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PubMed1992

Influence of the membrane surface on glycolipid conformation and dynamics. An interpretation of NMR results using conformational energy calculations.

Glycolipids constitute an important class of biomolecules that are involved in biomolecular recognition. The importance of carbohydrate head group conformation in such processes is well recognized. Glycolipids typically occur as minor components of the complex heterogeneous matrix of a biological membrane. As a result, the membrane surface may not only influence head group conformation but also serves as a spatial frame in which the glycolipid is oriented and recognized. In this study, conformational energy calculations have been used to assess the conformational space available to the glucose head group of 1,2-di-O-tetradecyl-3-O-(beta-D-glucopyranosyl)-sn-glycerol (beta-DTGL) in a liquid-crystalline membrane matrix. 2H NMR quadrupolar splittings are calculated and compared with those observed experimentally. This study demonstrates the importance of including surface interactions when considering the conformational space accessible to cell surface carbohydrates. The empirical approach taken here provides considerable insight at the molecular level, and offers the possibility of exploring even more complex systems.

Cell Membrane↗

PubMed2000

Optimization of adenosine deaminase assay by response surface methodology.

The effect of four variables (adenosine, glutamate dehydrogenase, phosphate buffer, and pH) on the measured catalytic concentration of adenosine deaminase (EC 3.5.4.4) was studied by Response Surface Methodology (RSM). This multivariate methodology offers an empirical approach to the study of enzyme assays and allows to detect the interaction between different variables of the system. Response-surface data showed maximum adenosine deaminase catalytic concentration at pH 7.2, adenosine 20 mmol/l, phosphate buffer 200 mmol/l and glutamate dehydrogenase 850 mu kat/l when pleural fluids were used as samples. Optimum conditions for a material containing purified adenosine deaminase from human erythrocytes differed only slightly from that obtained for the pleural fluid.

Adenosine↗

PubMed2002

[Community-acquired pneumonia: serum adenosine-deaminase activity in the aetiological diagnosis].

BACKGROUND: Adenosine deaminase (ADA) is a cytoplasmic enzyme which activity is increased in disorders that stimulate cells involved in the immune system. In community-acquired pneumonia (CAP), increased levels of serum ADA have been associated with the presence of atypical microorganisms as the source of the former. Previous studies have shown ADA increases in non-infectious diseases. We evaluated the factors that may influence plasmatic ADA (ADAp) levels in CAP patients. PATIENTS AND METHODS: A study with cases (245 episodes of CAP) and controls (49) was designed, and the differences in ADAp activity with regard to organisms, comorbidity factors and complications were analyzed. A logistic regression analysis was performed. RESULTS: CAP caused by atypical microorganisms were found to have increased ADAp values. Variables that independently increased ADAp levels were: atypical etiology (OR = 5.9), liver disease (OR = 5.8), diabetes mellitus (OR = 1.9), and prior antibiotic consumption (OR = 1.7). CONCLUSIONS: ADAp is an etiologic marker that could be useful in the empiric approach of the treatment of CAP.

Adenosine Deaminase↗

PubMed2001

Filtration behaviors of Giardia and Cryptosporidium--ionic strength and pH effects.

The laboratory-scale filtration tests of Giardia cysts and Cryptosporidium oocysts in both 2 mm-phi glass beads and 2 mm-phi polystyrene beads filters were conducted to investigate their filtration behaviors. The protozoan parasites were used as target particles, while the chemical system altered by changing the electrolyte concentration and pH. The results significantly indicate that ionic strength have a positive effect on the removal efficiencies for Giardia cysts and Cryptosporidium oocysts. The removal efficiency of two filters for Giardia cysts slightly decreased from pH 2.4 to 8.7 and decreased significantly in pH as pH up to 8.7, while that for Cryptosporidium slightly rippled beyond pH 8.7, and with the decrease in pH up to pH 8.7. The experimental collision efficiencies from the interactions between colloids and the filter media were calculated with a semi-empirical approach of the single sphere model and clean-bed filtration theory. The results also indicated that experimental collision efficiencies for (oo)cysts corresponded to the (oo)cysts removal efficiencies in all trials, and oocysts exhibits higher collision efficiencies than cysts.

Animals↗

PubMed2002

Incorporation of inorganic material in anoxic/aerobic-activated sludge system mixed liquor.

In the bioreactor of the nitrification denitrification (ND)-activated sludge system, the mixed liquor is made up of organic and inorganic materials. In the current design procedures and simulation models, the influent wastewater characteristics and biological processes that influence the bioreactor mixed liquor organic solids (as volatile suspended solids, VSS, or COD) are explicitly included. However, the mixed liquor total suspended solids (TSS, i.e. organic + inorganic solids) are calculated simply from empirical ratios of VSS/TSS. The TSS concentration is fundamental in the design of secondary settling tanks and waste activated sludge disposal. Clearly, the empirical approach to obtaining an estimate for TSS is not satisfactory within the framework of a fundamentally based model. Accordingly, the incorporation of the inorganic material present in the influent wastewater into ND-activated sludge system mixed liquor was investigated. From an experimental investigation into the distribution of inorganics in the influent, mixed liquor and effluent of a laboratory-scale ND-activated sludge system, it was concluded inter alia that (i) of the total inorganic solids in the influent, only a small fraction (2.8-7.5%) is incorporated into the mixed liquor, (ii) most of the inorganics in the influent (mean 88%) and effluent (mean 98.5%) are in the dissolved form, the balance being particulate, and (iii) the influent and effluent inorganic dissolved solids concentrations are closely equal (mean effluent to influent ratio 100%). Further, a number of models were developed to quantify the mixed liquor inorganic, and, hence, total solids. From an evaluation of these models against the experimental data, it would appear that the best approach to model the incorporation of inorganics into the activated sludge mixed liquor is to follow the concepts and principles used to develop the existing models for organic materials. With this approach, reasonably close correlation between predicted and measured data for mixed liquor and effluent inorganic concentrations were obtained.

Bioreactors↗

PubMed2002

Multi-metallic modelling for biosorption of binary systems.

In this paper a specially propagated biomass of Sphaerotilus natans was tested as adsorbent for binary solutions of Cu-Cd, Cu-Pb and Cu--Zn at different equilibrium pH. The experimental results outline the buffering effect of H+ at low pH. which masks the competition among metals. In each binary system the biomass affinity follows the acidic properties of the heavy metals probably due to an ionic exchange mechanism operating among active sites and metals in solution. The experimental results were fitted according to an empirical approach with growing complexity that outlines the inadequacy of the predictive models and the non-ideal interactions among metals.

Adsorption↗

PubMed2001

Detecting chlorophyll, Secchi disk depth and surface temperature in a sub-alpine lake using Landsat imagery.

Some bio-physical parameters, such as chlorophyll a concentration, Secchi disk depth and water surface temperature were mapped in the sub-alpine Lake Iseo (Italy) using Landsat Thematic Mapper (TM) data acquired on the 7 March 1997. In order to adequately investigate the water-leaving radiance, TM data were atmospherically corrected using a partially image-based method, and the atmospheric transmittance was measured in synchrony with the satellite passage. An empirical approach of relating atmospherically corrected TM spectral reflectance values to in situ measurements, collected during the satellite data acquisition, was used. The models developed were used to map the chlorophyll concentration and Secchi disk depth throughout the lake. Both models gave high determination coefficients (R2 = 0.99 for chlorophyll and R2 = 0.85 for the Secchi disk) and the spatial distribution of chlorophyll concentration and Secchi disk depth was mapped with contour intervals of 1 mg/m3 and 1 m, respectively. A scene-independent procedure was used to derive the surface temperature of the lake from the TM data with a root mean square error of 0.3 degrees C.

Atmosphere↗

PubMed1989

Understanding maps as symbols: the development of map concepts in children.

We expect that many readers encountered this article with the beliefs that maps are highly specialized devices primarily used for wayfinding; that they represent the spatial world in a single, correct form; that they are readily transparent; and that their sole contribution to psychology is their role in externalizing environmental cognition. By discussing the myriad functions and forms of maps, by highlighting their symbolic nature, and by considering some of the misconceptions about maps, we have attempted to demonstrate the value of maps for addressing a wide range of developmental questions. Our review of past research literature suggests that research conducted within individual disciplines has both strengths and limitations. Work in the psychological tradition is characterized by attention to important subject characteristics and to carefully described and implemented research designs, procedures, coding, and analyses. At the same time, this work reveals, at best, highly restricted views about maps, and at worst, fundamental misconceptions about maps. Work in the geographic and environmental traditions, in contrast, samples a broader range of map forms and functions, but it suffers from inattention to procedural details that makes the conclusions less compelling than they might otherwise be. A conventional wisdom is emerging from the work in both traditions: That children's map understanding occurs extremely early and extremely easily. The limitations of both research traditions, however, suggest the need for caution in accepting this view. Developmental and cartographic theories provide a compelling reason to reexamine the early and easy view and suggest the need for alternative conceptual and empirical approaches. We have argued that future work should integrate the traditions of psychology and geography. Illustrative data from an interdisciplinary program of research were presented. We described work demonstrating the gradual and difficult process of mastering the representational and geometric correspondences that link the map to its referent in the world. Our data suggest that there are significant achievements in map conceptualization (the understanding of the concept of a map), map identification (understanding the formal components of a map), and map utilization (the ability to use maps). Our data support the view that maps are not transparent and that children's abilities to understand, use, and create maps are linked to their developing representational and spatial skills. In concluding, we should acknowledge that we have deliberately pushed interpretations about understanding maps as symbolic representations to the extreme. The reason for this strategy is simple: We believe that work on maps--both in the public schools and in academia--is assumed to be an expendable and irrelevant luxury.(ABSTRACT TRUNCATED AT 400 WORDS)

Child Development↗

PubMed2004

Theories of visual awareness.

The past decade has provided a wealth of data for theorists of visual awareness. Two empirical approaches, both seeking to dissociate conscious from unconscious neural processes, have been particularly fruitful. The first has focused on the neural correlates of changes in experience occurring in the absence of change in external stimuli, for example during binocular rivalry; the second has investigated the neural correlates of unconscious processes such as blindsight. Several of the theories based on these data propose that visual consciousness arises from interactions between thalamo-cortical modules whose independent operation is unconscious; popular candidate 'modules' include visual regions in the 'ventral' visual pathway and parieto-frontal regions associated with action planning. These theories can be tested against recent findings from patients in the vegetative state, a state of 'wakefulness without awareness', which can follow major insults to the brain. The findings indicate that stimulus-evoked cortical activity occurs in the vegetative state, but tends to be limited in extent, is often restricted to primary sensory areas, and is poorly integrated with activity elsewhere in the cerebrum. The theories of visual awareness reviewed previously predict that such activity should not give rise to visual experience. This prediction is reassuring, but can we be sure that it is correct? Reflection on the indirect nature of the evidence available to theorists of visual awareness makes it doubtful that we can confidently specify the minimum conditions for awareness, unless we are prepared to modify our everyday concept of consciousness. O'Regan and Noe have recently proposed a sophisticated redefinition of visual awareness along these lines. Progress at this frontier of visual neuroscience requires that scientists and philosophers join forces to clarify the concepts of experience and consciousness.

Awareness↗

PubMed1998

Molecular basis of vaccination.

Vaccines represent the most cost-effective means to prevent infectious diseases. Most of the vaccines which are currently available were developed long before the era of molecular biology and biotechnology. They were obtained following empirical approaches leading to the inactivation or to the attenuation of microorganisms, without any knowledge neither of the mechanisms of pathogenesis of the disease they were expected to protect from, nor of the immune responses elicited by the infectious agents or by the vaccine itself. The past two decades have seen an impressive progress in the field of immunology and molecular biology, which have allowed a better understanding of the interactions occurring between microbes and their hosts. This basic knowledge has represented an impetus towards the generation of better vaccines and the development of new vaccines. In this monograph we briefly summarize some of the most important biotechnological approaches that are currently followed in the development of new vaccines, and provide details on an approach to vaccine development: the genetic detoxification of bacterial toxins. Such an approach has been particularly successful in the rational design of a new vaccine against pertussis, which has been shown to be extremely efficacious and safe. It has been applied to the construction of powerful mucosal adjuvants, for administration of vaccines at mucosal surfaces.

Adjuvants, Immunologic↗

PubMed2003

Genome-based design of a cell-free culture medium for Tropheryma whipplei.

Empirical approaches have guided the development of bacterial cultures. The availability of sequenced genomes now provides opportunities to define culture media for growth of fastidious pathogens with computer modelling of metabolic networks. A key issue is the possibility of growing host-dependent bacteria in cell-free conditions. The sequenced Tropheryma whipplei genome was analysed to identify specific metabolic deficiencies. We used this information to design a comprehensive medium that allowed three established T whipplei strains from culture with human cells and one new strain from a clinical sample to grow axenically. Genomic information can, therefore, provide sufficient clues for designing axenic media for fastidious and uncultured pathogens.

Actinomycetales↗

PubMed1992

The decline in new drug development.

The future depends on innovation, not imitation. New drug development can be encouraged in a number of ways (Table 4), and the rewards are great. Who knows what dramatic drug discoveries remain to be found in a new synthetic compound, a fresh soil sample, or a plant obtained from some pristine forest? In any event, let us all hope that the molecular roulette that has governed drug development in the past will be replaced by a more rational, and less empirical, approach.

Chemistry, Pharmaceutical↗

PubMed2003

Relationships among measures of treatment outcome in depressed patients.

BACKGROUND: Studies attempting to identify predictors of antidepressant response in patients with major depression have reported inconsistent results. One explanation may be the different definitions of outcome used. METHODS: 187 depressed subjects were recruited and were randomised to treatment with fluoxetine and nortriptyline. At baseline and 6 weeks, subjects completed Hamilton Depression Rating Scale HDRS-17 and 27, Montgomery Asberg Depression Rating Scale (MADRS), the Hopkins Symptom Checklist (SCL-90) and the Social Adjustment Scale (SAS) as well as the Clinical Global Impression Scale (CGI). Relationships among outcome measures were assessed. Receiver Operator Characteristic (ROC curves) were used to show the diagnostic ability of the MADRS and HDRS in predicting the clinician's rating. RESULTS: All outcome measures were moderately to highly correlated. All measures were significantly related to the clinician's global impression, but the strongest associations were with the MADRS score. Using ROC curves we showed that a score of 8 on the HDRS or 14 on the MADRS was the optimal compromise between sensitivity and specificity in dividing this sample into responders and non-responders. A 60% reduction in HDRS and MADRS scores rather than a 50% reduction appeared the most valid division between responders and non-responders. LIMITATIONS: We relied on clinician judgement as the validating criterion. The results only apply to a sample of moderately depressed outpatients. CONCLUSIONS: The MADRS score seemed to most accurately reflect a clinician's impression of change. Dividing a sample into responders and non-responders can be approached empirically.

Adult↗

PubMed2003

Comprehensive detection of bacterial populations by PCR amplification of the 16S-23S rRNA spacer region.

PCR amplification of the spacer region between the 16S and 23S rRNA genes is commonly employed for the analysis of bacterial communities. In this analysis, the intergenic spacers are amplified by PCR using primers complementary to conserved regions in the 3' 16S rDNA and 5' 23S rDNA. By this method, the observation of every bacterial population may be limited by several causes. To explore the extent of bacterial populations overlooked by this method, we have used an empirical approach. In a sample containing about 50 colonies, we tested the capability to amplify by PCR the spacers from each colony. We also examined the ability to observe the spacers from each colony in the product obtained after amplification of the DNA extracted from the whole sample, as it is usually performed by this method. Contrarily to our expectations that a significant fraction of colonies would not yield amplification products, spacers were successfully amplified from every colony of two different samples examined. Overall, our results suggest that in spite of well-based theoretical limitations, the analysis of bacterial communities by amplification of the spacer regions can render a comprehensive representation of the more abundant bacterial clades in the sample.

Bacteria↗

PubMed2003

Organ motion, set-up variation and treatment margins in radical radiotherapy of urinary bladder cancer.

BACKGROUND AND PURPOSE: A major challenge in conformal radiotherapy of bladder cancer is to determine adequate treatment margins. For this purpose, we therefore quantified the internal motion of the urinary bladder as well as the external patient set-up variation during a course of fractionated radiotherapy. In the light of the recently introduced ICRU-62 concept, the planning organ at risk volume, we also studied the internal motion of nearby organs at risk, the rectum and intestine. MATERIAL AND METHODS: Weekly CT scans and electronic portal images (EPIs) were sampled from 20 patients during radical, conformal bladder irradiation (60-64 Gy/2 Gy in five fractions weekly). The planning scans were acquired with 70 ml of bladder contrast instilled, and patients were instructed to void before the treatment/repeat scanning sessions. Internal motion of the bladder, rectum and intestine was measured by 3-D image matching of the repeat scans to the patients' planning scans. Internal margins (CTV-to-ITV) were determined using both a direct empirical approach and an analytically derived margin recipe. The external patient set-up variability was determined by 2-D matching of front and lateral EPIs to corresponding digitally reconstructed radiographs. RESULTS: A total of 149 CT scans (20 for planning, 129 during the treatment course) and 133 sets of EPIs were analysed. Bladder volumes were smaller during treatment than in the planning situation in 85% of the repeat scans. Nevertheless, we found the repeat scan bladder volumes to extend outside the planning scan bladder contours in 89% of the scans, on average with 9% of the volume (range: 0-47%). Eight patients (40%) had at least one repeat scan (25 scans in total) where displacements >15 mm were observed at one or more sides of the bladder. CTV-to-ITV margins of 10 mm inferior, 20 mm superior, 11 mm left, 8 mm right, 20 mm anterior and 14 mm posterior were required to simultaneously encompass all bladder deflections except for the largest outward deflection in all directions in 84% of the patients. Including patient set-up variation (CTV-to-PTV), we found that an additional safety margin of 2-6 mm had to be added in the various directions. The rectum expanded outside the planning contours in all repeat scans, on average with 24% of the volume (range: 2-69%). The volume of intestine found close to the bladder were significantly and negatively correlated to the bladder volume in almost half of the patients. CONCLUSION: This study documented both a large internal motion of the bladder and a substantial patient set-up variation. Our current treatment margins have been adjusted according to the findings of this study. Considerable variation in position and volume of the rectum and intestine was also documented.

Aged↗

PubMed2002

DNA repair and cisplatin resistance in non-small-cell lung cancer.

The results of cisplatin-based chemotherapy seem to have reached a plateau, and empirical approaches are targeting the inclusion of novel biological agents with different mechanisms of action, but their clinical benefit is still unknown. In preparing this review of cisplatin resistance, we posed two questions: Who are we writing for and why? We believe that medical oncologists should be involved in the reality of the growing list of genetic mechanisms of cancer and chemoresistance. Only by becoming familiar with these mechanisms will we be able to circumvent them. In this review, we provide some insight into DNA repair defects involved in non-small-cell lung cancer (NSCLC) and cisplatin effect. Some DNA repair genes, like ERCC1, have been shown to be crucial in predicting cisplatin resistance and can be used for tailoring cisplatin-based chemotherapy.

Antineoplastic Agents↗

PubMed2002

Future pharmacotherapy for post-traumatic stress disorder: prevention and treatment.

I have presented two complementary lines of speculation in this article. First, I have presented a public health model of resilience, prevention, acute intervention, and tertiary treatment to inform a pharmacotherapeutic strategy for PTSD in the future. Second, I have proposed a rational rather than an empirical approach to the clinical pharmacology of PTSD. Such an approach suggests that efforts be directed toward the development and testing of new classes of drugs designed to target the unique pathophysiology of PTSD.

Adrenergic Agents↗

PubMed2001

What are the limits of adjuvanticity?

Vaccines developed traditionally following empirical approaches have often limited problems of immunogenicity, probably due to the low level of purity of the active component(s) they contain. The application of new technologies to vaccine development is leading to the production of purer (e.g. recombinant) antigens which, however, tend to have a poorer immunogenicity as compared to vaccines of the previous generation. The search for new vaccine adjuvants involves issues related to their potential limits. Since the introduction of aluminium salts as vaccine adjuvants more than 70 years ago, only one adjuvant has been licensed for human use. The development of some of these new vaccine adjuvants has been hampered by their inacceptable reactogenicity. In addition, some adjuvants work strongly with some antigens but not with others, thus, limiting their potentially widespread use. The need to deliver vaccines via alternative routes of administration (e.g. the mucosal routes) in order to enhance their efficacy and compliance has set new requirements in basic and applied research to evaluate their efficacy and safety. Cholera toxin (CT) and labile enterotoxin (LT) mutants given along with intranasal or oral vaccines are strong candidates as mucosal adjuvants. Their potential reactogenicity is still matter of discussions, although available data support the notion that the effects due to their binding to the cells and those due to the enzymatic activity can be kept separated. Finally, adjuvanticity is more often evaluated in terms of antigen-specific antibody titers induced after parenteral immunization. It is known that, in many instances, antigen-specific antibody titers do not correlate with protection. In addition, very little is known on parameters of cell-mediated immunity which could be considered as surrogates of protection. Tailoring of new adjuvants for the development of vaccines with improved immunogenicity/efficacy and reduced reactogenicity will represent one of the major challenges of the ongoing vaccine-oriented research.

Adjuvants, Immunologic↗