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PubMed2004

Comparison of TCA and ICA techniques in fMRI data processing.

PURPOSE: To make a quantitative comparison of temporal cluster analysis (TCA) and independent component analysis (ICA) techniques in detecting brain activation by using simulated data and in vivo event-related functional MRI (fMRI) experiments. MATERIALS AND METHODS: A single-slice MRI image was replicated 150 times to simulate an fMRI time series. An event-related brain activation pattern with five different levels of intensity and Gaussian noise was superimposed on these images. Maximum contrast-to-noise ratio (CNR) of the signal change ranged from 1.0 to 2.0 by 0.25 increments. In vivo visual stimulation fMRI experiments were performed on a 1.9 T magnet. Six human volunteers participated in this study. All imaging data were analyzed using both TCA and ICA methods. RESULTS: Both simulated and in vivo data have shown that no statistically significant difference exists in the activation areas detected by both ICA and TCA techniques when CNR of fMRI signal is larger than 1.75. CONCLUSION: TCA and ICA techniques are comparable in generating functional brain maps in event-related fMRI experiments. Although ICA has richer features in exploring the spatial and temporal information of the functional images, the TCA method has advantages in its computational efficiency, repeatability, and readiness to average data from group subjects

Brain Mapping↗
PubMed2004

Onset and duration of cytomegalovirus immediate early 1 mRNA expression in the blood of renal transplant recipients.

Human cytomegalovirus (CMV) messenger (m) RNA expression in circulating leukocytes reflects directly viral activity in the human host. In this study, sixty-nine patients were monitored prospectively for CMV infection and mRNA expression during the first year after renal transplantation. Of the 69 recipients, 58 (84%) recipients were positive for CMV immediate early 1 (IE1) mRNA as detected by nucleic acid sequence-based amplification. The median onset of IE1 expression started at day 22 after transplantation and continued for a median duration of 82 days. IE1 mRNA expression started significantly earlier in recipients who developed an active CMV infection (P = 0.001) and in mycophenolate mofetil (MMF) treated recipients (P = 0.002). The duration of IE1 mRNA expression was significantly longer in recipients that had previously an early onset of IE1 mRNA expression (P = 0.001) and in recipients with active CMV infection (P = 0.007). Remarkably, longer prednisolone intake was correlated with a significantly (P = 0.02) shorter duration of IE1 expression compared to a longer duration of IE1 expression in recipients with only a short prednisolone intake. In recipients infected with glycoprotein B (gB) type 1 CMV strains, the duration of IE1 expression was significantly (P = 0.04) shorter compared to recipients infected with non-gB type 1 CMV strains (64 days vs. 150 days). The study indicates that multiple factors play a role in the onset and/or duration of CMV IE1 mRNA expression, for example, MMF treatment, prednisolone intake, and gB type of the specific CMV strain. The clinical significance of these correlations remains to be studied in more detail.

Adult↗
PubMed2005

NF-kappaB pathway protects cochlear hair cells from aminoglycoside-induced ototoxicity.

Cell death in outer hair cells of the mammalian inner ear induced by aminoglycoside antibiotics is mediated by reactive oxygen species (ROS) and can be prevented by antioxidants. The current study investigates the role of the nuclear factor (NF)-kappaB pathway in cell death or survival in adult CBA mice. Kanamycin (700 mg/kg subcutaneously, twice per day) progressively destroys hair cells but after 7 days of treatment auditory function and morphology are not yet affected significantly, permitting investigations of early events in drug-induced cell death. Immunostaining for 4-hydroxynonenal, indicative of lipid peroxidation, was elevated in the cochlea, but there was no effect on nitrotyrosine, a marker for peroxynitrite. NF-kappaB was increased at 3 hr, 3 days, and 7 days of treatment, with p50 and p65 proteins as its most abundant subunits. Immunoreactivity for p50 was present in nuclei of inner hair cells and supporting cells that survive the drug treatment. In contrast, nuclei of outer hair cells were devoid of label. Concomitant injections of antioxidants, however, such as 2,3-dihydroxybenzoic acid or salicylate (which prevent cell death induced by kanamycin), promoted the translocation of NF-kappaB into the nuclei of outer hair cells. In addition, kanamycin treatment decreased tyrosine phosphorylation of the inhibitory IkappaBalpha protein, leading to increased IkappaBalpha levels in the cochlea; the effect was reversed by cotreatment with antioxidants. These results suggest that changes in the redox state of the cochlea stimulate the activation of NF-kappaB and that this activation is cell protective.

Aldehydes↗
PubMed2006

Single-voxel 1H PRESS at 4.0 T: precision and variability of measurements in anterior cingulate and hippocampus.

The precision [coefficient of variation or CV (%) = 100SD/X] of single-voxel point resolved spectroscopic data was characterized bilaterally, in anterior cingulate and in hippocampus, at 4.0 T in a healthy subject. Data acquisition was replicated 10 times after voxel repositioning and readjusting higher order shims. Precision measurements show that the scan-to-scan precision is better in anterior cingulate than in hippocampus, with an average CV of 9.2% (for total NAA, tCho and Cr) in anterior cingulate and 13.9% in hippocampus. Variability measurements made by the same method in 24 healthy subjects and in 29 schizophrenia patients showed that there is substantial biological variability in metabolite levels, even in healthy subjects. Simple calculations suggest that more than 200 subjects would be needed to detect a 5% difference in NAA between patients and controls.

Adult↗
PubMed2004

What to add to nothing? Use and avoidance of continuity corrections in meta-analysis of sparse data.

OBJECTIVES: To compare the performance of different meta-analysis methods for pooling odds ratios when applied to sparse event data with emphasis on the use of continuity corrections. BACKGROUND: Meta-analysis of side effects from RCTs or risk factors for rare diseases in epidemiological studies frequently requires the synthesis of data with sparse event rates. Combining such data can be problematic when zero events exist in one or both arms of a study as continuity corrections are often needed, but, these can influence results and conclusions. METHODS: A simulation study was undertaken comparing several meta-analysis methods for combining odds ratios (using various classical and Bayesian methods of estimation) on sparse event data. Where required, the routine use of a constant and two alternative continuity corrections; one based on a function of the reciprocal of the opposite group arm size; and the other an empirical estimate of the pooled effect size from the remaining studies in the meta-analysis, were also compared. A number of meta-analysis scenarios were simulated and replicated 1000 times, varying the ratio of the study arm sizes. RESULTS: Mantel-Haenszel summary estimates using the alternative continuity correction factors gave the least biased results for all group size imbalances. Logistic regression was virtually unbiased for all scenarios and gave good coverage properties. The Peto method provided unbiased results for balanced treatment groups but bias increased with the ratio of the study arm sizes. The Bayesian fixed effect model provided good coverage for all group size imbalances. The two alternative continuity corrections outperformed the constant correction factor in nearly all situations. The inverse variance method performed consistently badly, irrespective of the continuity correction used. CONCLUSIONS: Many routinely used summary methods provide widely ranging estimates when applied to sparse data with high imbalance between the size of the studies' arms. A sensitivity analysis using several methods and continuity correction factors is advocated for routine practice.

Bayes Theorem↗
PubMed2005

Stream macroinvertebrate drift response to pulsed exposure of the synthetic pyrethroid lambda-cyhalothrin.

Outdoor experimental channels were used to study the behavioral changes of stream macroinvertebrates exposed to a pulse of the pyrethroid insecticide lambda-cyhalothrin. The primary end point was the number of macroinvertebrates drifting, but the mobility of macroinvertebrates caught in the drift also was assessed. A specified number of two insect species, Baetis rhodani and Leuctra fusca/digitata, and of the amphipod Gammarus pulex were introduced into small replicated subsections of the experimental channels. Macroinvertebrates were allowed to acclimatize for 26 h prior to a 60-min pulsed exposure to lambda-cyhalothrin. Measurement was initiated 2 h before pesticide application and continued for the following 24 h. Pulse concentrations of lambda-cyhalothrin of 0.001, 0.01, 0.1, and 1.0 microg L(-1) were applied, and each experiment was replicated 8 times. All three species responded to the pesticide pulse with catastrophic drift. The 0.001 microg L(-1) treatment caused a significant increase in the drift of Gammarus, whereas the drift response threshold was 0.01 microg L(-1) for the two insect species. Drift response onset followed the applied pulse concentration, with the highest concentrations resulting in more individuals of all species entering drift at an early stage. The majority of individuals caught in drift samples during low concentrations showed no change in mobility. At the two highest concentrations, however, both Baetis and Leuctra were in the process of being immobilized, with Leuctra the more sensitive of the two. In contrast, only a few of the Gammarus individuals caught showed changes in mobility after the high-concentration treatments. The present study shows that lambda-cyhalothrin is a potential hazard for macroinvertebrate populations in headwater streams. The clear species-specific responses indicate that sublethal doses have the potential to change the macroinvertebrate community structure.

Amphipoda↗
PubMed2002

Specific transduction of the leading edge cells of migrating epithelia demonstrates that they are replaced during healing.

As wounds in stratified epithelia close, the numbers of cells at the leading edge of migration decreases. It is not known whether cells at the leading edge are continually replaced or whether some retain their position at the leading edge over time. Replication-deficient adenovirus carrying the green fluorescent protein gene was applied to corneal epithelial wounds in mice and it was found that they primarily infect the leading edge cells of healing epithelium. Eighteen hr after viral transduction, green fluorescent protein expressing cells were located in the apical layer at varying distances behind the leading edge. These data indicate that leading edge cells are replaced during healing of stratified epithelia.

Adenoviridae↗
PubMed1995

Plus-strand DNA synthesis of the yeast retrotransposon Ty1 is initiated at two sites, PPT1 next to the 3' LTR and PPT2 within the pol gene. PPT1 is sufficient for Ty1 transposition.

Long terminal repeat elements and retroviruses require primers for initiation of minus and plus-strand DNA synthesis by reverse transcriptase. Here we demonstrate genetically that plus-strand DNA synthesis of the yeast Ty1 element is initiated at two sites located at the 5' boundary of the 3' long terminal repeat (PPT1) and near the middle of the pol gene in the integrase coding sequence (PPT2). A consequence of the presence of two PPTs is that Ty1 plus-strand DNA exists as segments at some time during replication. Three fragments have been identified: the plus-strand strong-stop DNA initiated at PPT1, a downstream fragment initiated at PPT2 and an upstream fragment spanning the 5'-terminal part of Ty1 and a portion of the TyB gene. Characterization of the 3' ends of the plus-strand DNA fragments reveals (1) that the upstream fragment is elongated beyond PPT2 creating a plus-strand overlap and (2) that the majority of plus-strand strong-stop DNA fragments bear a copy of the minus-strand primer binding site in agreement with the accepted model of retroviral genomic RNA reverse transcription. The two polypurine tracts, PPT1 and PPT2, have an identical sequence GGGTGGTA. Mutations replacing purines by pyrimidines in this sequence significantly diminish or abolish initiation of plus-strand synthesis. Ty1 elements bearing a mutated PPT2 sequence are not defective for transposition whereas mutations in PPT1 abolish transposition.

Base Sequence↗
PubMed1989

Sequence of centromere separation: characterization of multicentric chromosomes in a rat cell line.

The B1 cell line of rat cerebral endothelium origin exhibits several dicentric and multicentric chromosomes. These chromosomes, unlike multicentrics in mouse (Vig and Zinkowski 1986) do not show premature centromere separation. All centromeres deposit kinetochore proteins and appear to be functional. Even the centromeres which fail to migrate to the poles during anaphase and make side arm bridges bind to spindle microtubules. Some multicentric chromosomes show kinetochores spaced apart with intervening stretches of euchromatin while others are located adjacent to each other thus exhibiting tandem repeats and forming a "compound" kinetochore (Brinkeley et al. 1984). Also, unlike mouse multicentric chromosomes in which different pericentric regions and the centromeres replicate at different times, the rat chromosomes appear to replicate all pericentric and centric regions in a given multicentric simultaneously. The present studies indicate that centromeres in rat and mouse replicate during the last part of the S-phase and in continuation with the pericentric heterochromatin.

Animals↗
PubMed1982

Role of natural prostaglandins in the control of murine mammary tumor virus expression.

The regulation of murine mammary tumor virus (MuMTV) production by mammotropic hormones, hormonomimetic substances, and cyclic nucleotides was investigated. The virus produced in control and treated mammary tumor cell cultures was quantitated by measuring the supernatant reverse transcriptase activity in exogenous reaction using poly(rC).oligo(dG) as template-primer. Two days after exposure, the synthetic glucocorticoid, dexamethasone (DXMT), increased spontaneous MuMTV production at optimal concentration (0.1 mumol) up to ten times. Dibutyryl derivative of cyclic AMP had no effect on spontaneous MuMTV production, whereas the drug potentiated suboptimal concentrations of the glucocorticoid. Natural prostaglandins, potent agonists of adenylate cyclase catalyzing intracellular synthesis of cyclic AMP, enhanced both basal (up to five times) and DXMT-stimulated (up to 1.6 times) MuMTV replication. The MuMTV-stimulating activity of prostaglandins decreased in the order of PGA1 greater than PGE1 greater than PGB1 greater than PGF2 alpha. Prostaglandins can be replaced partially by norepinephrine and isoproterenol by enhancing the DXMT-mediated MuMTV stimulation, whereas these drugs remained without effect on spontaneous MuMTV production. Theophylline, an antagonist of cAMP-phosphodiesterase converting cAMP to AMP, enhanced the virus-stimulating activity of DXMT as well as of prostaglandins. The enhancement of MuMTV production by adenylate cyclase agonists do not correlate absolutely with the estimates of intracellular cAMP levels, since the highest amounts of cAMP has been repeatedly observed in cells treated with PGE1 and norepinephrine. The results indicate that besides hormones, other hormone-like substances and cyclic nucleotides may be involved in the complex mechanism of hormone-regulated MuMTV genome expression.

Adenocarcinoma↗
PubMed1978

The effects of dextroamphetamine on kinesthetic figural aftereffects.

The effect of dextroamphetamine, primarily a central stimulant, on kinesthetic figural aftereffects (KFAEs) was examined. The subjects were selected after preliminary testing with the Eysenck Personality Inventory and were classified into three groups: extraverts, ambiverts, and introverts. d-Amphetamine was used at three dose levels and a control group was included for purposes of comparison. The 3 X 4 randomized block design was replicated ten times. KFAEs were measured under two sets of conditions, i.e., before and after the induction experience. The results support the following conclusions: (1) neither personality grouping nor drug treatment during preinduction trials significantly affected KFAE; (2) both types of variables were, however, significantly related to behavior during the postinduction trials; (3) the extraverted subjects showed larger KFAEs than ambiverted and introverted subjects under placebo condition; (4) the extent of KFAE was reduced in extraverted and enhanced in introverted subjects under the influence of the drug; (5) there were significant interactions between the drug treatments and personality variables in effects on KFAE.

Adolescent↗
PubMed1983

Ultrastructural features of the murine cutaneous microvasculature after exposure to polychlorinated biphenyl compounds (PCBs) and benzo-(a)-pyrene (BAP).

Exposure to polychlorinated biphenyl compounds (PCBs) has resulted in a variety of cutaneous effects in several species. When mice were exposed to PCBs through the diet and to benzo-(a)-pyrene (BAP) by topical application, hyperkeratinization occurred in the epidermis and hyperkeratinized cysts occasionally formed, but alterations were also observed in the dermis and in small cutaneous blood vessels, particularly capillaries and venules. The luminal borders of the endothelial cells often became irregularly ruffled, and pinocytotic vesicles increased in number and varied considerably in size. Subjacent to the endothelium and pericytes, the basal laminae were either replicated many times or extensively thickened. These effects were attributable to PCBs but not to BAP with the methods and dosages employed. Although endotheliocytosis has been reported in birds exposed to PCBs, vascular effects have not been previously described in mammals treated with these compounds.

Animals↗
PubMed1997

Taping methods and tape types for securing oral endotracheal tubes.

PURPOSE: To evaluate tapes and taping methods with respect to the minimum force required to dislodge endotracheal tubes (ETTs). METHODS: A simulated face model consisting of a section of PVC pipe was used. The ETT was attached to a piezo-electric force transducer and pullout force was manually applied in a vertical, right or left direction. Five tape types were tested: Curity, Leukosilk, Hy.tape, Leukopore, and Transpore, Seven taping methods were used to secure the ETT. The methods differed with respect to tape width and whether the tape was split along its longitudinal axis. Each taping condition was replicated 20 times (7 methods x 5 tapes x 3 directions) for a total of 2100 pullout tests. RESULTS: Minimum forces to dislodge ETTs were higher (P < 0.05) with Curity tape (mean +/- SD; 135 +/- 75 N) than with the other tapes (Leukosilk: 93 +/- 51 N, Hy.tape: 78 +/- 34 N, Leukopore: 47 +/- 32, and Transpore: 37 +/- 23 N). The most secure taping method was achieved by taping the ETT, using 2.5 cm wide Curity tape, in a circumferential fashion to both the upper and lower borders of the simulated mouth opening, and reinforcing these tapes with two strips applied longitudinally across the borders of the mouth opening (method 7). Taping methods which involved splitting the tape along its longitudinal axis resulted in lower minimal pullout forces whenever the pullout force was directed towards the side of attachment (P < 0.05 vs right and vertical direction). CONCLUSION: There are differences in ETT pullout forces and mechanisms of dislodgement depending on taping method and tape type.

Humans↗
PubMed2001

Effects of Elevated Carbon Dioxide and Nitrogen Fertilization on Mycorrhizal Fine Roots and the Soil Microbial Community in Beech-Spruce Ecosystems on Siliceous and Calcareous Soil.

To study the responses of forests to global change, model ecosystems consisting of beech and spruce trees were maintained in open top chambers for 4 years under four conditions, namely with normal and elevated CO2 and with low and high nitrogen input, each replicated four times. Each open top chamber (height 3 m, diameter 3 m, soil depth 1.5 m) contained two separate soil compartments containing nutrient-poor siliceous and nutrient-rich calcareous soil. Here, we focus on the fine roots and the soil microbial community in these model ecosystems. At the time of planting, the fine roots were cut back according to forestry practice, and the newly formed roots were colonized by the indigenous soil microflora. After 4 years, the total biomass of fine roots, when averaged over all treatments, was almost the same in each of the two soil types; it was highest in the top 100 mm of soil (60%) and decreased sharply in deeper soil layers. Fungal biomass associated with the fine roots, consisting mainly of ectomycorrhizal fungi, was estimated using the ergosterol content as a marker. It was much higher in fine roots in the siliceous than in the calcareous soil, indicating considerably enhanced ectomycorrhiza formation in the nutrient-poor siliceous soil. Elevated atmospheric CO2 stimulated fine root production by ca. 85% and 43% in the top 100 mm of calcareous and siliceous soils respectively. Increased nitrogen input caused a slightly reduced production of fine root biomass in the calcareous soil but increased it by 33% in the siliceous soil. Marker substances for microorganisms were analyzed in the root-free soil. The amounts of carbon released by fumigation/extraction (a general marker for microbial biomass) and chitin (a marker for fungal biomass) were significantly higher in the top layer of the siliceous than of the calcareous soil, but they did not respond significantly to the treatments with elevated CO2 or the nitrogen fertilizer. The total concentration of the phospholipid fatty acids (PLFAs) and the number of the PLFAs did not differ between the two soil types. However, four of the eight most abundant PLFAs differed significantly between the two soil types. Principal component analysis revealed clearly separated clusters for the two soil types. Although analysis did not reveal any significant changes in response to the treatments, the concentration of the PLFA typical for ectomycorrhizal fungi was significantly higher under conditions of elevated CO2 in the nutrient-rich calcareous soil.

Journal Article↗
PubMed1997

Deletion of flanking ARS elements does not affect meiotic recombination at the HIS4 locus in yeast.

The HIS4-BIK1 interval on chromosome III of Saccharomyces cerevisiae contains a hotspot for meiotic recombination. Previous reports demonstrated that the initiating lesion is a double-stranded break which is subsequently processed in an asymmetric manner. Data presented here show that the efficiency of initiation of meiotic recombination is unaffected by the deletion of flanking ARS elements, and that the distribution of recombinants is not altered in strains heterozygous for these deletions. These results suggest that the initiation of recombination is not affected by the time of replication of the hotspot at HIS4. The data also indicate that altering the direction of replication-fork movement through the HIS4 region does not affect meiotic recombination.

Alcohol Oxidoreductases↗
PubMed2004

Effects of tonicity, digestive enzymes and bile salts, and nutrient media on the survival of excysted metacercariae of Echinostoma caproni.

The effects of tonicity, digestive enzymes and bile salts, and various nutrients added to Locke's solution were studied on the chemically excysted metacercariae of Echinostoma caproni. Metacercariae were maintained at 37.5 degrees C in multiwell chambers, ten per 0.5 ml of test solution; each experiment was replicated five times. Most metacercariae maintained in deionized water or Locke's 2x solution were dead within 2 h. About 85% and 55% of the metacercariae were alive at 8 h in Locke's 1x and Locke's 0.5x, respectively. Metacercariae of this species are osmoconformers, as is the case for adult digeneans. All metacercariae were dead in an acid saline or acid pepsin medium by 2 h. About 50% of the metacercariae were alive in an alkaline trypsin-bile salts medium at 4 h. These results suggest that the acidic pepsin environment in the stomach of a definitive host would be detrimental to the survival of excysted metacercariae, but prolonged survival in alkaline trypsin-bile salts would facilitate establishment of this larval stage in the mucosa of the host small intestine. Studies on excysted metacercariae in Locke's 1x supplemented with various nutrients showed that optimal survival occurred in Locke's plus 0.1% glucose and in Locke's 1x plus 1% hen's egg yolk. Significant survival of excysted metacercariae in Locke's 1x supplemented with either 0.1% proline, 0.1% threonine, or 0.1% serine did not occur.

Animals↗
PubMed2004

Bioinformatic analysis of primary endothelial cell gene array data illustrated by the analysis of transcriptome changes in endothelial cells exposed to VEGF-A and PlGF.

We recently published a review in this journal describing the design, hybridisation and basic data processing required to use gene arrays to investigate vascular biology (Evans et al. Angiogenesis 2003; 6: 93-104). Here, we build on this review by describing a set of powerful and robust methods for the analysis and interpretation of gene array data derived from primary vascular cell cultures. First, we describe the evaluation of transcriptome heterogeneity between primary cultures derived from different individuals, and estimation of the false discovery rate introduced by this heterogeneity and by experimental noise. Then, we discuss the appropriate use of Bayesian t-tests, clustering and independent component analysis to mine the data. We illustrate these principles by analysis of a previously unpublished set of gene array data in which human umbilical vein endothelial cells (HUVEC) cultured in either rich or low-serum media were exposed to vascular endothelial growth factor (VEGF)-A165 or placental growth factor (PlGF)-1(131). We have used Affymetrix U95A gene arrays to map the effects of these factors on the HUVEC transcriptome. These experiments followed a paired design and were biologically replicated three times. In addition, one experiment was repeated using serial analysis of gene expression (SAGE). In contrast to some previous studies, we found that VEGF-A and PlGF consistently regulated only small, non-overlapping and culture media-dependant sets of HUVEC transcripts, despite causing significant cell biological changes.

Cells, Cultured↗
PubMed2006

Early replication banding in Leporinus species (Osteichthyes, Characiformes) bearing differentiated sex chromosomes (ZW).

There are few examples of differentiated sex chromosomes in fishes. In the genus Leporinus, seven species present a highly differentiated ZW system, derived from heterochromatinization process. Cytogenetic analyses carried out in three of these fish species, Leporinus obtusidens, L. elongatus and L. reinhardti, through RBG-banding, showed late replication bands, coincident with heterochromatic regions in both Z and W chromosomes. A similar interstitial early replication segment was observed in the complex heterochromatic region along the Wq arms in the three species, which might correspond to a pseudoautosomal segment (SD, sex determining locus). Asynchrony related to the replication pattern among different Z chromosomes was not observed. When the identification of nuclear organizer regions by silver nitrate was performed over chromosomal preparations previously exposed to 5-bromo-2'-deoxyuridine (BrdU), remarkable positive signals at interstitial and telomeric position were observed on the q arms of W chromosomes in the species L. elongatus and L. reinhardti. The absence of 18S ribosomal RNA gene loci in this region, formerly demonstrated by FISH, indicates that this argentophilic behavior is putatively due to heterochromatin decondensation caused by BrdU incorporation, favoring such Ag+ reaction. Early and late replication bands were also observed in the heterochromatic portions of Z and W chromosomes, indicating that euchromatic and heterochromatic regions are interspersed. The present data suggest a significant level of heterochromatic complexity in the sex chromosomes of each species. On the other hand, the replication pattern shared by them supports a monophyletic origin.

Animals↗