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Classification of temporal patterns in dynamic biological networks.

A general method is presented to classify temporal patterns generated by rhythmic biological networks when synaptic connections and cellular properties are known. The method is discrete in nature and relies on algebraic properties of state transitions and graph theory. Elements of the set of rhythms generated by a network are compared using a metric that quantifies the functional differences among them. The rhythms are then classified according to their location in a metric space. Examples are given, and biological implications are discussed.

Models, Neurological↗

Chemical analysis of World Trade Center fine particulate matter for use in toxicologic assessment.

The catastrophic destruction of the World Trade Center (WTC) on 11 September 2001 caused the release of high levels of airborne pollutants into the local environment. To assess the toxicity of fine particulate matter [particulate matter with a mass median aerodynamic diameter < 2.5 microm (PM2.5)], which may adversely affect the health of workers and residents in the area, we collected fallen dust samples on 12 and 13 September 2001 from sites within a half-mile of Ground Zero. Samples of WTC dust were sieved, aerosolized, and size-separated, and the PM2.5 fraction was isolated on filters. Here we report the chemical and physical properties of PM2.5 derived from these samples and compare them with PM2.5 fractions of three reference materials that range in toxicity from relatively inert to acutely toxic (Mt. St. Helens PM; Washington, DC, ambient air PM; and residual oil fly ash). X-ray diffraction of very coarse sieved WTC PM (< 53 microm) identified calcium sulfate (gypsum) and calcium carbonate (calcite) as major components. Scanning electron microscopy confirmed that calcium-sulfur and calcium-carbon particles were also present in the WTC PM2.5 fraction. Analysis of WTC PM2.5 using X-ray fluorescence, neutron activation analysis, and inductively coupled plasma spectrometry showed high levels of calcium (range, 22-33%) and sulfur (37-43% as sulfate) and much lower levels of transition metals and other elements. Aqueous extracts of WTC PM2.5 were basic (pH range, 8.9-10.0) and had no evidence of significant bacterial contamination. Levels of carbon were relatively low, suggesting that combustion-derived particles did not form a significant fraction of these samples recovered in the immediate aftermath of the destruction of the towers. Because gypsum and calcite are known to cause irritation of the mucus membranes of the eyes and respiratory tract, inhalation of high doses of WTC PM2.5 could potentially cause toxic respiratory effects.

Air Pollutants↗

Fluorescence polarization immunoassays for metal ions.

Antibodies raised against a given metal ion complex of a polyaminopolycarboxylate chelating agent can display specificity for the immunizing chelate and, when used in conjunction with a fluorophore-labeled analog of that chelate, can form the basis for highly sensitive and specific methods for detecting that metal ion by competitive inhibition fluorescence polarization immunoassay (FPIA). Chelate complexes of ethylenediamine-N,N,N',N'- tetraacetic acid (EDTA) and of a hetrocyclic ring-substituted derivative of diethylenetriamine-N, N', N"-triacetic acid (DTTA) have been used to configure such assays for the heavy metal ions lead(II) and cadmium(II) respectively. Limits of detection for the 1:1 metal chelates under ideal conditions are 20 ppt for lead(II) and below 100 ppt for cadmium(II). Standard curves for 0 - 100 nM cadmium (II) chelate can be constructed in the presence of fixed 250 nM concentrations of the corresponding, potentially cross-reactive chelates of zinc(II), copper(II) and mercury(II). Cross-reactivity of the lead (II) FPIA with 15 non-target metals is below 0.2% in all cases except for mercury(II) (0.37%). These characteristics have allowed the development of FPIA methods for the quantitative analysis of lead in a variety of samples relevant to environmental monitoring, including soil, dust, solid wastes and drinking water. Although applied thus far to heavy metals that are of concern as toxic contaminants in the environment, anti-chelate FPIA methods are also in principle applicable to a wide variety of other metal ions, including precious metals and various transition and main group elements used or monitored in a range of industrial applications. As conventional methods for trace metal analysis based on atomic spectroscopy are relatively slow, expensive and cumbersome, anti-chelate FPIA methods have the potential to supplant many existing techniques and in so doing extend the use of immunoassay technology beyond the biomedical, veterinary and agricultural spheres in which it has historically found use.

Chelating Agents↗

Characterization of CD34+ human hemopoietic progenitor cells from the peripheral blood: enzyme-, carbohydrate- and immunocytochemistry, morphometry, and ultrastructure.

Following an immunomagnetic isolation and enrichment procedure, CD34+ cells were harvested from the peripheral blood of about 50 healthy donors. A battery of cytochemical staining reactions, monoclonal and carbohydrate-specific antibodies, proliferation markers and lectins was applied on smears and sections from paraffin-embedded pellets. Additionally, a morphometric analysis and ultrastructural investigation was carried out. More than 95% of the total yield of progenitor cells expressed CD34 and CD43 (MT1) and of these about 90% CD45 (LCA) and 25% CD45A (MT2). The CD34+/CD45RA-population was thought to represent very primitive, probably not lineage-restricted stem cells. On the other hand, reactivity with ANAE, CD11c, CD15, CD20, Ret40f, KiM1P, and CD61 (ranging between 1 to 20%) was considered to indicate a transition into more differentiated elements of hemopoiesis. The failure to detect any staining with proliferation markers (Ki-67/MIB 1, PCNA, KiS1) was in keeping with a quiescent status. Carbohydrate antigens revealed a pattern which underlines the fact that the CD34 and CD43 antigens belong to the family of heavily O-glycosylated sialomucins. Blood group antigens which are located at the peripheral regions of mucin-oligosaccharides (H type 2, Lewis, Lewis) could be demonstrated, but not A, B, Sialyl-Lewis and Lewis. Morphometric analysis revealed that CD34+ progenitors were larger than small lymphocytes. Electron microscopy showed a relatively primitive cytoplasmic organization and numerous tiny magnetic beads clustered at the plasma membrane.

Adult↗

Immunohistochemical localization of prostaglandin G/H synthase 1 and 2 in sheep placenta after glucocorticoid-induced and spontaneous labour.

Enhanced prostaglandin production and release by the placenta is an essential element in the normal transition to labour in many animal species. In sheep, expression of prostaglandin G/H synthase (PGHS) is the central enzyme regulating this process. In this study immunohistochemistry was used to examine the distribution of cells expressing PGHS-1 and PGHS-2 in ovine placenta in association with spontaneous parturition (n = 6) and glucocorticoid-induced labour (n = 5). Labour was induced in ewes after the intrafetal injection of betamethasone on day 131 of gestation. Animals administered an intrafetal injection of isotonic saline (n = 5) acted as non-labour controls. In placentomes collected from all groups, immunoreactive PGHS-1 was present in the mononuclear trophoblast cells of the fetal placenta. Cells in the maternal mesenchyme and epithelial syncytium were weakly immunopositive for this enzyme. PGHS-1 immunoreactivity was also demonstrated in the endothelial cells of the chorionic vessels. The PGHS-2 isozyme was localized exclusively to the trophoblast epithelial cells. Immunoreactive PGHS-2 was not detectable in the maternal epithelial syncytium or the stroma of the cotyledons. The binucleate cells of the fetal placenta were consistently immunonegative for both PGHS isozymes. These results indicate that the cellular localization of PGHS-1 and PGHS-2 in ovine placenta does not change during the last 15 days of pregnancy. Co-localization of these isozymes indicates that the source of arachidonic acid and the site of prostanoid formation are the same. Quantitation of the percentage area of positive staining for PGHS-1 and PGHS-2 using image analysis software demonstrated a significant increase in PGHS-2 in the fetal trophoblast after glucocorticoid-induced labour and spontaneous parturition. This finding indicates that increased formation of the PGHS-2 isozyme is responsible for the large increase in prostaglandin production by the ovine placenta at term labour.

Analysis of Variance↗

Flame atomic absorption spectrometric determination of trace amounts of nickel after extraction and preconcentration onto natural modified analcime zeolite loaded with 2-(5-bromo-2-pyridylazo)-5-diethylaminophenol.

Nickel is a moderately toxic element compared with other transition metals. However, inhalation of nickel and its compounds leads to serious problems, including cancer of the respiratory system and a skin disorder, nickel-eczema. Thus, attention has focused on the toxicity of nickel at low concentrations, and the development of reliable, analytical approaches for the determination of trace amounts of nickel is needed. This paper describes a simple, rapid, and sensitive flame atomic absorption spectrometric method for the determination of trace amounts of nickel in various samples after adsorption of its 2-(5-bromo-2-pyridylazo)-5-diethylaminophenol complex on a modified Analcime column in the pH range of 7.5-10.5. The retained analyte on the Analcime is recovered with 5.0 mL 2 M nitric acid and determined by flame atomic absorption spectrometry. The detection limit is 20 ng/mL, and the calibration curve is linear for analyte concentrations in the range of 0.1-8 microg/mL final solution, with a correlation coefficient of 0.9993. Eight replicate determinations of nickel at 2 microg/mL in the final solution gave an absorbance of 0.1222, with a relative standard deviation (RSD) of +/-1.2%. The interference of a large number of anions and cations was studied, and the proposed method was used for the determination of nickel in various standard reference samples. The accuracy of the proposed method was evaluated by analyzing standard reference samples, and the results were satisfactory (recoveries of >96%; RSD of <3.5%).

Absorption↗

[Spermatophyte flora in Hunshandake sand].

This paper studied the spermatophyte flora in the Hunshandake sand of central Inner Mongolia agriculture-animal husbandry ecotone, and compared it with the flora in whole Inner Mongolia. The results showed that there were 1191 species of spermatophyte in the sand, belonging to 402 genera and 84 families. The geographic element of the flora was of multiplicity, and predominant with temperate floristic element, among which, North Temperate distribution elements had a higher percentage, and Compositae and Gramineae had the greatest proportion. The temperate floristic element had a trend of laying in big families, indicating that the plant distribution of Hunshandake sand had adapted to the climate of this area. The dominant families of the spermatophyte belonged to different elements, but most of them were the worldwide element. The original of the element was very ancient, and the geographic element was complex and transitive. In addition, the plant flora was significantly vulnerable.

Biodiversity↗

Globalization, food and health in Pacific Island countries.

Pacific Island countries (PICs) are experiencing an epidemic of obesity and consequent chronic diseases. Despite investment in the development of National Plans of Action for Nutrition (NPANs) and interventions to promote healthy eating and physical activity, nutritional status appears to show little improvement. This paper presents a synthesis of the findings from two research papers that were prepared for a 2003 food safety and quality meeting in Nadi, Fiji. The findings indicate that although lifestyle behaviours might be the immediate cause of dietary imbalances, greater attention should focus on omnipresent influences of globalization as a critical element of the nutrition transition in the Pacific. In particular, those aspects of globalization mediated through the World Trade Organization (WTO) Agreements that are placing pressures on food security and fostering increased dependence on imported food of poor nutritional quality. Rapid, significant and sustainable improvements in public health in PICs require interventions that can tackle these underlying contributors to ill health. There are opportunities to explore the use of food regulatory approaches to influence the composition, availability and accessibility of food products. Within the context of the WTO Agreements the legitimacy of food regulatory approaches will depend upon the case to demonstrate the relationship between the intervention and the protection of food security and public health nutrition. The challenges in realising these opportunities are: 1) to have the capacity to construct a case, 2) meet the technical and financial demands to administer and enforce regulatory approaches, and 3) to take advantage of opportunities available and to be able to fully participate in the international policy-making process.

Chronic Disease↗

[Landscape pattern and its functioning after ecological reconstruction in black soil of northern China].

Taken Baiquan County in Heilongjiang Province as a case, this paper studied the effects of regional ecological reconstruction on agricultural landscape pattern and its functioning in soil and water conservation, with the spatial expression and quantity identification investigated based on Geographic Information System (GIS) and field data. The landscape pattern index in class scale, transition matrix of landscape elements, macrostructure of shelter-belt networks, and spatial distribution and hydrological characteristic of reservoirs and ponds in 1989 and 2002, as well as the effects of landscape pattern and its spatial configuration change on soil and water loss were compared. The results showed that artificial ecological reconstruction changed the quantity and spatial configuration of landscape patterns in regional scale, and exerted a significant effect on soil and water conservation. From 1989 to 2002, farmland area reduced 24 731.01 hm2, while forest land, grassland and water area increased 11 728.56, 1838.97 and 1190.97 hm2, respectively. The controlled eroded land increased by 55%, and the shelterbelt-protected farmland increased by 82.2%. The number and storage capacity of reservoirs and ponds added up to 1 490 and 2.4 x 10(8) m3, respectively, and 43.7% of intercepted surface runoff of whole landscape was collected.

China↗

Biosynthesis of truncated O-glycans in the T cell line Jurkat. Localization of O-glycan initiation.

Glycoproteins from the human T leukemia cells Jurkat were found to bind to the GalNAc alpha 1----Ser/Thr-specific lectin from Salvia sclarea seeds. The analysis of the O-linked saccharides of immunopurified leukosialin, the major [3H]glucosamine-labeled glycoprotein in Jurkat cell lysate, revealed the presence of mainly GalNAc alpha 1----Ser/Thr with only minor amounts (approximately 17%) of more complex O-glycans. A comparison between Jurkat and K562 cell glycosyltransferase involved in the biosynthesis of O-linked carbohydrates showed that a markedly lower activity of UDP-Gal:GalNAc alpha 1----Ser/Thr beta 1----3galactosyltransferase is apparently responsible for the presence of truncated O-glycans in the Jurkat cell line. The O-glycosylation defect makes Jurkat cells an ideal model to study the initiation of O-linked saccharides. Pulse-chase experiments with [35S] methionine showed that the addition of GalNAc to leukosialin is responsible for the decreased mobility of the mature glycoprotein on sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Furthermore, no biosynthetic intermediates between the O-glycan-free precursor and the fully O-glycosylated form could be detected either with an anti-leukosialin antiserum or with the GalNAc-specific lectin. Lowering the chase temperature to 15 degrees C completely inhibited the transfer of GalNAc to the peptide core indicating that O-glycan initiation takes place in the first Golgi elements and not in transitional vesicles between endoplasmic reticulum and Golgi. In addition, treatment of the cells with monensin did not inhibit GalNAc transfer to leukosialin apoprotein. These results indicate that the initiation of O-glycosylation in Jurkat cells starts in the cis-Golgi stacks.

Acetylgalactosamine↗

Zinc: biochemistry, physiology, toxicology and clinical pathology.

Among the transition and group II elements the abundance of zinc in biology is second only to that of iron. It is present in and indispensable to all forms of life. Knowledge regarding the biological occurrence and function of zinc, the development of methods that permit its detection and those aspects of biochemistry which have allowed an appreciation of the manner in which it participates in generating biological specificity have grown exponentially in the last two decades. The recognition that zinc is an essential, coenzyme-like component of many enzymes, indispensable to their function, is reminiscent of the role of some vitamins. Technical advances in the isolation and characterization of enzymes in general and metalloenzymes in particular were basic to the rapid growth of zinc metallobiochemistry during the last two decades. Zinc is now known to be an integral component of a large variety of proteins and enzymes and, hence, the total zinc content of tissues cannot serve as a guide to the multiple functions of the metal. Zinc participates in a wide variety of metabolic processes including carbohydrate, lipid, protein and nucleic acid synthesis or degradation. Most recently, zinc proteins have been shown to be involved in the transcription and translation of the genetic material, perhaps accounting for its essentiality to all forms of life. A number of zinc proteins have been described whose function is not known as yet. Among these, the metallothioneins are prominent. They are widely distributed, of low molecular weight (approximately 6700), and their content of cadmium and/or zinc as well as sulfur is exceptionally high.(ABSTRACT TRUNCATED AT 250 WORDS)

Animals↗

Progress in the use of elemental diets in infants and children.

The clinical use of elemental diets to provide adequate nutrition in the infant or child in a catabolic state will, undoubtedly, increase as experience confirms the effectiveness and safety of this technique. The value of total parenteral nutrition and nutrition given through the peripheral vein should, in no way, be underestimated, since many infants and children will still require this form of nutrition during periods when the intestine is not available for alimentation. The use of elemental diets in the transitional period between total parenteral nutrition and more conventional feedings as well as in providing nutritional support when the intestine is totally or partially available provides a method of earlier discontinuance of parenteral nutrition and, hence, decreases the incidence of mechanical, metabolic and septic complications associated with intravenously administered nutrition. Each patient should be considered individually and a decision made as to whether or not enteral hyperalimentation can be used in place of, or in conjunction with, parenteral nutrition.

Amino Acids↗

Acral arteriovenous tumor.

A unique, superficial, lobulated, benign vascular tumor of the skin, found in the acral areas of adult males, is described. The combination of three different elements--arterial, venous, and transitional vascular channels--make up the predominant histologic features of this tumor. The transition of fibromuscular channels indicates a venous lesion, but the acral location of the lesions and the structure and staining characteristics suggest that the lesion is a hamartomatous proliferation of the Sucquet-Hoyer canal of the true glomus.

Adult↗

Primitive neuroectodermal tumor arising in an ovarian mature cystic teratoma: immunohistochemical and electron microscopic studies.

The occurrence of a malignant neuroectodermal tumor in a mature cystic teratoma is extremely rare. Five cases of ovarian primitive neuroectodermal tumors (PNET) or neuroepitheliomas have been reported. In two, the tumor was adjacent to foci of a mature teratomatous element. We present the immunohistochemical profile and electron microscopic study of an ovarian mature cystic teratoma with PNET or malignant neuroepithelioma. The transition between the mature neural elements and the malignant PNET presents a model for monodermic neuroepithelial differentiation and explains the histogenesis of this unusual tumor.

Adult↗

Development of parameter sets for semi-empirical MO calculations of transition metal systems: iron parameters for iron-sulfur proteins.

A semi-empirical parameter set for iron has been developed which is appropriate for the study of iron-sulfur proteins having a single iron atom, by fitting to density-functional theory (DFT) calculations obtained for a series of small models of iron-containing proteins. These parameters are obtained using a modified BFGS optimisation procedure previously used to obtain semi-empirical parameters for the main group elements. The modifications to this procedure for obtaining parameters for transition metal atoms are outlined. In addition to modifications to the semi-empirical core repulsion function, which yield significant improvements in the calculation of molecular structures, compared to the standard core repulsion function, are outlined. The reported parameters are then tested on a set of model complexes containing a variety of ligands and show good agreement with both DFT and experimental data for these species.

Algorithms↗

Synthesis and characterisation of the first transition metal complex of zoxazolamine (2-amino-5-chlorobenzoxazole): the X-ray crystal structure determination of [ZnCl2(eta 1-Nbenzoxazole-2-amino-5-chlorobenzoxazole)2].

The synthesis and characterisation (NMR, X-ray, elemental analysis) of the first transition metal complex of Zoxazolamine (1: 2-amino-5-chlorobenzoxazole), viz. [ZnCl(2)(1)(2)] (2) is described; complex 2 is obtained in 77% yield from the treatment of 1 with ZnCl(2) in acetone solution. The Zn compound is a mononuclear species (X-ray) with a distorted tetrahedral array of ligands around the metal centre with the title ligand bound to Zn via the benzoxazole ring N-atom. The structural properties of 2 are discussed in relation to other mononuclear Zn halide complexes.

Journal Article↗

The 5'-end transitional CpGs between the CpG islands and retroelements are hypomethylated in association with loss of heterozygosity in gastric cancers.

BACKGROUND: A loss of heterozygosity (LOH) represents a unilateral chromosomal loss that reduces the dose of highly repetitive Alu, L1, and LTR retroelements. The aim of this study was to determine if the LOH events can affect the spread of retroelement methylation in the 5'-end transitional area between the CpG islands and their nearest retroelements. METHODS: The 5'-transitional area of all human genes (22,297) was measured according to the nearest retroelements to the transcription start sites. For 50 gastric cancer specimens, the level of LOH events on eight cancer-associated chromosomes was estimated using the microsatellite markers, and the 5'-transitional CpGs of 20 selected genes were examined by methylation analysis using the bisulfite-modified DNA. RESULTS: The extent of the transitional area was significantly shorter with the nearest Alu elements than with the nearest L1 and LTR elements, as well as in the extragenic regions containing a higher density of retroelements than in the intragenic regions. The CpG islands neighbouring a high density of Alu elements were consistently hypomethylated in both normal and tumor tissues. The 5'-transitional methylated CpG sites bordered by a low density of Alu elements or the L1 and LTR elements were hypomethylated more frequently in the high-level LOH cases than in the low-level LOH cases. CONCLUSION: The 5'-transitional methylated CpG sites not completely protected by the Alu elements were hypomethylated in association with LOH events in gastric cancers. This suggests that an irreversible unbalanced decrease in the genomic dose reduces the spread of L1 methylation in the 5'-end regions of genes.

5' Flanking Region↗