Combined in-fermenter extraction and cross-flow microfiltration for improved inclusion body processing

In this study we demonstrate a new in-fermenter chemical extraction procedure that degrades the cell wall of Escherichia coli and releases inclusion bodies (IBs) into the fermentation medium. We then prove that cross-flow microfiltration can be used to remove 91% of soluble contaminants from the released IBs. The extraction protocol, based on a combination of Triton X-100, EDTA, and intracellular T7 lysozyme, effectively released most of the intracellular soluble content without solubilising the IBs. Cross-flow microfiltration using a 0.2 mum ceramic membrane successfully recovered the granulocyte macrophagecolony stimulating factor (GM-CSF) IBs with removal of 91% of the soluble contaminants and virtually no loss of IBs to the permeate. The filtration efficiency, in terms of both flux and transmission, was significantly enhanced by infermenter Benzonase(R) digestion of nucleic acids following chemical extraction. Both the extraction and filtration methods exerted their efficacy directly on a crude fermentation broth, eliminating the need for cell recovery and re-suspension in buffer. The processes demonstrated here can all be performed using just a fermenter and a single cross-flow filtration unit, demonstrating a high level of process intensification. Furthermore, there is considerable scope to also use the microfiltration system to subsequently solubilise the IBs, to separate the denatured protein from cell debris, and to refold the protein using diafiltration. In this way refolded protein can potentially be obtained, in a relatively pure state, using only two unit operations. (C) 2004 Wiley Periodicals Inc.

Identification of "pathologs" (disease-related genes) from the RIKEN mouse cDNA dataset using human curation plus FACTS, a new biological information extraction system

Background: A major goal in the post-genomic era is to identify and characterise disease susceptibility genes and to apply this knowledge to disease prevention and treatment. Rodents and humans have remarkably similar genomes and share closely related biochemical, physiological and pathological pathways. In this work we utilised the latest information on the mouse transcriptome as revealed by the RIKEN FANTOM2 project to identify novel human disease-related candidate genes. We define a new term patholog to mean a homolog of a human disease-related gene encoding a product ( transcript, anti-sense or protein) potentially relevant to disease. Rather than just focus on Mendelian inheritance, we applied the analysis to all potential pathologs regardless of their inheritance pattern. Results: Bioinformatic analysis and human curation of 60,770 RIKEN full-length mouse cDNA clones produced 2,578 sequences that showed similarity ( 70 - 85% identity) to known human-disease genes. Using a newly developed biological information extraction and annotation tool ( FACTS) in parallel with human expert analysis of 17,051 MEDLINE scientific abstracts we identified 182 novel potential pathologs. Of these, 36 were identified by computational tools only, 49 by human expert analysis only and 97 by both methods. These pathologs were related to neoplastic ( 53%), hereditary ( 24%), immunological ( 5%), cardio-vascular (4%), or other (14%), disorders. Conclusions: Large scale genome projects continue to produce a vast amount of data with potential application to the study of human disease. For this potential to be realised we need intelligent strategies for data categorisation and the ability to link sequence data with relevant literature. This paper demonstrates the power of combining human expert annotation with FACTS, a newly developed bioinformatics tool, to identify novel pathologs from within large-scale mouse transcript datasets.

Quantification of carbamazepine, carbamazepine-10,11-epoxide, phenytoin and phenobarbital in plasma samples by stir bar-sorptive extraction and liquid chromatography

A sensitive and reproducible stir bar-sorptive extraction and high-performance liquid chromatography-UV detection (SBSE/HPLC-UV) method for therapeutic drug monitoring of carbamazepine, carbamazepine-10,11-epoxide, phenytoin and phenobarbital in plasma samples is described and compared with a liquid:liquid extraction (LLE/HPLC-UV) method. Important factors in the optimization of SBSE efficiency such as pH, extraction time and desorption conditions (solvents, mode magnetic stir, mode ultrasonic stir, time and number of steps) assured recoveries ranging from 72 to 86%, except for phenytoin (62%). Separation was obtained using a reverse phase C-18 column with UV detection (210 nm). The mobile phase consisted of water: acetonitrile (78:22, v/v). The SBSE/HPLC-UV method was linear over a working range of 0.08-40.0 mu g mL(-1) for carbamazepine, carbamazepine-10,11-epoxide and phenobarbital and 0.125-40.0 mu g mL(-1) for phenytoin, The intra-assay and inter-assay precision and accuracy were studied at three concentrations (1.0, 4.0 and 20.0 mu g mL(-1)). The intra-assay coefficients of variation (CVs) for all compounds were less than 8.8% and all inter-CVs were less than 10%. Limits of quantification were 0.08 mu g mL(-1) for carbamazepine, carbamazepine-10,11-epoxide and phenobarbital and 0.125 mu g mL(-1) for phenytoin. No interference of the drugs normally associated with antiepileptic drugs was observed. Based on figures of merit results, the SBSE/HPLC-UV proved adequate for antiepileptic drugs analyses from therapeutic levels. This method was successfully applied to the analysis of real samples and was as effective as the LLE/HPLC-UV method. (c) 2008 Elsevier B.V. All rights reserved.

Simultaneous analysis of parabens in cosmetic products by stir bar sorptive extraction and liquid chromatography

A sensitive and precise stir bar sorptive extraction (SBSE) combined with LC (SBSE/LC) analysis is described for simultaneous determination of methyl, ethyl, propyl, and butyl parabens in commercial cosmetic products in agreement with the European Union Cosmetics Directive 76/768/EEC. Important factors in the optimization of SB SE efficiency are discussed, such as time and temperature of extraction, pH, and ionic strength of the sample, matrix effects, and liquid desorption conditions by different modes (magnetic stirring, ultrasonic). The LOQs of the SBSE/LC method ranged from 30 to 200 ng/mg, with linear response over a dynamic range, from the LOQ to 2.5 mu g/mg, with a coefficient of determination higher than 0.993. The interday precision of the SBSE/LC method presented a coefficient of variation lower than 5%. The effectiveness of the proposed method was proven for analysis of commercial cosmetic products such as body creams, antiperspirant creams, and sunscreens.

Rifampicin determination in plasma by stir bar-sorptive extraction and liquid chromatography

A sensitive and reproducible stir bar-sorptive extraction and high performance liquid chromatography-UV detection (SBSE/HPLC-UV) method for therapeutic drug monitoring of rifampicin in plasma samples is described and compared with a liquid:liquid extraction (LLE/HPLC-UV) method. This miniaturized method can result in faster analysis, higher sample throughput, lower solvent consumption and less workload per sample while maintaining or even improving sensitivity. Important factors in the optimization of SBSE efficiency such as pH, temperature, extraction time and desorption conditions (solvents, mode magnetic stir, mode ultrasonic stir, time and number of steps) were optimized recoveries ranging from 75 to 80%. Separation was obtained using a reverse phase C(8) column with UV detection (254 nm). The mobile phase consisted of methanol:0.25 N sodium acetate buffer, pH 5.0 (58:42, v/v). The SBSE/HPLC-UV method was linear over a working range of 0.125-50.0 mu g mL(-1). The intra-assay and inter-assay precision and accuracy were studied at three concentrations (1.25, 6.25 and 25.0 mu g mL(-1)). The intra-assay coefficients of variation (CVs) for all compounds were less than 10% and all inter-CVs were less than 10%. Limits of quantification were 0.125 mu g mL(-1). Stability studies showed rifampicin was stable in plasma for 12 h after thawing; the samples were also stable for 24 h after preparation. Based on the figures of merit results, the SBSE/HPLC-UV proved to be adequate to the rifampicin analyses from therapeutic to toxic levels. This method was successfully applied to the analysis of real samples and was as effective as the LLE/HPLC-UV method. (C) 2009 Elsevier B.V. All rights reserved.

Ultrasound imaging in rehabilitation: Just a fad?

Real-time ultrasound imaging provides an unrivalled opportunity to observe muscle morphology and contraction. This has obvious potential for clinical practice and the tool is beginning to be adopted into physical therapy. The implementation of ultrasound imaging has become particularly widespread for assessment of size and activation of deep trunk muscles, such as the transversus abdominis and lumbar multifidus, and for assessment of the pelvic floor muscles. The obvious benefit for these areas is that ultrasound permits observation of muscles that are difficult to assess through noninvasive means. This realization of the clinical potential of ultrasound imaging has been paralleled by an explosion of clinical and physiological research. However, despite the enthusiasm for utilization of ultrasound imaging, a question that is critical to address is whether ultrasound can actually improve rehabilitation.

The systematic use of intraoperative vascular Doppler ultrasound during microsurgical subinguinal varicocelectomy improves precise identification and preservation of testicular blood supply

Objective: To evaluate the impact of systematic use of intraoperative Doppler ultrasound during microsurgical subinguinal varicocele repair. Design: Prospective clinical study. Setting: Andrology laboratory and male infertility section of the urology department of a tertiary care hospital. Patient(s): Two hundred and thirteen men with clinical varicocele. Intervention(s): Subinguinal microsurgical varicocele ligation using an intraoperative vascular Doppler flow detector. Main Outcome Measure(s): Number of veins ligated, lymphatic spared, arteries identified or accidentally ligated. Result(s): A statistically significant greater number of arteries were identified and preserved when intraoperative vascular Doppler was used. In addition, the average number of internal spermatic veins ligated was statistically significantly greater in the same group. Accidental artery ligation occurred in two cases (1.1%) in which the Doppler was not applied. There was no statistically significant difference in number of lymphatics spared between groups. Conclusion(s): Our findings showed that concomitant use of intraoperative vascular Doppler during microsurgical varicocelectomy allows more arterial branches to be preserved, and more internal spermatic veins are likely to be ligated. This device should be considered an attractive tool to improve surgical outcomes and safety. (Fertil Steril (R) 2010; 93: 2396-9. (C)2010 by American Society for Reproductive Medicine.)

Is the ultrasound-estimated bladder weight a reliable method for evaluating bladder outlet obstruction?

OBJECTIVE To evaluate the correlation between ultrasound-estimated bladder weight (UEBW) in patients with different degrees of bladder outlet obstruction (BOO). METHODS We evaluated 50 consecutive non-neurogenic male patients with lower urinary tract symptoms (LUTS) referred to urodynamic study (UDS). All patients self-answered the International Prostate Score Symptoms (IPSS) questionnaire. After the UDS, the bladder was filled with 150 mL to determine UEBW. Patients with a bladder capacity under 150 mL, a previous history of prostate surgery or pelvic irradiation, an IPSS score <8, a bladder stone or urinary tract infection were excluded. After a pressure-flow study, the Schafer linear passive urethral resistance relation nomogram was plotted to determine the grade of obstruction: Grades I-II/VI were defined as mild obstruction, Grades III-IV/VI as moderate obstruction, and Grades V-VI/VI as severe obstruction. RESULTS The UEBW was 51.7 +/- 26.9, 54.1 +/- 30.0 and 54.8 +/- 28.2 in patients with mild, moderate and severe BOO, respectively (P = 0.130). The UEBW allowed us to define four groups: (i) UEBW < 35 g; (ii) 35 g <= UEBW < 50 g; (iii) 50 g <= UEBW < 70 g; and (4) UEBW >= 70 g. We did not find any differences in age, prostate weight, IPSS, PVR, cystometric bladder capacity, presence of detrusor overactive and degree of obstruction in the aforementioned groups. CONCLUSION Despite the fact that some studies have emphasized the value of UEBW as an efficient non-invasive method for evaluating lower urinary tract obstruction, our study suggests that UEBW does not present any individual correlation with LUTS or objective measurements of BOO.

Chemical treatment of Escherichia coli .1. Extraction of intracellular protein from uninduced cells

Extraction of intracellular protein from Escherichia coli is traditionally achieved by mechanical disruption. A chemical treatment that destroys the integrity of the bacterial cell wall and could provide an alternative technique is examined in this study. Treatment with a combination of the chelating agent ethylenediaminetetraacetate (EDTA) (greater than 0.3 mM) and the chaotropic agent urea (6 M) is highly effective at releasing protein from uninduced E. coli. The 6 M urea in the presence of 3 mM EDTA can release cytoplasmic protein from both logarithmic-phase and stationary-phase E. coli cells at levels equivalent to mechanical disruption. The concentrations of the two chemical agents were the major variables affecting the maximum levels of protein release. Several minor variables and interactions were also identified. The kinetics of protein release is first order. For 2, 4, and 6 M urea with 3 mM EDTA, the time constant is approximately 2.5 min independent of urea concentration. Kinetics for 3 mM EDTA without urea is considerably slower, with a time constant of 12.3 min. (C) 1997 John Wiley & Sons, Inc.

Extraction of electrical characteristics from pixels of multifrequency EIT images

Computer modelling has shown that electrical characteristics of individual pixels may be extracted from within multiple-frequency electrical impedance tomography (MFEIT) images formed using a reference data set obtained from a purely resistive, homogeneous medium. In some applications it is desirable to extract the electrical characteristics of individual pixels from images where a purely resistive, homogeneous reference data set is not available. One such application of the technique of MFEIT is to allow the acquisition of in vivo images using reference data sets obtained from a non-homogeneous medium with a reactive component. However, the reactive component of the reference data set introduces difficulties with the extraction of the true electrical characteristics from the image pixels. This study was a preliminary investigation of a technique to extract electrical parameters from multifrequency images when the reference data set has a reactive component. Unlike the situation in which a homogenous, resistive data set is available, it is not possible to obtain the impedance and phase information directly from the image pixel values of the MFEIT images data set, as the phase of the reactive reference is not known. The method reported here to extract the electrical characteristics (the Cole-Cole plot) initially assumes that this phase angle is zero. With this assumption, an impedance spectrum can be directly extracted from the image set. To obtain the true Cole-Cole plot a correction must be applied to account for the inherent rotation of the extracted impedance spectrum about the origin, which is a result of the assumption. This work shows that the angle of rotation associated with the reactive component of the reference data set may be determined using a priori knowledge of the distribution of frequencies of the Cole-Cole plot. Using this angle of rotation, the true Cole-Cole plot can be obtained from the impedance spectrum extracted from the MFEIT image data set. The method was investigated using simulated data, both with and without noise, and also for image data obtained in vitro. The in vitro studies involved 32 logarithmically spaced frequencies from 4 kHz up to 1 MHz and demonstrated that differences between the true characteristics and those of the impedance spectrum were reduced significantly after application of the correction technique. The differences between the extracted parameters and the true values prior to correction were in the range from 16% to 70%. Following application of the correction technique the differences were reduced to less than 5%. The parameters obtained from the Cole-Cole plot may be useful as a characterization of the nature and health of the imaged tissues.

Evaluating SVM and MLDA in the extraction of discriminant regions for mental state prediction

Pattern recognition methods have been successfully applied in several functional neuroimaging studies. These methods can be used to infer cognitive states, so-called brain decoding. Using such approaches, it is possible to predict the mental state of a subject or a stimulus class by analyzing the spatial distribution of neural responses. In addition it is possible to identify the regions of the brain containing the information that underlies the classification. The Support Vector Machine (SVM) is one of the most popular methods used to carry out this type of analysis. The aim of the current study is the evaluation of SVM and Maximum uncertainty Linear Discrimination Analysis (MLDA) in extracting the voxels containing discriminative information for the prediction of mental states. The comparison has been carried out using fMRI data from 41 healthy control subjects who participated in two experiments, one involving visual-auditory stimulation and the other based on bimanual fingertapping sequences. The results suggest that MLDA uses significantly more voxels containing discriminative information (related to different experimental conditions) to classify the data. On the other hand, SVM is more parsimonious and uses less voxels to achieve similar classification accuracies. In conclusion, MLDA is mostly focused on extracting all discriminative information available, while SVM extracts the information which is sufficient for classification. (C) 2009 Elsevier Inc. All rights reserved.

Prospective randomized trial of EUS versus ERCP-guided common bile duct stone removal: an interim report (with video)

Background: EUS is being increasingly utilized for the diagnosis of choledocholithiasis and microlithiasis, especially in patients with biliary colic. Simultaneously, there is also a rising interest in the use of EUS for therapeutic interventions. Objectives: Our goal was to assess the effectiveness of EUS-directed common bile duct (CBD) stone removal to compare its safety and effectiveness with ERCP-directed intervention. Design: interim results of a prospective, randomized, single-center blinded clinical trial. Setting: A single tertiary care referral center. Patients: Fifty-two patients with uncomplicated CBD stones were prospectively randomized to CBD cannulation and stone removal under EUS or ERCP guidance. Main Outcome Measurements and Interventions: Primary outcome measure was the rate of successful cannulation of the CBD. Secondary Outcome measures included Successful removal of stones and overall complication rates. Results: CBD cannulation followed by stone extraction was successful in 23 of 26 patients (88.5%) in the EUS group (1) versus 25 of 26 patients (96.2%) in the ERCP group (11) (95% CI, -27.65%, 9.88%). Overall, there were 3 complications in the EUS group and 4 complications in the ERCP group. Limitation: The current study is an interim report from a single center report and performed by a single operator. Conclusions: Our preliminary analysis indicates that Outcomes following EUS-guided CBD stone retrieval are equivalent to those following ERCP EUS-related adverse events are similar to those following ERCP. ERCP and EUS-guided stone retrieval appears to be equally effective for therapeutic interventions of the bile duct. Additional studies are required to validate these preliminary results and to determine predictors of success of EUS-guided stone removal. (Gastrointest Endosc 2009;69:238-43.)

Transvaginal ultrasound for diagnosis of deeply infiltrating endometriosis

Deeply infiltrating endometriosis is the clinical form of the disease that is generally associated with conditions of more intense pain and may require more complex surgical management, consequently resulting in greater risks to the patient. In recent years, various investigators have confirmed the usefulness of methods such as magnetic resonance imaging (MRI), transrectal ultrasound and transvaginal ultrasound (TVUS) for the diagnosis of deep endometriotic lesions. The objectives of the present study are to describe the method used to perform TVUS for the detection of deeply infiltrating endometriosis, and to discuss the clinical benefits that the data obtained may offer clinicians providing care for patients suspected of having this type of endometriosis. (C) 2008 International Federation of Gynecology and Obstetrics. Published by Elsevier Ireland Ltd. All rights reserved.

Ultrasound detection rate of single umbilical artery in the first trimester of pregnancy

Objective To determine accuracy of first trimester detection of single umbilical artery (SUA). Methods The number of vessels in the umbilical cord was examined in a prospective cohort of 779 singleton, low-risk, unselected pregnancies, in the first (11-13 weeks) and second (17-24 weeks) trimesters, using both power and color Doppler and after delivery, by placental histopathologic exam. Concordance between first and second trimester findings to postnatal diagnoses was compared by calculating kappa coefficients. Results There was medium concordance between the findings in the first trimester and the postnatal diagnoses (kappa = 0.52) and high concordance (kappa = 0.89) for the second trimester scan. Sensitivity, specificity, positive and negative predictive values for the findings in the first trimester were 57.1, 98.9, 50.0 and 99.2% and for the second trimester were 86.6, 99.9, 92.9 and 99.7%. Conclusion Sensitivity and positive predictive value of first trimester scan to identify an isolated SUA in a prospective unselected population was poor. Diagnosis of isolated SUA as well as a definitive judgment about the presence of associated anomalies would still require a scan in the second trimester. Copyright (C) 2011 John Wiley & Sons, Ltd.