The predominant cellular fatty acids of these seven strains were

The predominant cellular fatty acids of these seven strains were branched-chain saturated and unsaturated fatty acids and straight-chain saturated and mono-unsaturated fatty acids, namely iso-C15:0 (7.5%), iso-C15:1��10c (7.5%), iso -C17:1��7c (6.1%), C15:0 (14.3%), C16:1��7c (19.2%), iso -C15:0 3-OH (8.6%), iso-C16:0 3-OH (6.5%) and iso -C17:0 3-OH (4.5%) [1]. The isoprenoid quinones of C. algicola were not determined, but for C. pacifica the presence of MK-6 as the major lipoquinone was described [3]. Polar lipids not have been studied. Genome sequencing and annotation Genome project history This organism was selected for sequencing on the basis of its phylogenetic position [24], and is part of the Genomic Encyclopedia of Bacteria and Archaea project [25].

The genome project is deposited in the Genomes OnLine Database [12] and the complete genome sequence is deposited in GenBank. Sequencing, finishing and annotation were performed by the DOE Joint Genome Institute (JGI). A summary of the project information is shown in Table 2. Table 2 Genome sequencing project information Growth conditions and DNA isolation C. algicola IC166T, DSM 14237, was grown in DSMZ medium 514 (BACTO marine broth) [26] at 15��C. DNA was isolated from 0.5-1 g of cell paste using MasterPure Gram-positive DNA purification kit (Epicentre MGP04100) following the standard protocol as recommended by the manufacturer with modification st/DL for cell lysis as described in Wu et al. [25]. DNA is available through the DNA Bank Network [27]. Genome sequencing and assembly The genome was sequenced using a combination of Illumina and 454 sequencing platforms.

All general aspects of library construction and sequencing can be found at the JGI website [28]. Pyrosequencing reads were assembled using the Newbler assembler version 2.3-PreRelease-09-14-2009-bin (Roche). The initial Newbler assembly consisting of 128 contigs in two scaffolds was converted into a phrap assembly by [29] making fake reads from the consensus, to collect the read pairs in the 454 paired end library. Illumina GAii sequencing data (710 Mb) was assembled with Velvet [30] and the consensus sequences were shredded into 1.5 kb overlapped fake reads and assembled together with the 454 data. The 454 draft assembly was based on 263.4Mb 454 draft data and all of the 454 paired end data. Newbler parameters are -consed -a 50 -l 350 -g -m -ml 20.

The Phred/Phrap/Consed software package [29] was used for sequence assembly and quality assessment in the subsequent AV-951 finishing process. After the shotgun stage, reads were assembled with parallel phrap (High Performance Software, LLC). Possible mis-assemblies were corrected with gapResolution [28], Dupfinisher [31], or sequencing cloned bridging PCR fragments with subcloning or transposon bombing (Epicentre Biotechnologies, Madison, WI).

After observing the overlain first-order derivative spectra with

After observing the overlain first-order derivative spectra with scaling factor = 4 and ���� = 4 for NBM and PRCM [Figure 3], zero crossing points of drugs were selected for the analysis of other drugs. The first wavelength selected was 261 nm (zero crossing of NBM), where PRCM showed considerable absorbance. The second wavelength selected was 248.2 nm (zero crossing of PRCM), where NBM showed considerable absorbance. Figure 2 Overlain zero-order absorption spectra of 12 ��g/ml nabumetone and 12 ��g/ml paracetamol in methanol Figure 3 Overlain first-order derivative spectra of 12 ��g/ml nabumetone and 12 ��g/ml paracetamol in methanol Calibration curves For each drug, linearity was observed by diluting appropriate aliquots of the working standard stock solution 0.15, 0.3, 0.45, 0.6, 0.

75, and 0.9 ml into a series of 10-ml volumetric flasks with methanol to get a final concentration range of 3�C18 ��g/ml separately for both NBM and PRCM. The samples were scanned in the wavelength range 200400 nm, and the first-order derivative of the spectrum was taken. The dA/d�� of each of these solutions was measured at the selected wavelength and plotted against concentration to obtain the calibration graph. The statistical parameters of the calibration curve, such as correlation coefficient, regression equation, limit of detection, and limit of quantitation, for NBM and PRCM are given in Table 1. Table 1 Optical characteristics of the proposed method (first-order derivative method) Analysis of tablet formulation Twenty tablets were weighed accurately and powdered.

A powder equivalent of 12 mg of NBM (containing 12 mg of PRCM) was weighed and transferred to a 100-ml volumetric flask. Then it was dissolved in 25 ml of methanol by shaking the flask for 15 min, and the volume was made up to the mark with methanol. The solution was filtered through Whatman filter paper no. 41. A 1.0 ml aliquot of the sample stock solution was transferred to a 10-ml standard volumetric flask, and the volume was made up to the mark with methanol. The sample solution of the final concentration of 12 ��g/ml of NBM (containing 12 ��g/ml of PRCM) was analyzed by the first-order derivative spectroscopic method, and absorbance was measured at 261 and 248.2 nm. The procedure was repeated six times for sample analysis. The concentrations of NBM and PRCM were calculated from the calibration graph.

The results of analysis are given in Table 2. Table 2 Results of commercial formulation analysis (n = 3) METHOD VALIDATION Accuracy Batimastat The accuracy of the proposed method was determined by performing recovery study at 80, 100, and 120% level for NBM and PRCM. The recovery study was done by adding pure drug solution to the preanalyzed tablet formulation, and concentrations of NBM and PRCM were determined by using the calibration graph. The values of percent relative standard deviation and recovery studies were showing satisfactory accuracy.

250 ��g Precision Validation of the method for precision was mea

250 ��g. Precision Validation of the method for precision was measured by using standard solutions containing lumefantrine at concentrations covering the entire calibration range. Further the method was validated for instrumental precision, intraday precision, and interday precision. Instrumental precision was studied by repeated analysis (n = 10), of lumefantrine standard solution (6.250 ��g/ml) on the same day. The RSD for instrumental precision was 0.10 %. The precision of the method in terms of intraday variation (%CV) was determined by analyzing lumefantrine standard solutions in the range (1.250-12.500 ��g/ml) three times on the same day. Interday precision (%CV) was assessed by analyzing these solutions (1.250-12.500 ��g/ml) on three different days over a period of one week. The results of the precision studies are shown in Table 2. Table 2 Summary of precision and accuracy Accuracy The accuracy of the method was established by use of standard addition method i.e., measurement of recovery at three different concentration levels. 80%, 100%, and 120% of the standard drug solutions were added to the solution of known concentration and the percentage recovery was then determined. The results are summarized in Table 2. Specificity The optimized mobile phase gave a very good resolution of lumefantrine, indicating the specificity of the method. A typical absorbance spectrum of the drug is shown in [Figure 2]. The optimized solvent system yielded a symmetrical peak for the drug with RF 0.59 [Figure 3]. To achieve the best detection sensitivity, wavelength 266 nm was selected for detection. Figure 2 Absorption spectrum of lumefantrine scanned at 190-400 nm Figure 3 Representative chromatogram of standard lumefantrine at 266 nm Ruggedness and robustness Ruggedness is a measure of the reproducibility of a test result under normal, expected operating conditions from instrument to instrument and from analyst to analyst. Robustness is a measure of the capacity of a method to remain unaffected by small but deliberate variations in the method conditions. The %RSD was recorded less than 2%, thus indicating reliability of the method. Reproducibility The repeatability of sample application was assessed by spotting drug solution (10 ��l) seven times on an HPTLC plate then development of plate and recording the peak height and area for the spots. The %RSD for peak height and peak area values of lumefantrine were found to be 0.49% and 0.98%, respectively. Repeatability of measurement of peak height and area were determined by spotting 10-��l standard drug solution on the HPTLC plate and developing the plate. The separated spot was scanned seven times without changing the position of the plate. %RSD for measurement of peak height and peak area of lumefantrine was 0.53 and 1.05, respectively. Stability studies To test the stability of drugs on the HPTLC plates, analyte was tested against freshly prepared solutions.

Therefore, we strongly recognized the necessity to improve the ne

Therefore, we strongly recognized the necessity to improve the new SILC technique without using the Abiraterone molecular weight SILS Port. 3. Three-Port Method via Umbilical Incision Next, we selected the 3-port method, which makes use of three 5mm ports (Ethicon, Brunswick, NJ, USA) (Figure 2) via umbilical incision. The same forceps, graspers, or electrical devices were used as when using the SILS Port. This technique was able to shorten the length of the umbilical scar by approximately 5mm in comparison to the use of the SILS Port; however, the conflicts between the operative instruments and the scope and between the surgeon and the assistant were not improved. As a result, it was found that the ideal technique for SILC would involve the insertion of only two ports via umbilical incision and would have the surgeon and the assistant located on opposite sides of the patient.

Figure 2 External view of 3-port LC via umbilical incision. 4. Two-Port via Umbilical Incision A 15mm vertical skin incision was made through the center of the umbilicus. After the fascia was exposed, two 5mm ports were introduced at separate sites, one on the left side for the 5mm laparoscopic flexible scope and one on the right side for a forceps or grasper to dissect the gallbladder. The instruments used in this technique were the same as in the conventional 4-port LC. A 2mm loop-type retractor was inserted from the right subcostal arch to present Calot’s triangle by extending Hartman’s pouch. A nylon suture with a straight needle to which a Roeder knot [10] was added to the end was inserted through a 5mm left side port.

The fundus of the gallbladder was tightened with the Roeder knot, and then the straight needle was inserted from the abdominal cavity to the right subcostal abdominal wall (Figure 3). The gallbladder was elevated by raising this nylon suture, and a good surgical field was obtained (Figure 4). The surgeon operated both one instrument and the 5mm flexible scope by herself, and the assistant made a good surgical field such as Calot’s triangle via the traction of the gallbladder using a fine loop retractor and nylon suture. This technique relieved the interference between the surgeon and the assistant and between the forceps themselves. To extract the exfoliated gallbladder, one 5mm port was removed, and an endoscopic retrieval bag was inserted directly with an original hole, and the gallbladder was then extracted.

No intraperitoneal drainage was used. The fascial defect of the umbilicus incision was repaired with approximately two stitches, and an intradermal suture was performed on the skin. The treatment of the small scar made by the 2mm loop-type retractor and nylon suture was unnecessary. This technique represents minimally invasive surgery that combines low invasiveness and Entinostat with a scarless outcome. Figure 3 External view of 2-port LC.


These BTB06584? were compared to 14 patients undergoing conventional mitral surgery [36]. They found no significant difference in the cerebral microembolic rate between either technique. The Consensus Statement of the International Society of Minimally Invasive Coronary Surgery (ISMICS) 2010, based on a systematic review and meta-analysis of all available randomized and nonrandomized comparative trials of isolated mini versus conventional mitral valve surgery (two randomized trials and 33 nonrandomized studies for a total of 35 studies) [68], associated some adverse clinical outcomes with mini MVS compared with conv-MVS, including stroke, aortic dissection, and groin wound/vasculature complications. The absolute risk increase of stroke for mini MVS versus conv-MVS was 0.9% overall (2.1% versus 1.

2%, RR 1.79, 95% CI 1.35�C2.38; 13 studies, level B). Subanalysis of two propensity comparison studies also showed significant increase of stroke of 1% with mini MVS compared with conv-MVS (1.9% versus 0.9%, RR 2.02, 95% CI 1.40�C2.94; two studies, level B) [69]. These findings are similar to those recently reported by a recent Society of Thoracic Surgeons-Adult Cardiac Surgical Database (STS-ACSD) publication made on 28,143 patients undergoing isolated mitral valve operations that examined the associations between operative strategy and the increased risk of stroke in the less-invasive group [70]. The markedly higher rate of permanent perioperative stroke in the less-invasive group compared with the conventional sternotomy group in unadjusted, adjusted, and propensity analyses was the most significant finding of this study.

The adjusted OR for permanent stroke was 1.96 for less-invasive compared with conventional sternotomy operations in the multivariable analysis, and the likelihood of stroke was similarly increased in the propensity analysis. Among the 4,322 LIMV operations, there were 41 excess strokes compared with the propensity-matched group having conventional mitral valve operations. Additional analyses demonstrated a threefold higher risk of stroke for less-invasive operations performed without aortic occlusion (beating- or fibrillating-heart), which comprised 12% of the less invasive group. Femoral cannulation was not an independent predictor of stroke [70]. Grossi et al.

[71] using an informal strategy of intraoperative echocardiographic analysis of the aortic arch and the descending aorta in 714 minimally invasive mitral valve procedures had excellent results from this Entinostat approach avoiding the use of femoral perfusion when there was significant atherosclerotic burden [71]. In this cohort, where 30% of patients were >70 years of age, 15% were reoperations, and 12% were multivalve operations, femoral perfusion was used in nearly 80% of patients, with a 2.9% incidence of stroke.

Non-coding genes and miscellaneous features were predicted using

Non-coding genes and miscellaneous features were predicted using tRNAscan-SE [36], RNAMMer [37], Nilotinib Leukemia Rfam [38], TMHMM [39], and SignalP [40]. Additional gene prediction analyses and functional annotation were performed within the Integrated Microbial Genomes (IMG-ER) platform [41]. Genome properties The genome is 7,784,016 nucleotides with 63.40% GC content (Table 3) and comprised of 1 scaffold (Figure 3a, Figure 3b) of 2 contigs. From a total of 7430 genes, 7,372 were protein encoding and 58 RNA only encoding genes. Within the genome, 274 pseudogenes were also identified. The majority of genes (74.10%) were assigned a putative function whilst the remaining genes were annotated as hypothetical. The distribution of genes into COGs functional categories is presented in Table 4.

Table 3 Genome Statistics for Bradyrhizobium sp. strain WSM471. Figure 3a Graphical circular map of the chromosome of Bradyrhizobium sp. strain WSM471. From outside to the center: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs … Figure 3b Graphical circular map of the plasmid of Bradyrhizobium sp. strain WSM471. From outside to the center: Genes on forward strand (color by COG categories as denoted by the IMG platform), Genes on reverse strand (color by COG categories), RNA genes (tRNAs … Table 4 Number of protein coding genes of Bradyrhizobium sp. strain WSM471 associated with the general COG functional categories.

Acknowledgements This work was performed under the auspices of the US Department of Energy Office of Science, Biological and Environmental Research Program, and by the University of California, Lawrence Berkeley National Laboratory under contract No. DE-AC02-05CH11231, Lawrence Livermore National Laboratory under Contract No. DE-AC52-07NA27344, and Los Alamos National Laboratory under contract No. DE-AC02-06NA25396. We gratefully acknowledge the funding received from the Murdoch University Strategic Research Fund through the Crop and Plant Research Institute (CaPRI) and the Centre for Rhizobium Studies (CRS) at Murdoch University. The authors would like to thank the Australia-China Joint Research Centre for Wheat Improvement (ACCWI) and SuperSeed Technologies (SST) for financially supporting Mohamed Ninawi��s PhD project.

Biological fixation of inert atmospheric dinitrogen gas is a process that can only be performed by certain prokaryotes in the domains Archaea and Bacteria. By far the greatest amounts of nitrogen (N) are fixed by specialized soil bacteria (root nodule bacteria or rhizobia) that form proto-cooperative, non-obligatory symbiotic relationships with legumes [1]. Indeed, these symbioses contribute Batimastat ~40 million tonnes of N annually to support global food production [2]. Species of the legume genus Trifolium (clovers) are amongst the most widely cultivated pasture legumes.

The cumulative prominence by respondent (ranging from 0-5) was th

The cumulative prominence by respondent (ranging from 0-5) was then used to calculate the mean prominence for each category. Thematically similar individual categories were grouped under specific headings (e.g. related to dehydration among somatic symptoms) for the analysis selleck of broader concepts of experience, meaning and behaviour. Calculation of the grouped prominence followed the same procedure as with the individual variables. To identify significant differences for cholera between the two sites and between sexes, a non-parametric statistic, the Wilcoxon rank-sum test, was used when comparing prominence variables; the Pearson Chi2 and Fisher’s exact test were applied when comparing proportions.

This particular approach to comparing prominence, which has been widely used in other cultural epidemiological studies, takes more information about a category into account than a simple comparison of frequencies of report without considering how they are reported. A similar series of questions were asked to elicit shigellosis-related illness experience, meaning and help-seeking behaviour. The same categories that were coded for cholera were also coded for shigellosis. Comparative analysis between the two conditions considered only spontaneously reported categories, because the interview coded only spontaneous responses for shigellosis. The proportion of positive responses by category was tabulated individually for each vignette, and for a report in both vignettes. To determine whether a category was associated more with one vignette than the other, McNemar’s Chi2 test for paired data was used.

To examine whether or not individual categories were differentiated between both conditions, Cohen’s kappa was calculated. The kappa statistic indicates the strength of agreement for a categorical assessment, corrected for agreement by chance. The analysis identified the two conditions as distinct for a category if the kappa coefficient was below 0.4, a level commonly accepted as a threshold for moderate agreement [22]. Narrative information was written down during the interview in Kiswahili, then translated into English and typed in a word processor. The qualitative software MAXQDA, version 2007, was used for managing the textual data and to facilitate further analyses of findings from quantitative data. Quantitative data was entered twice and verified in Epi Info software, version 3.

4.3, and cleaned. Statistical analyses were done with Stata, version 10. Sample size The sample size calculation was based on comparison of mean prominence of categories of distress, perceived causes, self treatment and outside help seeking for peri-urban�Crural and female�Cmale differences. Entinostat The detection of a difference of 0.5 between prominence means with equal standard deviations of 1.

This is in contrast to IL-10?/?NOD?/? mice in which only 6 of 20

This is in contrast to IL-10?/?NOD?/? mice in which only 6 of 20 (30%) mice had developed colitis (Fig. 1A). At 18 wk of age, the reduction in the incidence of colitis in IL-10?/?NOD2?/? mice was associated with significant reduction in serum amyloid A, EMD 1214063 a nonspecific marker of inflammation (Fig. 1B). FIGURE 1. Chronic colitis is ameliorated in IL-10?/?NOD2?/? mice. The development of colitis was investigated in IL-10?/? and IL-10?/?NOD2?/? mice. (A) The incidence of clinical colitis … IBD and colitis in IL-10?/? mice are characterized by increased mucosal inflammatory cytokine levels arising primarily from the immune cell infiltrate. At 6 wk of age, there was no significant difference in colonic cytokine levels in IL-10?/? mice compared with IL-10?/?NOD2?/? mice.

However, by 10 wk of age, levels of IL-12p70, TNF-��, and IL-1�� were significantly elevated in the colons of IL-10?/? mice when compared with IL-10?/?NOD2?/? mice of the same age. Moreover, proinflammatory colonic cytokine levels remained attenuated in older (18-wk) IL-10?/?NOD2?/? mice, thus confirming amelioration of spontaneous colitis (Fig. 1D). To look specifically at progression of intestinal inflammation, we analyzed the colon for histopathological changes in 6-, 10-, and 18-wk-old mice. At 6 wk of age, histological analysis revealed a small inflammatory cell infiltrate restricted to the lamina propria at the base of the crypts and elongated crypts (mild damage) in a small number of IL-10?/? mice (3 of 11) and IL-10?/?NOD2?/? mice (1 of 11).

However, there was no significant difference in histopathology between IL-10?/? and IL-10?/?NOD2?/? at 6 wk of age (Fig. 1C), concurring with the slight, but nonsignificant, increase in colon cytokines observed in IL-10?/? mice compared with IL-10?/?NOD2?/? mice (Fig. 1D). By 10 wk of age, the incidence (11 of 12) and severity of histopathology had increased in IL-10?/? mice, characterized by increased inflammatory cell infiltrate and crypt elongation associated with goblet cell depletion along the length of the colon (Fig. 1E, ,1F).1F). In contrast, 5 of 11 IL-10?/?NOD2?/? mice had no histopathology, and those that did had limited inflammation and epithelial damage, resulting in significantly less histopathology scores (Fig. 1C). At 18 wk, IL-10?/? mice had marked mucosal thickening, epithelial hyperplasia, and crypt abscesses involving distal and proximal colon (Fig.

1E, ,1F).1F). Severe epithelial damage was associated with increased immune infiltrate extending into the submucosa and the presence of immune cell foci. This is in contrast to colons from 18-wk-old IL-10?/?NOD2?/? mice that had significantly less mucosal damage and immune cell infiltrate. Taken together these data demonstrate that deletion of NOD2 in IL-10?/? mice AV-951 ameliorates spontaneous chronic colitis.

Correlation analysis of gFOBT and SEPT9 in the same healthy sampl

Correlation analysis of gFOBT and SEPT9 in the same healthy samples showed specificity of 70.6% (12/17 negative) for gFOBT and 76.5% (13/17 negative) for CHIR99021 IC50 SEPT9. For CRC, all of the patients were SEPT9 positive (100%; 22/22) whereas only 68.2% (15/22) were positive by gFOBT. Compared to gFOBT, we found the CEA assay was more precise for detecting CRC, with 85.2% specificity, but was also less sensitive (51.8%). CEA is the most widely used serum tumor marker for CRC monitoring. This antigen is expressed on the surface of the colonic epithelial cells and in the case of malignancy, CEA is expressed on the whole cell surface and excreted at high levels into the bloodstream [22]. Elevated preoperative CEA is associated with reduced survival after surgical resection of CRC.

Monitoring of CEA in the postoperative period can help to identify patients with metastasis, although its sensitivity for pulmonary metastasis is less than for hepatic metastasis [23]. The primary use of CEA is in follow-up of CRC after surgical or chemotherapy treatment. In our study, only 51.8% (14/27) of CRC patients showed elevated CEA levels. From the comparison of CEA and Septin 9 in the same patients, the specificity of the CEA assay was 85.2% (23/27), higher than the Septin 9 specificity (70.4%; 19/27); however Septin 9 was much more sensitive (100%; 27/27) in cancer samples than CEA (51.8%; 14/27). Hence serum CEA is not as a reliable method for CRC screening as Septin 9 [24]. Septins have been originally detected in cell division cycle mutant yeast, but recently it is become known that Septin proteins play role in several cellular functions.

They have been implicated in neoplasia, neurological and infectious diseases [25]. Previous studies used the first generation Septin 9 detection kit (Epi proColon 1.0) and found Septin 9 positivity in 9% of healthy subjects and 73% of CRC patients [14]�C[17]. In our study, new generation Septin 9 blood test, the Epi proColon 2.0 was used. The advantages of Epi proColon 2.0 kit are fewer handling steps, shorter time to result and increased clinical performance compared to the first generation test [26]. In the present study, we first analyzed the data using the high sensitivity (1/3 analysis method) as described previously [16]. In the current study only 4 of the 92 (4.3%) CRC cases showed SEPT9 negativity, all of them stage I CRC, and the test had 95.

6% sensitivity for CRC. Its specificity (84.8%) was similar to that found for CEA (Table 3). Seventy-eight of the 92 (84.8%) healthy subjects were negative for Septin 9. Healthy subjects that were positive for Septin 9 did not show any sign of colonic disease at the GSK-3 time of colonoscopy. However, it remains to be seen whether they will develop any illness in the future. Septin 9 was sufficiently sensitive to detect early stage CRC as well. For stage I CRC, 95.6% were identified by Septin 9 methylation, and all of the stage II CRC samples showed positive test results.

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