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Results for “protocol optimization”

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PubMed1999

Different phases of renal enhancement: role in detecting and characterizing renal masses during helical CT.

Although helical CT offers greater flexibility in data acquisition and reconstruction than does conventional axial CT, new opportunities for error must be understood so that optimal protocols are used that minimize the likelihood of misdiagnosis. Most nonrenal abdominal helical CT scans are obtained late in the corticomedullary phase of renal enhancement because of the preferable enhancement of other parenchymal organs. CT evaluation of the kidneys during the corticomedullary phase or at an intermediate phase between the corticomedullary and nephrographic phases has significant limitations. Therefore, dedicated renal CT performed for the detection of suspected renal masses or for the characterization of known renal masses must include images obtained during later phases of enhancement (i.e., nephrographic or excretory phase). Nephrographic or excretory phase images appear to be similar to one another but superior to corticomedullary phase images in the ability to both detect and characterize renal masses. Corticomedullary phase images should always be obtained when information about the renal vasculature is desired or when there is a possibility that a detected renal mass may represent an aneurysm or an arteriovenous malformation or fistula. Optimal technique of helical CT for staging renal cancers may require use of both corticomedullary and nephrographic or excretory phase images, although work in this area is still preliminary.

Artifacts↗

PubMed1999

Amplification of MelanA messenger RNA in addition to tyrosinase increases sensitivity of melanoma cell detection in peripheral blood and is associated with the clinical stage and prognosis of malignant melanoma.

An improved protocol for reverse transcription-polymerase chain reaction (RT-PCR), amplifying tyrosinase and MelanA/MART-1 mRNA from peripheral blood, was used to test 340 blood samples from 225 patients with malignant melanoma for the presence of circulating tumour cells. Positive results for tyrosinase or MelanA were obtained in 19% of patients in stage I (n = 74), 31% in stage II (n = 45), 29% in stage III (n = 48) and 52% in stage IV (n = 58). Amplification of MelanA in addition to tyrosinase resulted in a 30% enhanced sensitivity of melanoma cell detection compared with amplification of tyrosinase alone. The sensitivity was further enhanced by analysis of at least two blood samples per patient and performing at least two PCR analyses per sample. During a median follow-up of 4 months, patients with a positive PCR showed a 2. 4-fold increased risk for relapse compared with PCR-negative patients. These data indicate that the detection of circulating melanoma cells in peripheral blood using our optimized protocol for RT-PCR correlated with the clinical stage of disease and is therefore likely to be a prognostic marker for recurrence. MelanA is a sensitive additional marker to tyrosinase in detecting micrometastases using RT-PCR.

Adolescent↗

PubMed2003

Modelling a minimal residual disease-based treatment strategy in childhood acute lymphoblastic leukaemia.

The measurement of minimal residual disease (MRD) in childhood acute lymphoblastic leukaemia offers the promise of individualized, risk-stratified treatment, but an optimal protocol needs establishing. A model was developed to explore certain unanswered questions. The model assumes that all patients have MRD assessed after induction chemotherapy and children above a certain threshold are offered intensive chemotherapy. Using parameter estimates derived from published studies of MRD, the model predicted event-free survival (EFS) rates, relapse rates and treatment-related mortality for a cohort of children in the first presentation who were Philadelphia chromosome negative. Using the level of MRD after induction in order to decide on the use of intensive therapy resulted in an increase in EFS rates of up to 2.9 per 100 children, although if the error of the MRD measurement were too great, the benefit was almost nullified. Taking and analysing more than one marrow sample from the patient for the MRD measurement, in order to reduce sampling and measurement error, improved EFS by a further 1.1 patients per 100 treated, and decreased the number of patients offered intensive therapy by up to 2.6 per 100 treated. The optimal threshold for offering intensive therapy was in the range of 10-3.5- 10-4.5 cells if the intensive treatment-related mortality was 13-18% (allograft options), but 10-5- 10-6 cells if it was less than 8% (intensified chemotherapy). Using MRD to target patients at a high risk of relapse improved EFS rates, but the accuracy of measurements was of critical importance.

Antineoplastic Agents↗

PubMed1996

Group B streptococcus and pregnancy.

Group B streptococcus is a significant pathogen for both mother and child. routine urine culture in pregnancy will identify and allow treatment of women with asymptomatic bacteriuria. An optimal protocol for the prevention of neonatal sepsis has not yet been developed. While intrapartum antimicrobial prophylaxis appears to provide the best potential, each of the currently suggested protocols has significant drawbacks. Drawbacks include the potential for missing high-risk carriers, failure to treat a significant proportion of those destined to deliver an affected infant because no risk factors are present, and empirical treatment of a large proportion of the population in order to present significant disease in a few. Until an effective program of immunization becomes available, intrapartum prophylaxis of group B streptococcal carriers appears to offer the best hope of reducing the incidence of neonatal disease. Caregivers should adopt a uniform practice with regard to screening and prophylaxis. It is essential that any broad-based screening program include an evaluation of efficacy as well as complications including the development of new etiologic agents as causes of neonatal sepsis and the emergence of resistant bacteria. Further, mothers and newborns should be evaluated for drug adverse reactions and the impact of intrapartum prophylaxis on the use of prolonged empirical broad-spectrum antimicrobial therapy on the asymptomatic infant. Additional research is necessary regarding the required duration of therapy for optimal effect of intrapartum prophylaxis, the need for postnatal prophylaxis of the asymptomatic neonate, and the optimal agent for neonatal prophylaxis (penicillin versus broad-spectrum agents) if neonatal therapy is necessary after intrapartum prophylaxis.

Female↗

PubMed2003

[Endoluminal diode laser vein damage: preclinic study for vein insufficiency].

BACKGROUND: The ex-vivo phase of this research aims to define fibre laser activity ranges with the intent of using a safety protocol on the operating table to ensure maximum results in occluding the vein lumen with minimum necessary energy parameters. METHODS: The study was performed on 20 human saphenous veins removed during phlebological surgery. A 1 mm diameter optical fibre was inserted in the vein to the proximal extremity where administration of laser energy began along the vein axis. The veins were subdivided into three groups based on the parameters used: Group 1: treated with 20 Watt power; Group 2, treated with 15 Watt power; Group 3, treated with 10 Watt power. On conclusion of the procedure the veins were immersed in formalin and sent for histological examination. RESULTS: The greatest endothelial damage was observed in the group of veins treated with fluence above 300 J/cm(2), in which carbonisation of the endothelium was observed; in those treated with lower fluence (200-100 J/cm(2)) damage consisted in coagulation necrosis and interstitial oedema; at fluence of 100 J/cm(2) endothelial damage was less uniform. CONCLUSIONS: Experimental evidence would appear to support the hypothesis that the optimal protocol is below 300 J/cm(2) fluence with 15 Watt power and pulse train 100-300 ms.

Adult↗

PubMed1998

Incidence and impact of Clostridium difficile infection in the UK, 1993-1996.

Questionnaires were sent to 360 UK medical microbiologists to determine the incidence of Clostridium difficile infection in the UK between 1993-1996, and to establish the current laboratory testing protocols. Replies were received from 104 laboratories (29% response rate), 86, 7, 4 and 3% of which are in England, Scotland, Wales and Northern Ireland, respectively. The laboratories serve a total of approximately 90,000 hospital beds (median 750). C. difficile testing was performed by 83% of the laboratories, and 52, 45 and 31% used toxin A +/- B kits, cell cytotoxicity, and culture +/- isolate toxigenicity testing methods, respectively. Forty-seven percent of laboratories only performed testing when specifically requested, 19% if antibiotic use was stated, 15% tested all diarrhoeal specimens, and 14% examined all specimens except those from infants and community patients. The annual totals of positive C. difficile reports and cases increased from 3132 to 12,775, and from 1576 to 8211, respectively, between 1993-1996. In 1993 C. difficile infection caused ward closures in 5% of hospitals but 16% in 1996. Antibiotic policy changes, due to C. difficile infection, occurred in 21% of hospitals in 1996 compared with only 4% in 1993. C. difficile infection appears to be increasing markedly in the UK with major implications on hospital inpatient activity. Wide variations in laboratory selection and testing methods are likely to be masking the true epidemiology of C. difficile infection, and consensus is required on optimal protocols.

Aged↗

PubMed1997

Induction of superovulation in cyclic rats by administration of decreasing doses of recombinant follicle stimulating hormone (Org32489).

The objective of this study was to set up a superovulation protocol in adult cyclic rats by using recombinant human follicle stimulating hormone (rhFSH; Org32489). Good results were obtained by treatment with decreasing doses of rhFSH (2.5 to 0.5 IU) during the dioestrus period. The number of corpora lutea (CL) found in rats treated with this protocol was 43.5 +/- 3.4; this is more than three times the number in saline-treated control rats (13.0 +/- 0.4). Fertilization of oocytes after superovulation was as good as after normal ovulation in terms of number of 2-cell stage embryos found 2 days after mating. The absolute number of implantations was twice the number observed in saline-treated control rats (23.3 +/- 1.8 versus 10.6 +/- 0.5); therefore the number of implantations per CL was lower in superovulated rats. The serum concentrations of luteinizing hormone (LH), endogenous FSH and oestradiol-17beta were decreased during rhFSH treatment, while the inhibin serum concentration was increased. The progesterone serum concentration was increased on the days of pro-oestrus and oestrus after treatment. No difference was observed in the testosterone serum concentration. Pretreatment with 10 IU rhFSH at oestrus before giving the decreasing doses of rhFSH during dioestrus reduced the ovulatory response. Finally, treatment with a constant low dose of rhFSH instead of a decreasing dose of rhFSH did not result in spontaneous ovulation. However, ovulation induction by means of a human chorionic gonadotrophin bolus resulted in superovulation in six out of eight rats. It is concluded that superovulation in cyclic rats can be achieved using rhFSH treatment. However, it was found that the type of rhFSH regimen was very important to achieve appropriate stimulation. The optimal protocol was treatment with decreasing doses of rhFSH during dioestrus. The oocytes retrieved could be fertilized as well as oocytes of saline-treated control rats. The results also indicate that treatment with higher doses of rhFSH might induce a desensitization for FSH and LH.

Animals↗

PubMed1996

Temporal and molecular characteristics of lacZ mutations in somatic tissues of transgenic mice.

In order to help establish criteria for optimizing protocols for in vivo mutation studies, lacZ transgenic mice (Muta mouse) were treated with five consecutive daily doses of ethylnitrosourea (50 mg/kg), sampled at times up to 55 days after treatment, and mutant frequencies and DNA sequences determined for liver and bone marrow. In the bone marrow, the mutant frequency rose very rapidly in the first 5 days after treatment to 34 times the control frequency. Subsequently, there was a brood peak where the mutant frequency did not vary significantly, although it did appear to begin to decline after 45 days. In contrast, in the liver, the peak mutant frequency (11 times the control frequency) was not achieved until 35 days, after which there appeared to be a slow decline up to 55 days, which was not statistically significant. Once the maximum mutant frequency was reached, the mutation spectra in the two tissues were indistinguishable. In contrast to the G:C-->A:T transitions in 5'-CpG sites characteristic of untreated mice, A:T-->T:A transversions and A:T-->G:C transitions were prominent in both liver and bone marrow of ENU-treated mice, suggesting the involvement of unrepaired O2- and O4-ethylthymine adducts. In addition, G:C-->T:A transversions were induced in liver. This study demonstrates the possibility that although tissues may have different mutation fixation times, a single mutation fixation time equal to the longest time may be appropriate for in vivo mutation studies, provided that the mutation frequency does not decline appreciably after the peak is reached. This study also illustrates the necessity of ensuring that mutation characteristics are determined after optimal fixation has occurred.

Animals↗

PubMed1998

Different modalities of spa therapy for skin diseases at the Dead Sea area.

BACKGROUND: Balneology and spa therapy, although not accepted as well-established treatment modalities in dermatology, are used throughout the world. The therapeutic properties for skin and rheumatic diseases of the Dead Sea area may be attributed to unique climatic characteristics and unique natural resources. The mechanisms by which a broad spectrum of diseases are alleviated by spa therapy may involve mechanical, thermal, and chemical effects. OBJECTIVE: To review and discuss various spa therapy modalities, used at the Dead Sea area for a wide spectrum of skin diseases. CONCLUSIONS: Existing evidence indicates the therapeutic potential of Dead Sea spa therapy modalities for psoriasis and psoriatic arthritis. A beneficial effect is hinted at for other skin diseases, but the absence of relevant methodological and clinical information precludes the drawing of any scientific conclusions. It is essential to establish therapeutic guidelines to determine the optimal treatment modality for each disease, and the optimal protocol of each treatment component, adjusted individually for each patient, with respect to remission and long-term adverse effects.

Balneology↗

PubMed1999

Dual colour fluorescence in situ hybridization to paraffin-embedded samples to deduce the presence of the der(X)t(X;18)(p11.2;q11.2) and involvement of either the SSX1 or SSX2 gene: a diagnostic and prognostic aid for synovial sarcoma.

Identification of the t(X;18)(p11.2;q11.2) and the fusion gene products, SYT-SSX1 and SYT-SSX2, associated with a high proportion of synovial sarcomas, has been shown to be a useful diagnostic aid. This study demonstrates the application of dual colour fluorescence in situ hybridization to paraffin-embedded samples to deduce the presence of the derivative X chromosome and also the position of the breakpoint on chromosome X at either the SSX1 or the SSX2 gene. This used region specific markers from chromosomes X and 18 and an optimized protocol involving microwave exposure. Novel and rapid scoring criteria were validated which circumvented potential problems of nuclear truncation and defining cell boundaries. This involved blind analysis of two negative sarcoma samples and three synovial sarcomas in which corresponding frozen material had been previously shown to have the translocation involving different SSX genes. Six new cases diagnosed as synovial sarcoma were also analysed; two monophasic and two biphasic case were deduced to have a breakpoint in the SSX1 gene, one monophasic case an SSX2 breakpoint, and one case did not show rearrangement of the region. The ability to analyse formalin-fixed, paraffin-embedded samples in this way has practical implications for aiding the diagnosis of difficult cases, recently ascribed prognostic relevance, and allows further retrospective studies to be carried out. The methodology is also applicable to the identification of other tumour specific translocations in paraffin-embedded material.

Adult↗

PubMed1999

Electrohydrodynamically induced aggregation during constant and pulsed field capillary electrophoresis of DNA.

We present a study aimed at understanding the factors affecting the separation of large DNA molecules by capillary electrophoresis in polymer solutions. In a first series of experiments, a systematic study of the effect of operational parameters on the development of an electrohydrodynamic instability resulting in DNA aggregation and spurious peaks in the electropherograms is presented. The results are discussed in regard to a recent theory of electrohydrodynamic instabilities in macroion suspensions, recently proposed by Isambert et al. Overall, the results provide strong support to the theory. Some situations of interest for applications, and not explicitly considered in the theory, such as asymmetric field pulsing and the use of polymer additives in the buffer, were also considered. Furthermore, robust optimized protocols for high resolution separation of DNA in the range of 100 base pairs to 160 kilobase pairs, are proposed. As predicted by the model, it is shown that using a concentrated isoelectric buffer (histidine) strongly reduces aggregation as compared to the use of a conventional buffer at the same concentration, and allows separation of DNA from 100 bp to 160 kbp in less than 10 min. We also present a systematic study of the dependence of the mobility vs DNA size, pulse frequency, and field strength. The results are discussed with respect to the Biased Reptation with Fluctuations model and a good agreement is obtained. Copyright 1999 John Wiley & Sons, Inc.

Journal Article↗

PubMedDate not supplied

Concentration of viral vectors by co-precipitation with calcium phosphate.

BACKGROUND: The envelope glycoproteins, surface unit (SU) and transmembrane (TM) of the murine leukemia virus (MLV) are not covalently linked and tend to dissociate upon high-speed centrifugation, leading to loss of vector infectivity. This study describes a gentle and simple method to concentrate MLV vectors or HIV vectors pseudotyped with MLV envelopes. Having a fast and inexpensive method to concentrate large volumes of vector supernatant will facilitate in vivo experiments and clinical trials that require high titer vector stocks. METHODS: The methods employed in the study were co-precipitation of viral supernatant with calcium phosphate, low-speed centrifugation, dialysis, and infection assays with Lac-Z transducing vectors. RESULTS: Murine leukemia virus vectors and HIV vectors pseudotyped with vesicular stomatitis virus glycoprotein (VSV.G) or MLV envelopes were concentrated successfully using the calcium phosphate co-precipitation method. Parameters that influence virus yield and the reproducibility of the method were investigated. The optimized protocol involves virus harvest in serum-free media, co-precipitation using 60mM calcium chloride, pelleting at 2,000 g, resuspending the pellet in a small volume of 0.1M EDTA-saline, and dialysis against saline to remove EDTA. Volumes were decreased from 300 ml to 10 ml, with 50-100% recovery, and titers can be concentrated up to 1,000-fold. CONCLUSIONS: The calcium phosphate co-precipitation method to concentrate virus is applicable to retrovirus and lentivirus preparations. It uses simple techniques and does not require expensive equipment. Multiple rounds of co-precipitation can be carried out if required.

Animals↗

PubMed2002

Multiwell in-gel protein digestion and microscale sample preparation for protein identification by mass spectrometry.

In-gel peptide digestion has become a widely used technique for characterizing proteins resolved by two-dimensional gel electrophoresis. Peptides generated from gel pieces are frequently contaminated with detergent and salts. Prior to matrix-assisted laser desorption/ionization-time of flight mass spectrometry analysis, these contaminants are removed using micro scale C18 sample preparation columns. In this paper, data are presented to demonstrate the application of a solvent resistant MultiScreen 96-well plate with a low peptide binding membrane and ZipTip micropipette based sample preparation. Recoveries of peptides (m/z of 1000 to 5000 Da) derived from standard protein protease digests, were estimated at various stages of the analytical process. An optimized protocol has been established and all the reagents and consumables have been packaged in a ready to use commercial kit. Data will be presented to show the application of this technology package to accelerate the throughput of protein characterization by protease fragmentation.

Blood Protein Electrophoresis↗

PubMed2002

Bioprocess applications of a Sindbis virus-based temperature-inducible expression system.

The production and study of toxic proteins requires inducible expression systems with low basal level expression and high inducibility. Here, we describe bioprocess applications of the pCytTS temperature-regulatable Sindbis virus replicon-based expression system. We used green fluorescent protein as a marker protein to optimize the selection of stable transfected clones with increased expression levels. Using the optimized protocol, clones were constructed that produced the growth-inhibiting, anti-viral protein interferon beta (beta-IFN). Selected clones were analyzed for temperature-dependent beta-IFN production in adherent and suspension cultures in serum free medium. Specific expression levels were around 1.0 x 10(5) IU/10(6) cells/day (0.5 microg/10(6) cells/day) in suspension cultures and over 1.5 x 10(6) IU/mL/day (7.5 microg/mL/day) in hollow fiber reactors using adherent cells. Hexahistidine-tagged beta-IFN purified from T-flask cultures was highly glycosylated and showed high specific activity. beta-IFN mRNA amplified by the viral replicase for 10 days did not show an accumulation of mutations. These data suggest the applicability of the pCytTS-inducible expression system for the production of high-quality glycoproteins in different reactors.

Animals↗

PubMedDate not supplied

Contrast-to-noise ratio in functional MRI of relative cerebral blood volume with sprodiamide injection.

The purpose of this study was to investigate the dependence of contrast-to-noise ratio (CNR) on the dose and rate of sprodiamide injection in magnetic resonance relative cerebral blood volume (rCBV) imaging. rCBV maps for 35 normal volunteers were constructed from dynamic MR image sets acquired with echo-planar spin-echo imaging after intravenous injection of sprodiamide. Doses of .1, .2, and .3 mmol/kg, at rates of 2 ml/second and 5 ml/second, were tested. CNRs and blood/volume ratios of gray to white matter were computed. CNR depended on dose (P < .0001) but was independent of injection rate (P < .69). rCBV ratios of gray to white matter were dose independent (P < .38) and rate independent (P < .97). The dependence of CNR on dose, but not injection rate, has practical implications in optimal protocol design. The independence of gray/white ratios supports the theory underlying the generation of rCBV maps.

Adult↗

PubMed1992

Liver tissue characterization by in vitro NMR: tissue handling and biological variation.

The extraction of reliable and useful relaxation time data for tissue characterization by NMR requires strict protocols, optimized for each type of biological tissue, which include parameters like storage duration and temperature as well as measurement parameters. Spin-lattice relaxation times in liver tissue vary not only with NMR frequency but also with their "time-after-excision characteristics," while spin-spin relaxation times are almost independent of most parameters which influence T1 at 20 MHz in normal liver tissue (e.g., species, sex, circadian rythm, starvation). T2, however, being more sensitive to water content and pH changes, is well suited for detecting nonspecific tissue alterations (e.g., due to ischemia, chemical toxins). Following the suggestions outlined herein, investigation of at least 120 min of time-after-excision (storage) effects allows the significant distinguishing of various physiological differences in normal liver tissue as well as improvement of early detection of liver pathologies.

Animals↗

PubMed1992

Optimization of non-isotopic in situ hybridization on formalin-fixed, paraffin-embedded material using digoxigenin-labelled probes and transgenic tissues.

The sensitivity of non-isotopic in situ hybridization (NISH), particularly on formalin-fixed, paraffin-embedded (FFPE) clinical tissues, has been the subject of controversy. Generally, NISH has been regarded as being less sensitive than radiolabelled procedures, although some reports have contradicted this. Accordingly, tissues from mice which were transgenic for variable amounts of the human alpha-1-antitrypsin gene were used to optimize the NISH procedure and to estimate the sensitivity. This approach showed that prolonged incubation of slides in final substrate resulted in high sensitivity--about 13 kb of target DNA. However, this prolonged incubation crucially depended on achieving minimal non-specific background staining. Many factors affected the degree of background staining, but five were particularly important. First, the method of mounting cut sections onto slides. Second, the length of the probe (ideally less than 400 bp). Third, the procedure for proteolytic digestion. Fourth, the denaturation technique, and fifth, the quality of the dextran sulphate used in the hybridization mix. The optimized protocol showed variable patterns of mRNA distribution in the transgenic mouse livers, while DNA distribution appeared uniform.

Animals↗

PubMed2001

Optimization of quartz tube pyrolysis atmospheric pressure ionization mass spectrometry for the generation of bacterial biomarkers.

Experimental procedures were investigated to improve the efflux of biomolecule pyrolyzates from quartz tube pyrolysis under atmospheric pressure ionization mass spectrometry conditions. Heating regimes, airflows, and ion focusing parameters were optimized to increase the informative mass spectral signals generated from the pyrolysis of Gram-positive bacterial spores and vegetative cells. Dipicolinic acid (DPA) is found in 5-15% by weight in Gram-positive Bacillus spores, and the parameter optimization procedures provided an intense mass spectral signature of the m/z 168 protonated DPA molecule with a minimization of pyrolytic and ionization fragments. Moreover, mass spectral information from the optimization protocols yielded peaks and mass patterns characteristic of DNA and RNA nitrogen bases, protein diketopiperazines, and amino sugars.

Bacillus↗