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PubMed2006

Chemometrical investigation of the presence and distribution of organochlorine and polyaromatic compounds in sediments of the Ebro River Basin.

A multivariate statistical data analysis, using principal component analysis, of historical data from 1996 to 2003 concerning the concentration of different polycyclic aromatic hydrocarbons and organochlorine compounds in sediment samples from different sampling sites of the Ebro River Basin was performed under the UE funded project AQUATERRA. Three major contamination sources were identified and their composition and distribution profiles were resolved. The first contamination profile was mostly loaded by polycyclic aromatic hydrocarbons, the second contamination profile was loaded by some organochlorine compounds and the third contamination profile was more specifically loaded by naphthalene. Samples from the different geographical regions of the Ebro River Basin were grouped according to the contamination described by these three major profiles.

Europe↗
PubMed2001

Multi-element sewer slime impact pattern--a quantitative characteristic enabling identification of the source of heavy metal discharges into sewer systems.

The capability of sewer slime to accumulate heavy metals from municipal wastewater can be exploited to identify the sources of sewage sludge pollution. Former investigations of sewer slime looked for a few elements only and could, therefore, not account for deviations of the enrichment efficiency of the slime or for irregularities from sampling. Results of ICP-MS multi element determinations were analyzed by multivariate statistical methods. A new dimensionless characteristic "sewer slime impact" is proposed, which is zero for unloaded samples. Patterns expressed in this data format specifically extract the information required to identify the type of pollution and polluter quicker and with less effort and cost than hitherto.

Algorithms↗
PubMed1996

Heavy metals and nutrients in coastal, surface seawaters (Gulf of Trieste, Northern Adriatic Sea): an environmental study by factor analysis.

Trace metals and nutrients were monitored voltammetrically and spectrophotometrically during a one-year period (1992/93) in the filtered fraction of coastal surface seawaters sampled with a monthly frequency at 6 different sites in the Gulf of Trieste (Northern Adriatic Sea), to evaluate the degree of pollution in an area receiving industrial, agricultural and urban wastes. The sites devoted to hatcheries of edible mussels are of particular interest. A multivariate statistical analysis of the collected concentration data by the principal component method allows to identify the sources and typology of pollution, and to discriminate between the quality of waters at the different sampling sites. The coastal waters in the Gulf of Trieste seem to be comparable to, or better than, waters of analogous areas in the Mediterranean Sea.

Journal Article↗
PubMed2002

Trends in codon and amino acid usage in Thermotoga maritima.

The usage of synonymous codons and the frequencies of amino acids were investigated in the complete genome of the bacterium Thermotoga maritima using a multivariate statistical approach. The GC3 content of each gene was the most prominent source of variation of codon usage. Surprisingly the usage of UGU and UGC (synonymous triplets coding for Cys, the least frequent amino acid in this species) was detected as the second most prominent source of variation. However, this result is probably an artifact due to the very low frequency of Cys together with the nonbiased composition of this genome. The third trend was related to the preferential usage of a subset of codons among highly expressed genes, and these triplets are presumed to be translationally optimal. Concerning the amino acid usage, the hydropathy level of each protein (and therefore the frequency of charged residues) was the main trend, while the second factor was related to the frequency of usage of the smaller residues, suggesting that the cell economy strongly influences the architecture of the proteins. The third axis of the analysis discriminated the usage of Phe, Tyr, Trp (aromatic residues) plus Cys, Met, and His. These six residues have in common the property of being the preferential targets of reactive oxygen species, and therefore the anaerobic condition of T. maritima is an important factor for the amino acid frequencies. Finally, the Cys content of each protein was the fourth trend.

Amino Acids↗
PubMed2005

Proteome composition in Plasmodium falciparum: higher usage of GC-rich nonsynonymous codons in highly expressed genes.

The parasite Plasmodium falciparum, responsible for the most deadly form of human malaria, is one of the extremely AT-rich genomes sequenced so far and known to possess many atypical characteristics. Using multivariate statistical approaches, the present study analyzes the amino acid usage pattern in 5038 annotated protein-coding sequences in P. falciparum clone 3D7. The amino acid composition of individual proteins, though dominated by the directional mutational pressure, exhibits wide variation across the proteome. The Asn content, expression level, mean molecular weight, hydropathy, and aromaticity are found to be the major sources of variation in amino acid usage. At all stages of development, frequencies of residues encoded by GC-rich codons such as Gly, Ala, Arg, and Pro increase significantly in the products of the highly expressed genes. Investigation of nucleotide substitution patterns in P. falciparum and other Plasmodium species reveals that the nonsynonymous sites of highly expressed genes are more conserved than those of the lowly expressed ones, though for synonymous sites, the reverse is true. The highly expressed genes are, therefore, expected to be closer to their putative ancestral state in amino acid composition, and a plausible reason for their sequences being GC-rich at nonsynonymous codon positions could be that their ancestral state was less AT-biased. Negative correlation of the expression level of proteins with respective molecular weights supports the notion that P. falciparum, in spite of its intracellular parasitic lifestyle, follows the principle of cost minimization.

Amino Acids↗
PubMed2001

Origin and evolution of GBV-C/hepatitis G virus and relationships with ancient human migrations.

The GB virus C/hepatitis G virus (GBV-C/HGV) is a newly identified human RNA virus, belonging to the Flaviviridae family. Persistent infection by GBV-C/HGV is common in humans, and genetically divergent isolates have been identified in different parts of the world. Due to the absence of a real pathogenic role of GBV-C/HGV in liver disease and its extremely low mutation rate, this virus is a potential marker to trace prehistoric links between human populations. In this study, origin and evolution of GBV-C/HGV were examined using a set of fully sequenced strains of worldwide origin. A first phylogenetic analysis, addressed to the short (255 nucleotides) NS5A overlapping coding region by the neighbor-joining method, suggested an ancient African origin of GBV-C/HGV. This notion was confirmed when the same analysis was applied to the genomic regions showing the lowest rate of synonymous substitutions, covering one-fourth (2184 nucleotides) of the total coding potential of the virus genome. By using a multivariate statistical method and extending the analysis to the complete coding region, fine details of the evolutionary history of GBV-C/HGV were further elucidated. By this approach, isolates from Southeast Asia appeared to be the most closely related to those of African origin, consistent with a major route of ancient human migrations from Africa to southeastern parts of the Asian continent.

Base Sequence↗
PubMed2003

Assessment of effects of chromated copper arsenate (CCA)-treated timber on nontarget epibiota by investigation of fouling community development at seven European sites.

To assess the effect of the anti-marine-borer timber preservative CCA (a pressure-impregnated solution of copper, chromium, and arsenic compounds) on nontarget epibiota, fouling community development was investigated. Panels of Scots pine treated to target retentions of 12, 24, and 48 kg CCA per m3 of wood (covering the range of retentions recommended for marine use) plus untreated controls were submerged at seven coastal sites (Portsmouth, UK; La Tremblade [two sites], France; Ria Formosa, Portugal; Sagres, Portugal; Kristineberg, Sweden; Athens, Greece). The fouling community on the surfaces of the panels was assessed both qualitatively and quantitatively after 6, 12, and 18 months of exposure. Multivariate statistical methods were used to compare community structure between panel treatments. Panels treated to the three CCA loadings supported very similar fouling assemblages, which in most cases had higher numbers of taxa and individuals than assemblages on untreated panels. No detrimental effects on epibiota due to CCA preservatives were detected at any of the treatment levels at all seven exposure sites, suggesting that the range of environmental conditions at the sites had no bearing on preservative impact on fouling biota. Differences in community structure between CCA-treated and untreated panels may be due to enhanced larval settlement on CCA-treated timber by some species as a result of modifications to the surface properties of the timber by the preservative. Possible reasons for the higher numbers of certain species on the surface of CCA-treated panels are discussed.

Animals↗
PubMed2006

Ecological effects of spring and late summer applications of lambda-cyhalothrin on freshwater microcosms.

The aim of the study was to compare the effects of the pyrethroid insecticide lambda-cyhalothrin (treated at 10, 25, 50, 100, 250 ng active ingredient a.i./L) on a drainage ditch ecosystem in spring and late summer. Microcosms (water volume approximately 430 L) were established using enclosures in a 50-cm-deep experimental ditch system containing communities typical of macrophyte-dominated freshwater ecosystems. Effects on macroinvertebrates, zooplankton, phytoplankton, macrophytes, and community metabolism were assessed and evaluated using univariate and multivariate statistical techniques. The macroinvertebrate community responded most clearly to treatment and, as anticipated, insects and crustaceans were among the most sensitive organisms. Statistical analysis showed that the underlying community structure was significantly different between the spring and summer experiments. However, the most sensitive species (Chaoborus obscuripes and Gammarus pulex) were abundant in spring as well as in late summer. In spring and late summer, only slight and transient effects were observed at the community level in the 10-ng/L treatment. Overall, the study did not show substantial differences in the responses of sensitive taxa between spring and late summer treatments, and effects thresholds were similar irrespective of season of treatment.

Animals↗
PubMed2001

Multi-elemental concentrations in tissues of Japanese common squid (Todarodes pacificus).

Forty-five elements were determined in mantle muscle and liver of juvenile Japanese common squid, Todarodes pacificus, collected from three locations in and near Japanese coasts, using a high-resolution inductively coupled plasma mass spectrometer (HR-ICP-MS) and an inductively coupled plasma atomic emission spectroscope (ICP-AES). Multivariate statistical techniques were applied to discriminate populations of squids from these three locations by treating absolute and relative concentrations of trace elements. Significant differences were found in the concentrations of elements, particularly for some alkaline and alkaline earth elements in the muscle and liver and for some 3d transition elements in the liver of three groups of squids. Squids from the Pacific Ocean could be distinguished from those of the Sea of Japan by discriminant function analysis of elemental concentrations. Based on the analysis, the squids collected from the Nemuro Strait in Japan were predicted to belong to those from the Sea of Japan. Elemental concentrations and discriminant function analysis can be used to identify subpopulations and migratory routes of squids.

Animals↗
PubMed2001

Investigating Influential Factors on Bacterioplankton Community Composition: Results from a Field Study of Five Mesotrophic Lakes.

In order to investigate which biotic and abiotic factors may have an impact on the community composition of bacterioplankton, five mesotrophic lakes were studied. The composition of the bacterioplankton communities was determined by denaturing gradient gel electrophoresis (DGGE) of 16S rDNA. Multivariate statistical analyses of the gel patterns, in relation to each other and to the chemical, biological, and physical parameters of the lakes, were performed. The analyses showed that the import of allochthonous bacteria and the interaction with other plankton organisms (for example, grazing) in the lakes probably had an impact on the composition of the communities.

Journal Article↗
PubMed2005

Microbial community growth and utilization of carbon constituents during thermophilic composting at different oxygen levels.

Composting is characterized by dramatic changes in microbial community structure, to a high extent driven by changes in temperature and in the composition of the organic substrate. This study focuses on the interrelationships between decomposition of major classes in the organic material and dynamics in microbial populations during thermophilic composting of source-separated organic household waste. Experiments were performed in a 200-L laboratory reactor at 16, 2.5, and 1% O(2) in the compost atmosphere. Major classes of carbon constituents were analyzed by chemical methods, and the microbial biomass and community structure determined by fatty acid analyses with phospholipid fatty acids (PLFA) and total ester-linked fatty acids (EL) methods. At all three O(2) levels, the process was characterized by a rapid increase in microbial activity and biomass in the early thermophilic phase, although this period was delayed at the lower O(2) concentrations. Starch and fat were the main substrates utilized at all three O(2) levels during this period. The depletion of the starch fraction coincided with the beginning of a microbial biomass decrease, suggesting that starch is an important carbon substrate for the growth of thermophilic microorganisms during composting. Growth yields in the microbial community based on consumption of major carbon constituent classes in the high-activity period fell between 22 and 28%. Multivariate statistical analysis of changes in fatty acid composition revealed small, but statistically significant differences in the microbial community succession. At 16% O(2), 10 Me fatty acids from Actinomycetes and cyclopropyl fatty acids (from Gram-negative bacteria) became more important with time, whereas 18:1 omega 7t was characteristic at 2.5 and 1% O(2), indicating a more stressed bacterial community at the lower O(2) concentrations. Although adequate composting was achieved at O(2) levels as low as 2.5 and 1%, it is not recommended to compost at such low levels in large-scale systems, because the heterogeneous gas transport through the material in these systems might lead to anaerobic conditions and inefficient composting.

Actinobacteria↗
PubMed1999

High-cell-density cultivation of microorganisms.

High-cell-density cultivation (HCDC) is required to improve microbial biomass and product formation substantially. An overview of HCDC is given for microorganisms including bacteria, archae and eukarya (yeasts). Problems encountered by HCDC and their possible solutions are discussed. Improvements of strains, different types of bioreactors and cultivation strategies for successful HCDC are described. Stirred-tank reactors with and without cell retention, a dialysis-membrane reactor, a gas-lift reactor and a membrane cyclone reactor used for HCDC are outlined. Recently modified traditional feeding strategies and new ones are included, in particular those for unlimited growth to very dense cultures. Emphasis is placed on robust fermentation control because of the growing industrial interest in this field. Therefore, developments in the application of multivariate statistical control, artificial neural networks, fuzzy control and knowledge-based supervision (expert systems) are summarized. Recent advances using Escherichia coli--the pioneer organism for HCDC--are outlined.

Archaea↗
PubMed1998

The significance of an increase in soluble interleukin-2 receptor level in colorectal cancer and its biological regulating role in the physiological switching of the immune response cytokine network from TH1 to TH2 and back.

Current research has still not clarified the biological role of soluble interleukin(IL)-2 receptor (sIL-2R) and the significance of its increase in the serum of colon cancer patients compared to healthy subjects. To address these questions at the immunological level in a group of patients and healthy subjects, we determined the sIL-2R level in the serum and its release from peripheral blood mononuclear cells (PBMC) as a function of tumour necrosis factor (TNF) alpha, IL-1 alpha, IL-1 beta, IL-2, interferon (IFN) gamma, IL-4, IL-6 and IL-10 levels in the serum and PBMC production; and PBMC proliferative responses to IL-2, IL-4 and anti-CD3 monoclonal antibody (CD3), variously combined. The level of sIL-2R in patients' serum was higher than in healthy subjects and correlated with the stage of advancement. Moreover, while in healthy subjects the serum level of sIL-2R was not significantly correlated with other parameters, in patients it was positively related to IL-4, IL-6 and IL-10 serum levels, PBMC IL-4 production and to the PBMC proliferative response to CD3 and CD3 + IL-2; it was negatively correlated to IL-2 serum level and IL-1 beta PBMC release. A negative connection between IFN gamma serum level and the PBMC production of sIL-2R was also found. This suggests that the increase of sIL-2R in the serum of patients, compared to healthy subjects, is involved in the inappropriate expansion of the T helper (TH2) suppressive immune response, which we previously reported. The multivariate statistical method supported the above suggestions and we also found that, in healthy subjects, the up- and down-regulation of sIL-2R in the serum within the physiological ranges seems to have a regulating role in the relationships between TNF alpha, IFN gamma and IL-4, IL-6, contributing to the operation of the cytokine network between TH1 and TH2 cells. However, in patients compared to healthy subjects the increased sIL-2R serum level seems to direct the immune response towards a suppressive type, which may be due to an alteration in the above-mentioned physiological regulating role.

Adult↗
PubMed2004

Scoring CT/HRCT findings among asbestos-exposed workers: effects of patient's age, body mass index and common laboratory test results.

We studied the effects of age, body mass index (BMI) and some common laboratory test results on several pulmonary CT/HRCT signs. Five hundred twenty-eight construction workers (age 38-80, mean 63 years) were imaged with spiral and high resolution CT. Images were scored by three radiologists for solitary pulmonary nodules, signs indicative of fibrosis and emphysema, ground glass opacities, bronchial wall thickness and bronchiectasis. Multivariate statistical analyses were adjusted for smoking and asbestos exposure. Increasing age, blood haemoglobin value and erythrocyte sedimentation rate correlated positively with several HRCT signs. Increasing BMI was associated with a decrease in several signs, especially parenchymal bands, honeycombing, all kinds of emphysema and bronchiectasis. The latter finding might be due to the suboptimal image quality in obese individuals, which may cause suspicious findings to be overlooked. Background data, including patient's age and body constitution, should be considered when CT/HRCT images are interpreted.

Adult↗
PubMed2003

Long-term outcome of hydrocephalus management in myelomeningoceles.

BACKGROUND: The cerebrospinal fluid (CSF) shunt remains an important ongoing management problem in myelomeningocele (MMC) patients. We reviewed the long-term shunt treatment outcome in a prospectively followed group of MMC patients from a single institution. METHOD: Patients prospectively entered into a hydrocephalus database with a diagnosis of MMC from the years 1987 to 1996 were selected. All data was verified from the medical records and additional details about the shunt surgery were collected. The outcome of shunt failure was categorized as shunt obstruction, shunt infection, presence of loculated ventricles, overdrainage, and other. All deaths were recorded and causation identified. Univariate analysis for shunt failure risk factors was accomplished using Log rank statistics. Multivariable analysis was performed for each repeated failure level using a conditional Cox regression model. RESULTS: One hundred and twenty (64%) out of 189 MMC patients experienced a first shunt failure with a median time of 303 days; 29 (24%) of the failures were due to shunt infection (the procedure infection rate being 15%). Sixty-one patients experienced a second shunt failure, 38 a third and 36 had four or more. Multivariable analysis of risk factors failed to demonstrate any clear risk factors for either first or subsequent shunt failure. Fifteen patients died, 13 from either shunt or Chiari 1 complications. CONCLUSION: Shunt complications remain an important cause of morbidity and mortality in MMC patients, particularly shunt infection.

Adolescent↗
PubMed1999

High tibial osteotomy: factors influencing the duration of satisfactory function.

In 94 patients 112 knees were examined after high tibial osteotomy for varus and valgus gonarthrosis. Preoperatively, there were 71 varus and 23 valgus deformities. The mean follow-up period was 9.0 years (range 2-21 years). Concerning the pain on walking and the pain at rest, we noted good and excellent results in 73% and 65%, respectively. The radiological evaluation showed an improvement or a persistence of the stage of arthrosis in 69.5% of the reviewed cases. The results according to the HSS score as an objective parameter showed in over 50% an improvement of the patients' situation. The data were subjected to multivariate statistical analysis in which three of four evaluated risk factors were found to be associated with the duration of pain-free survival: certain preoperative injuries, preoperative meniscopathies and a deterioration of the stage of arthrosis (P < 0.05). There was no significance for weight in excess of 10% above the normal body mass index (BMI) limits. However, in a Kaplan-Meier survival analysis this parameter could be determined as a significant factor for a reduced pain-free survival interval (P < 0.05): patients with a BMI of more than 10% above normal limits had a pain-free period of 5.07 years, whereas those with a BMI of less than 10% had a pain-free period of 7.80 years.

Adolescent↗
PubMed2005

Prognostic factors in laryngotracheal injury following intubation and/or tracheotomy in ICU patients.

The aim of this study was to determine the incidence of laryngotracheal injuries following intubation and/or tracheotomy in intensive care unit (ICU) patients and to analyze their prognostic factors. This prospective study includes the clinical data and endoscopic exploration of 654 ICU patients who underwent oro-tracheal intubation between September 1992 and February 1999. The prognostic factors for upper airway injuries were analyzed using a multivariate statistical study. Endoscopic exploration of the upper airway 6 to 12 months after extubation revealed laryngotracheal injuries in 30 of the 280 patients examined (11%). The most important factors influencing the development of laryngotracheal lesions were the duration of the oro-tracheal intubation and the length of time in the ICU. Patients at high risk of developing injuries were those with pathological background, a non-neurological or non-surgical (medical) admission or upper-airway injuries at an early stage. The length of oro-tracheal intubation is the most important factor in the development of laryngotracheal injuries. Consequently, it is essential to establish a time limit to perform tracheotomy in ICU patients. Such timing should be adapted to each patient and pathology.

Female↗
PubMed2004

Plasma homocysteine, MTHFR C677T, CBS 844ins68bp, and MTHFD1 G1958A polymorphisms in spontaneous cervical artery dissections.

Mild hyperhomocysteinemia is a probable risk factor for atherosclerotic diseases and stroke. Recently, associations of elevated plasma homocysteine concentrations in the acute phase and of MTHFR 677 TT genotype with spontaneous cervical artery dissections (sCAD) have been reported. The purpose of this study was to test this hypothesis in the currently largest sample of patients with sCAD, taking into account known factors influencing plasma homocysteine levels. Ninety-five patients with past sCAD were compared with 95 age- and sex-matched healthy individuals. Homocysteine, vitamin B6, B12, folate, and polymorphisms of methylenetetrahydrofolate reductase (MTHFR C677T), cystathionine beta-synthase (CBS 844ins68bp) and methylenetetrahydrofolate dehydrogenase/methenyltetrahydrofolate cyclohydrolase/formyltetrahydrofolate synthetase (MTHFD1 G1958A) were assessed and any associations were analysed using multivariate statistics. The occurrence of sCAD was associated with elevated homocysteine levels with an odds ratio of 1.327 per 20 % percentile. Homocysteine levels were influenced by gender, smoking status, occurrence of hypertension, vitamin B12 and folate levels, and by the MTHFR TT genotype. MTHFR, CBS 844ins68bp, and MTHFD1 G1958A genotype were not independently associated with the occurrence of sCAD. These data suggest that elevated homocysteine is associated with the occurrence of sCAD. The MTHFR C677T polymorphism is associated with the homocysteine level.

Adult↗