," position the casing over the stump in the rotary table, and grip the top of the casing without making a threaded connection. The drive tool supports the full torsional and axial load for running the casing and provides the ability to circulate the well at any time to wash and ream to bottom as tight hole or fill is encountered. The top drive provides the rotary power to make up and rotate the casing.

The new portable casing-running system had been used on more than 430 jobs for more than 40 operators in nine countries (at the end of 2004) to run more than 3 million ft of casing of various weights, grades, and connection types, with sizes ranging from 4½ to 16 in. These jobs encompass wells from vertical holes to high-angle extended-reach wells and include both onshore and offshore applications. The system has been completely mechanized on one casing-drilling rig to allow the driller to routinely pick up casing from the pipe racks and make connections without human contact with the pipe.