bluuebunny/crossref_metadata_2025_split huggingface dataset:
Metabolic engineering and protein directed evolution increase the yield of L‐phenylalanine synthesized from glucose in Escherichia coli
Authors: Báez‐Viveros José Luis , Osuna Joel , Hernández‐Chávez Georgina , Soberón Xavier , Bolívar Francisco , Gosset Guillermo 
Published: July 2004

AbstractL‐phenylalanine (L‐Phe) is an aromatic amino acid with diverse commercial applications. Technologies for industrial microbial synthesis of L‐Phe using glucose as a starting raw material currently achieve a relatively low conversion yield (YPhe/Glc). The purpose of this work was to study the effect of PTS (phosphotransferase transport system) inactivation and overexpression of different versions of feedback inhibition resistant chorismate mutase‐prephenate dehydratase (CM‐PDT) on the yield (YPhe/Glc) and productivity of L‐Phe synthesized from glucose. The E. coli JM101 strain and its mutant derivative PB12 (PTS−Glc+ phenotype) were used as hosts. PB12 has an inactive PTS, but is capable of transporting and phosphorylating glucose by using an alternative system constituted by galactose permease (GalP) and glucokinase activities (Glk). JM101 and PB12 were transformed with three plasmids, harboring genes that encode for a feedback inhibition resistant DAHP synthase (aroGfbr), transketolase (tktA) and either a truncated CM‐PDT (pheAfbr) or its derived evolved genes (pheAev1 or pheAev2). Resting‐cells experiments with these engineered strains showed that JM101 and PB12 strains expressing either pheAev1 or pheAev2 genes produced l‐Phe from glucose with YPhe/Glc of 0.21 and 0.33 g/g, corresponding to 38 and 60% of the maximum theoretical yield (0.55 g/g), respectively. In addition, in both engineered strains the reached qPhe high levels of 40 mg/g‐dcw*h. The metabolic engineering strategy followed in this work, including a strain with an inactive PTS, resulted in a positive impact over the YPhe/Glc, enhancing it nearly 57% compared with its PTS+ counterpart. This is the first report wherein PTS inactivation was a successful strategy to improve the YPhe/Glc. © 2004 Wiley Periodicals, Inc.
Serum‐free large‐scale transient transfection of CHO cells
Authors: Derouazi Madiha , Girard Philippe , Van Tilborgh Frédéric , Iglesias Keyvan , Muller Natalie , Bertschinger Martin , Wurm Florian M. 
Published: July 2004

AbstractTo date, methods for large‐scale transient gene expression (TGE) in cultivated mammalian cells have focused on two transfection vehicles: polyethylenimine (PEI) and calcium phosphate (CaPi). Both have been shown to result in high transfection efficiencies at scales beyond 10 L. Unfortunately, both approaches yield higher levels of recombinant protein (r‐protein) in the presence of serum than in its absence. Since serum is a major cost factor and an obstacle to protein purification, our goal was to develop a large‐scale TGE process for Chinese hamster ovary (CHO) cells in the absence of serum. CHO‐DG44 cells were cultivated and transfected in a chemically defined medium using linear 25 kDa PEI as a transfection vehicle. Parameters that were optimized included the DNA amount, the DNA‐to‐PEI ratio, the timing and solution conditions for complex formation, the transfection medium, and the cell density at the time of transfection. The highest levels of r‐protein expression were observed when cultures at a density of 2.0 × 106 cells/ml were transfected with 2.5 μg/ml DNA in RPMI 1640 medium containing 25 mM HEPES at pH 7.1. The transfection complex was formed at a DNA:PEI ratio of 1:2 (w/w) in 150 mM NaCl with a 10‐min incubation at room temperature prior to addition to the culture. The procedure was scaled up for a 20‐L bioreactor, yielding expression levels of 10 mg/l for an intracellular protein and 8 mg/l for a secreted antibody. © 2004 Wiley Periodicals, Inc.
Study of dye decolorization in an immobilized laccase enzyme‐reactor using online spectroscopy
Authors: Kandelbauer Andreas , Maute Oliver , Kessler Rudolf W. , Erlacher Angelika , Gübitz Georg M. 
Published: July 2004

AbstractDecolorization of textile dyes by a laccase from Trametes modesta immobilized on γ‐aluminum oxide pellets was studied. An enzyme reactor was equipped with various UV/Vis spectroscopic sensors allowing the continuous online monitoring of the decolorization reactions. Decolorization of the dye solutions was followed via an immersion transmission probe. Adsorption processes were observed using diffuse reflectance measurements of the solid carrier material. Generally, immobilization of the laccase does not seem to sterically affect dye decolorization. A range of commercial textile dyes was screened for decolorization and it was found that the application of this enzymatic remediation system is not limited to a certain structural group of dyes. Anthrachinonic dyes (Lanaset Blue 2R, Terasil Pink 2GLA), some azo dyes, Indigo Carmine, and the triphenylmethane dye Crystal Violet were efficiently decolorized. However, the laccase displayed pronounced substrate specificities when a range of structurally related model azodyes was subjected to the biotransformation. Azodyes containing hydroxy groups in ortho or para position relative to the azo bond were preferentially oxidized. The reactor performance was studied more closely using Indigo Carmine. © 2004 Wiley Periodicals, Inc.
Development of a dedicated risk-adjustment scoring system for colorectal surgery (colorectal POSSUM)
Authors: Tekkis P P , Prytherch D R , Kocher H M , Senapati A , Poloniecki J D , Stamatakis J D , Windsor A C J 
Published: July 2004

Abstract

Background
The aim of the study was to develop a dedicated colorectal Physiological and Operative Severity Score for the enUmeration of Mortality and morbidity (CR-POSSUM) equation for predicting operative mortality, and to compare its performance with the Portsmouth (P)-POSSUM model.

Methods
Data were collected prospectively from 6883 patients undergoing colorectal surgery in 15 UK hospitals between 1993 and 2001. After excluding missing data and 93 patients who did not satisfy the inclusion criteria, 4632 patients (68·2 per cent) underwent elective surgery and 2107 had an emergency operation (31·0 per cent); 2437 operations (35·9 per cent) for malignant and 4267 (62·8 per cent) for non-malignant diseases were scored. Stepwise logistic regression analysis was used to develop an age-adjusted POSSUM model and a dedicated CR-POSSUM model. A 60 : 40 per cent split-sample validation technique was adopted for model development and testing. Observed and expected mortality rates were compared.

Results
The operative mortality rate for the series was 5·7 per cent (387 of 6790 patients) (elective operations 2·8 per cent; emergency surgery 12·0 per cent). The CR-POSSUM, age-adjusted POSSUM and P-POSSUM models had similar areas under the receiver–operator characteristic curves. Model calibration was similar for CR-POSSUM and age-adjusted POSSUM models, and superior to that for the P-POSSUM model. The CR-POSSUM model offered the best overall accuracy, with an observed: expected ratio of 1·000, 0·998 and 0·911 respectively (test population).

Conclusion
The CR-POSSUM model provided an accurate predictor of operative mortality. External validation is required in hospitals different from those in which the model was developed.
Pylorus-preserving pancreaticoduodenectomy for advanced duodenal disease in familial adenomatous polyposis
Authors: Gallagher M C , Shankar A , Groves C J , Russell R C G , Phillips R K S 
Published: July 2004

AbstractBackgroundAlthough only 5 per cent of patients with familial adenomatous polyposis (FAP) die from duodenal cancer, a recent study indicated that the mortality rate is much higher in patients with Spigelman stage IV disease. This has prompted an increased rate of referral for excisional surgery and an analysis of the results.MethodsBetween January 1994 and June 2002, 16 patients with FAP (mean age 55 years; eight men) were referred to a single surgeon for pylorus-preserving pancreaticoduodenal resection for Spigelman stage IV duodenal adenomatosis.ResultsOne patient died from multiple organ failure after relaparotomy for haemorrhage and a jejunal perforation; other major complications included anastomotic leak (one), primary haemorrhage (one), lymphatic leak (one), chylous ascites (one), pulmonary embolus (two) and prolonged delayed gastric emptying that required total parenteral nutrition (three). Overall there were 11 major complications in eight patients. Two patients developed insulin-dependent diabetes and one postprandial dumping. Postoperative histological examination revealed five unsuspected cancers, which led to four deaths within 3 years of surgery. One patient died 2 months after surgery from pulmonary thromboembolism and another at 5 months from an inoperable brain tumour. Nine of the 16 patients were alive and well at a mean of 38 months after surgery.ConclusionThe choice between continued endoscopic surveillance and excisional surgery for Spigelman stage IV duodenal disease remains finely balanced.
Functional and physiological outcome following transanal repair of rectocele
Authors: Heriot A G , Skull A , Kumar D 
Published: July 2004

Abstract

Background
Rectoceles are traditionally repaired transvaginally and sexual dysfunction can be a significant complication. The aim of this study was to evaluate the functional and physiological outcome following transanal repair of rectoceles.

Methods
Forty-five patients of mean age 57·1 (range 34–78) years with a symptomatic anterior rectocele, selected by contrast retention greater than 15 per cent on isotope defaecography, underwent transanal repair of rectocele. Preoperative and postoperative symptoms were assessed by means of a questionnaire. A proportion of patients underwent anorectal physiology and isotope defaecography before and after surgery.

Results
Median(range) follow-up was 24 (2–50) months. One patient developed a wound infection after surgery. Thirty-five patients reported an excellent, good or fair result, with seven reporting a moderate and three a poor result. There was a reduction in incomplete evacuation (P &lt; 0·001) confirmed by isotope defaecography (mean(s.d.) rectal emptying before surgery 57(14) per cent versus 76(9) per cent after surgery; P = 0·020), and a reduction in vaginal (P &lt; 0·001) and perineal (P = 0·004) digitation. Symptomatic feeling of prolapse (vaginal bulging) was significantly improved (P &lt; 0·001). There was no increase in incontinence (P = 0·688). Resting and squeeze anal canal pressures were unchanged after operation. Surgery did not result in sexual dysfunction.

Conclusion
Transanal repair of rectocele is a safe alternative to posterior colporrhaphy. It provides improvement in symptoms, reflected by anatomical improvement with minimal complications and no increase in dyspareunia.
Therapeutic strategy for signet ring cell carcinoma of the stomach
Authors: Kunisaki C , Shimada H , Nomura M , Matsuda G , Otsuka Y , Akiyama H 
Published: July 2004

AbstractBackgroundReports of clinicopathological characteristics and prognosis in patients with signet ring cell carcinoma (SRC) of the stomach are conflicting.MethodsA retrospective review was undertaken of 1450 patients with gastric cancer who had undergone gastrectomy. Of 1113 patients who underwent a curative gastrectomy, 174 had SRC (early, 120; advanced, 54) and 939 had other types of gastric carcinoma. Clinicopathological features, prognostic factors and surgical outcome in patients with SRC and non-SRC were compared.ResultsIn patients with early gastric cancer, age, histological type, and number and anatomical extent of lymph node metastases independently affected prognosis. Patients with SRC had a significantly better survival rate than those with non-SRC, although there was no difference in the extent or number of lymph node metastases. Mucosal tumours with a diameter of 40 mm or less and submucosal lesions with a diameter of 20 mm or less were not associated with lymph node metastasis. SRC in advanced disease was frequently poorly differentiated or scirrhous, but macroscopic appearance was not an independent prognostic factor.ConclusionEarly SRC of the stomach is associated with a better prognosis than non-SRC. Conversely, in advanced gastric cancer histological type cannot be used to establish a definitive therapeutic strategy.
Identifying cause of quality defect in cheese using qualitative variables in a statistical experimental design
Authors: Wikström Malin , Sjöström Michael 
Published: July 2004

AbstractStatistical experimental design was used to identify the stage or stages in a cheesemaking process that caused a quality defect. A full factorial design with five qualitative variables was constructed and a total of 32 experiments, each representing a unique combination of treatments, were then evaluated by a trained sensory panel. The average score for each sample was used as a response, and classical multiple linear regression (MLR) was used to find the relationship between the treatments (X) and the rate of quality defect (y). Evaluation of the design and the regression coefficients clearly showed that one of the factors, process step 3 (x3) at location B, was mainly responsible for high rates of the quality defect. In addition, process step 5 at location B, especially in combination with process step 2 or 4 at location A or step 3 at location B, increased the rate of quality defect in the cheese. The other factors had little or no effect. Copyright © 2004 John Wiley & Sons, Ltd.
Strategies for implementation and validation of on‐line models for multivariate monitoring and control of wood chip properties
Authors: Jonsson Pär , Sjöström Michael , Wallbäcks Lars , Antti Henrik 
Published: July 2004

AbstractHere we present an approach for on‐line control and monitoring of pulpwood chip properties based on near infrared (NIR) spectroscopy and multivariate data analysis. In addition, this paper suggests how to deal with large multivariate data sets in order to extract information which can be used as a basis for changes in raw material or process conditions in the drive towards more optimal intermediate or end product properties within the pulp and paper industry. The pulpwood chips used as raw material in a pulp and paper making process were characterized at‐ and on‐line using NIR spectroscopic measurements. Collected NIR spectra were used in multivariate calibration models for prediction of the moisture content as well as the between‐ and within‐species variation in the studied raw material. Statistical experimental design was used to form a calibration data set including most of the variation occurring in a ‘real’ on‐line situation. NIR spectra for all designed samples were measured at‐line and the estimated calibration models were used for carrying out predictions on‐line. Predictions of the moisture content (% dry weight) as well as the percentage contents of pine and sawmill chips in the raw material were carried out using partial least squares projections to latent structures (PLS) methodology. NIR spectra were collected subsequently on‐line once every minute, and, to reduce the problem with noise in the time series predictions, the measured signals were filtered using a moving average of 100 predicted values. This provided smoother predictions more suitable for process monitoring and control. To validate the quality of the predictions, wood chips from the studied process were sampled and analysed in the laboratory before being subjected to predictions in the on‐line model. Comparison of the filtered on‐line predictions with the results obtained from the laboratory measurements indicated that moisture and pine chip contents could be well predicted by the on‐line model, while predictions of sawmill chip content showed less promising results. Copyright © 2004 John Wiley & Sons, Ltd.
Potentialities of multivariate approaches in genome‐based cancer research: identification of candidate genes for new diagnostics by PLS discriminant analysis
Authors: Musumarra G. , Barresi V. , Condorelli D. F. , Fortuna C. G. , Scirè S. 
Published: July 2004

AbstractPartial least squares discriminant analysis (PLS‐DA) provides a sound statistical basis for the selection, from an original 9605‐data set, of a limited number of gene transcripts most effective in discriminating different tumour histotypes. The potentialities of the PLS‐DA approach are pointed out by its ability to identify genes which, according to current knowledge, are associated with cancer development. Moreover, PLS‐DA was able to identify MUC 13 and S100P proteins as candidates for the development of new colon cancer diagnostics. Various genes with unknown function and ESTs (expressed sequence tags), found to be important in discriminating genes for colon, leukaemia, renal and central nervous system tumour cells, are indicated as deserving high priority in future molecular studies. Copyright © 2004 John Wiley & Sons, Ltd.
Use of software to facilitate pharmaceutical formulation—experiences from a tablet formulation
Authors: Lindberg Nils‐Olof , Gabrielsson Jon 
Published: July 2004

AbstractThis paper exemplifies the benefits of using experimental design together with software to facilitate the formulation of a tablet for specific purposes, from screening to robustness testing. By applying a multivariate design for the screening experiments, many excipients were evaluated in comparatively few experiments. The formulation work was generally based on designed experiments. Most of the experiments were fractional or full factorial designs, generated and evaluated in Modde with the centre point replicated. The robustness of the formulation was evaluated with experimental designs on two different occasions. Tested flavours were found to have limited influence on the important responses, which was key information in order to proceed with that particular composition. The formulation was also robust towards normal batch‐to‐batch variation of the excipients and the active pharmaceutical ingredient. A process step was investigated and, by applying experimental design and keeping in mind previous findings, important information could be gained from the study. The different studies yielded good and very useful models. Established relationships between design factors and responses provided information that was vital for the project. In cases of poor models, essential information regarding robustness was obtained. Copyright © 2004 John Wiley & Sons, Ltd.
Onion design and its application to a pharmaceutical QSAR problem
Authors: Eriksson Lennart , Arnhold Thomas , Beck Bernd , Fox Thomas , Johansson Erik , Kriegl Jan M. 
Published: July 2004

AbstractStatistical molecular design (SMD) is an efficient tool for selecting informative, representative and diverse sets of molecular structures to be used in conjunction with QSAR, combinatorial technologies and other areas of research depending on optimization of molecular properties. Onion design represents a recent addition to the plethora of designs encountered in the SMD toolbox. It is a flexible design approach relying on a combination of the best properties of other design families, notably the model support property of D‐optimal design and the uniform coverage ability of space‐filling design. The onion design splits the candidate set into a number of subsets (‘shells’ or ‘layers’), and a D‐optimal selection is made from each shell. This makes it possible to select representative sets of molecular structures throughout any property space with reasonable design sizes. The number of selected molecules is easily controlled by varying (i) the number of shells and (ii) the model on which the design is based. The applicability of onion design to a pharmaceutical QSAR problem is reported. The example data set contains 967 drug‐like molecules. The biological activity under investigation is the inhibition of the major human drug‐metabolizing enzyme cytochrome P450 3A4. Onion design is used to select an informative training set. QSAR modeling is accomplished by means of multivariate data analysis tools. Copyright © 2004 John Wiley & Sons, Ltd.
Quantification of pollution levels by multiway modelling
Authors: Flåten Geir Rune , Grung Bjørn , Kvalheim Olav M. 
Published: July 2004

AbstractEnvironmental surveys are performed regularly in environmental monitoring of possible industrial pollution. The seabed pollution from industry in or near water, e.g. offshore oil production, can be biologically monitored as benthic species, and their diversity can be used as indicators of pollution. The community disturbance index (CDI) was recently proposed as a quantitative measure of pollution calculated from the benthic data. However, the CDI and other measurements are not optimal for quantifying the changes in level of environmental stress over several years. In this work it is suggested that the total environmental stress over several monitoring surveys can be determined by modelling the natural variation for a set of non‐polluted sites. The suggested approach uses a multiway method (Tucker3) to describe the natural variation, and the three‐way extension of CDI to quantify the pollution. Implicitly, the traditional soft independent modelling of class analogies (SIMCA) classification is extended to its three‐way counterpart. The proposed method is tested on the data from four subsequent surveys performed at the North Sea oil field Embla. Copyright © 2004 John Wiley & Sons, Ltd.
Peptide studies by means of principal properties of amino acids derived from MIF descriptors
Authors: Cruciani Gabriele , Baroni Massimo , Carosati Emanuele , Clementi Monica , Valigi Roberta , Clementi Sergio 
Published: July 2004

AbstractThe paper derives a new set of principal properties (PPs) for coded amino acids from GRID maps and experimental data. The three scales characterize side chains according to their polarity (PP1), size/hydrophobicity (PP2) and H‐bonding capability (PP3) and can be used profitably both for describing and designing peptide series. The new parameters are further used to develop modified auto‐ and cross‐covariance transforms which appear to be even more suitable for the stated goals, as they label each peptide according to its bonding capabilities. Copyright © 2004 John Wiley & Sons, Ltd.
Prediction and spectral profile estimation in multivariate calibration
Authors: Trygg Johan 
Published: July 2004

AbstractDirect and indirect calibration have been compared with respect to both prediction and model interpretation. This included their ability to estimate the pure spectral profile of each known constituent in a mixture of different metal–ion complexes. In the examples, the predictions by indirect calibration, represented by the PLS and O‐PLS methods, were consistently better than those of direct calibration, exemplified by the CLS method. It was further demonstrated that indirect calibration is equally capable to direct calibration in estimating the pure spectral profiles, as long as the unknown systematic variation is properly handled. A linear transformation of the regression coefficient matrix, given by K = B(BTB)−1, is all that is needed. Note that this does not only apply to spectral data, but any situation where the Y‐variables can be assumed to additively contribute to the variation in the X matrix. Throughout the examples, the O‐PLS method was able to maintain good spectral profile estimates and predictions. This indicates that O‐PLS may be the approach for simultaneous good prediction and interpretation of complex multivariate systems. Copyright © 2004 John Wiley & Sons, Ltd.