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J E Thomas

Publications and source records attributed to J E Thomas.

At least 37 records · Page 2Linked to original sources
PubMed2002

Experimental simulation of two-particle quantum entanglement using classical fields.

We experimentally demonstrate simulation of two entangled quantum bits using classical fields of two frequencies and two polarizations. Multiplication of optical heterodyne beat signals from two spatially separated regions simulates coincidence detection of two particles. The product signal so obtained contains several frequency components, one of which can be selected by bandpass frequency filtering. The bandpassed signal contains two indistinguishable, interfering contributions, permitting simulation of four polarization-entangled Bell-like states. These classical field methods may be useful in small scale simulations of quantum logic operations that require multiparticle entanglement without collapse.

Journal Article↗
PubMed2002

Detection of Helicobacter pylori DNA in drinking water biofilms: implications for transmission in early life.

AIMS: To provide evidence of water quality as a risk factor for acquisition of Helicobacter pylori in early life, and to identify evidence for its presence within pots used to store drinking water. METHODS AND RESULTS: A prospective cohort study of 65 infants was conducted in the rural village of Keneba, The Gambia. Age of H. pylori colonization was determined and water pot biofilms were tested for H. pylori by sequencing of amplified DNA. Use of supplemental water was a strong risk factor for H. pylori colonization in infants (OR 4.71, 95% CI 1.17-22.5). DNA with 95% homology to the 16S rRNA gene of H. pylori was isolated from biofilms of water pots. CONCLUSIONS: Drinking water may be a reservoir for H. pylori in areas of the developing world where water quality is poor. Early introduction of water, particularly if stored in, or collected from contaminated sources, may be associated with an increased rate of H. pylori colonization.

Base Sequence↗
PubMed2001

Identification and characterisation of PEX6 orthologues from plants.

The sunflower (Helianthus annuus) orthologue of PEX6, an AAA ATPase essential for the biogenesis of peroxisomes in yeasts and mammals, was isolated. HaPex6p is immunologically related to Pichia pastoris Pex6p. Like other genes involved in peroxisome biogenesis and function HaPEX6 mRNA and protein levels peak in early post-germinative growth and mRNA levels also increase in senescent tissue. HaPEX6 identifies probable orthologues in Arabidopsis and rice.

ATPases Associated with Diverse Cellular Activitie↗
PubMed2001

Molecular characterisation of Banana mild mosaic virus, a new filamentous virus in Musa spp..

Banana mild mosaic virus (BanMMV) is a previously undescribed filamentous virus infecting Musa spp. The complete genome has been sequenced from PCR clones and consists of 7352 nucleotides, encoding five open reading frames (ORFs) of 205, 25.5, 12.4, 8.0 and 26.8 kDa, respectively. BanMMV was most closely related to fovea- and carlaviruses, based on phylogenetic analysis using a portion of the viral replicase. Analysis of other parts of the genome revealed similarities with fovea-, carla- and potexviruses, but the virus was not clearly aligned to any previously recognised genus.

3' Untranslated Regions↗
PubMed2001

Degradation of 1,3-dichloropropene by a soil bacterial consortium and Rhodococcus sp. AS2C isolated from the consortium.

A bacterial consortium capable of degrading the fumigant 1,3-D ((Z)- and (E)- 1,3-dichloropropene) was enriched from an enhanced soil. This mixed culture degraded (Z)- and (E)-1,3-D only in the presence of a suitable biodegradable organic substrate, such as tryptone, tryptophan, or alanine. After 8 months of subculturing at 2- to 3-week intervals, a strain of Rhodococcus sp. (AS2C) that was capable of degrading 1,3-D cometabolically in the presence of a suitable second substrate was isolated. (Z)-3-chloroallyl alcohol (3-CAA) and (Z)-3-chloroacrylic acid (3-CAAC), and (E)-3-CAA and (E)-3-CAAC were the metabolites of (Z)- and (E)- 1,3-D, respectively. (E)- 1,3-D was degraded faster than (Z)- 1,3-D by the strain AS2C and the consortium. AS2C also degraded (E)-3-CAA faster than (Z)-3-CAA. Isomerization of (E)- 1,3-D to (Z)- 1,3-D or the (Z) form to the (E) form did not occur.

Allyl Compounds↗
PubMed2001

The African enigma: low prevalence of gastric atrophy, high prevalence of chronic inflammation in West African adults and children.

BACKGROUND: Helicobacter pylori infection is very common in Africa, yet peptic ulcer disease and gastric malignancy are rare. AIM: The aim of this study was to quantify mucosal responses to H. pylori in Gambian adults and children and to estimate the prevalence of antibodies to bacterial virulence factors (cagA and vacA) in a symptomatic population. PATIENTS AND METHODS: Adults (mean 36 SD 12 years) with dyspepsia and children (mean 1.4 years SD 0.4 years) with malnutrition underwent gastroscopy with biopsy. Blood was simultaneously drawn for cagA and vacA antibody status. Histopathological scoring used the modified Sydney classification. RESULTS: Both adults (n = 45) and children (n = 37) mainly demonstrated chronic mild antral inflammation. Only 2/83 cases of focal atrophy (GA) and 4/83 cases of intestinal metaplasia (IM) were observed. Adults tended to demonstrate more frequent acute (AI) and chronic inflammation (CI) (38% compared with 18% and 85% compared with 72%, respectively). Sixty-seven percent of children were cagA IgG+ and 21% vacA IgG+ and 93% of adults were IgG cagA+ and 86% vacA+. There were no differences in mucosal responses between those who were cagA or vacA positive compared with those who were negative. CONCLUSION: Gambian adults and children mount a CI response to H. pylori but GA, IM and AI are uncommon. cagA and vacA are commonly expressed in Gambian strains of H. pylori. Further studies are needed in order to confirm that GA and IM are not late findings in old age.

Adolescent↗
PubMed2001

Capsaicin vanilloid receptor-1 mediates substance P release in experimental pancreatitis.

We examined whether the capsaicin vanilloid receptor-1 (VR1) mediates substance P (SP) release from primary sensory neurons in experimental pancreatitis. Pancreatitis was achieved by 12 hourly injections of caerulein (50 microg/kg ip) in mice. One group received capsazepine (100 micromol/kg sc), a competitive VR1 antagonist, at 4-h intervals. Neurokinin-1 receptor (NK1R) internalization in acinar cells, used as an index of endogenous SP release, was assessed by immunocytochemical quantification of NK1R endocytosis. The severity of pancreatitis was assessed by measurements of serum amylase, pancreatic myeloperoxidase (MPO) activity, and histological grading. Caerulein administration caused significant elevations in serum amylase and pancreatic MPO activity, produced histological evidence of pancreatitis, and caused a dramatic increase in NK1R endocytosis. Capsazepine treatment significantly reduced the level of NK1R endocytosis, and this was associated with similar reductions in pancreatic MPO activity and histological severity of pancreatitis. These results demonstrate that repeated caerulein stimulation causes experimental pancreatitis that is mediated in part by stimulation of VR1 on primary sensory neurons, resulting in endogenous SP release.

Amylases↗
PubMed2001

AKT-1, -2, and -3 are expressed in both normal and tumor tissues of the lung, breast, prostate, and colon.

PURPOSE: The AKT/PKB kinase controls many of the intracellular processes that are dysregulated in human cancer, including the suppression of apoptosis and anoikis and the induction of cell cycle progression. Three isoforms of AKT have been identified: AKT-1, -2, and -3. Selective up-regulation of AKT-3 RNA expression has been reported in hormone-independent breast and prostate cancer cell lines suggesting that AKT-3 expression may be increased with breast or prostate tumor progression. To determine whether AKT-3 RNA expression is selectively up-regulated in human cancers and whether the patterns of AKT RNA expression may change with tumor development, we examined AKT isoform expression by RT-PCR in human cancer cell lines, primary human cancers, and normal human tissues. EXPERIMENTAL DESIGN: AKT-1, -2, and -3 RNA expression was examined by RT-PCR. Because up-regulated AKT-3 expression has been implicated in human breast and prostate cancer progression, we also examined AKT-3 expression levels by semiquantitative RT-PCR using matched normal/tumor first-strand cDNA pairs from colon, breast, prostate, and lung cancers. RESULTS: Our data reveal that the overwhelming majority of both normal and tumor tissues express all three of the AKT isoforms. Moreover, semiquantitative RT-PCR of matched normal/tumor pairs confirmed similar AKT-3 RNA expression levels in both normal and tumor tissue. CONCLUSIONS: Our data show that both normal and tumor tissues express all three of the AKT isoforms and indicate that tumorigenesis does not involve a dramatic shift in the RNA expression patterns of the three AKT isoforms.

Breast↗
PubMed2000

Time-resolved phase-space distributions for light backscattered from a disordered medium.

We demonstrate time-resolved measurement of optical phase-space distributions as a new probe for investigating the propagation of light in disordered media. Phase-space techniques measure the joint transverse position and momentum distribution of the scattered light, and are sensitive to the spatially varying phase and amplitude of the field. Using this method we investigate light backscattered from a random medium. The measurements indicate that the weakly localized component is a phase conjugate of the incident light field. A new model of backscatter, based on Wigner phase-space distributions, elucidates the spatial and angular behavior of the localized and unlocalized components.

Biomedical Engineering↗
PubMed2000

Development of a multiplex immunocapture PCR with colourimetric detection for viruses of banana.

A multiplex, immunocapture PCR (M-IC-PCR) was developed for the simultaneous detection of three viruses from crude sap extracts of banana and plantain (Musa spp.). A reverse transcription step was required for Banana bract mosaic virus and Cucumber mosaic virus, which have ssRNA genomes. The detection of Banana bunchy top virus (ssDNA genome) was not adversely affected by inclusion in this step. All the three viruses could be detected simultaneously from a mixed infection. Identification and detection of individual viruses was achieved through the visualisation of discretely sized PCR amplicons by gel electrophoresis. Alternatively, a colourimetric microplate detection system utilising digoxigenin-labelled virus-specific probes was used. The latter assay was up to five times more sensitive than detection by gel electrophoresis and between 25 and 625 times more sensitive than ELISA for the various viruses. Careful selection of PCR primers was necessary to ensure the detection of a wide range of virus isolates and to avoid detrimental interactions between heterologous templates and primers.

Badnavirus↗
PubMed2000

Ataxic dysarthria.

Although ataxic dysarthria has been studied with various methods in several languages, questions remain concerning which features of the disorder are most consistent, which speaking tasks are most sensitive to the disorder, and whether the different speech production subsystems are uniformly affected. Perceptual and acoustic data were obtained from 14 individuals (seven men, seven women) with ataxic dysarthria for several speaking tasks, including sustained vowel phonation, syllable repetition, sentence recitation, and conversation. Multidimensional acoustic analyses of sustained vowel phonation showed that the largest and most frequent abnormality for both men and women was a long-term variability of fundamental frequency. Other measures with a high frequency of abnormality were shimmer and peak amplitude variation (for both sexes) and jitter (for women). Syllable alternating motion rate (AMR) was typically slow and irregular in its temporal pattern. In addition, the energy maxima and minima often were highly variable across repeated syllables, and this variability is thought to reflect poorly coordinated respiratory function and inadequate articulatory/voicing control. Syllable rates tended to be slower for sentence recitation and conversation than for AMR, but the three rates were highly similar. Formant-frequency ranges during sentence production were essentially normal, showing that articulatory hypometria is not a pervasive problem. Conversational samples varied considerably across subjects in intelligibility and number of words/ morphemes in a breath group. Qualitative analyses of unintelligible episodes in conversation showed that these samples generally had a fairly well-defined syllable pattern but subjects differed in the degree to which the acoustic contrasts typical of consonant and vowel sequences were maintained. For some individuals, an intelligibility deficit occurred in the face of highly distinctive (and contrastive) acoustic patterns.

Adolescent↗
PubMed2000

Differences in genotypes of Helicobacter pylori from different human populations.

DNA motifs at several informative loci in more than 500 strains of Helicobacter pylori from five continents were studied by PCR and sequencing to gain insights into the evolution of this gastric pathogen. Five types of deletion, insertion, and substitution motifs were found at the right end of the H. pylori cag pathogenicity island. Of the three most common motifs, type I predominated in Spaniards, native Peruvians, and Guatemalan Ladinos (mixed Amerindian-European ancestry) and also in native Africans and U.S. residents; type II predominated among Japanese and Chinese; and type III predominated in Indians from Calcutta. Sequences in the cagA gene and in vacAm1 type alleles of the vacuolating cytotoxin gene (vacA) of strains from native Peruvians were also more like those from Spaniards than those from Asians. These indications of relatedness of Latin American and Spanish strains, despite the closer genetic relatedness of Amerindian and Asian people themselves, lead us to suggest that H. pylori may have been brought to the New World by European conquerors and colonists about 500 years ago. This thinking, in turn, suggests that H. pylori infection might have become widespread in people quite recently in human evolution.

Amino Acid Isomerases↗
PubMed2000

Diagnostic value of immunocytochemistry in leptomeningeal tumor dissemination.

Differentiating chronic aseptic meningitis from leptomeningeal carcinomatosis or gliomatosis can be difficult, particularly when the differentiation is based solely on routine cytologic examination. The diagnosis of cerebrospinal fluid tumor dissemination in at-risk patients requires cytologic examination of cerebrospinal fluid and radiography of the leptomeninges. Routine cytologic examination alone has proven less than desirable, in most instances providing confirmation in as little as 50% of cases in the first lumbar puncture. This percentage increases to 85% to 90% after multiple lumbar punctures. We retrospectively reviewed 2 cases of leptomeningeal dissemination (one gliomatosis, the other carcinomatosis) with initial false-negative test results. However, after further examination of the cerebrospinal fluid by selected battery of immunocytochemical stains, both cases were identified as positive for malignancy (ie, false negatives). Immunocytochemistry can be useful in distinguishing chronic aseptic meningitis from leptomeningeal carcinomatosis or gliomatosis in patients at risk or when abnormal cells are seen on routine cerebrospinal fluid cytologic examination.

Adult↗
PubMed2000

The interventional neuroradiology suite as an operating room.

The evolution of new neurointerventional techniques, along with improved imaging and catheter developments, has changed the interventional suite into a subspecialized operating room. This article discusses this operating room as a combination of neuroanesthesia, neuromonitoring, nursing, and technician support coordinated by the neruointerventionalist. The coordination of elective and emergent intervention is also discussed, from conception to completion of the plan, including arteriovenous emoblization, endovascular aneurysm obliteration, intra-arterial thrombolysis, extracranial and intracranial carotid angioplasty, and stenting. Specific examples are illustrated, including pharmacologic intervention complementing these techniques.

Cerebrovascular Disorders↗
PubMed2000

Endosaccular thrombosis of cerebral aneurysms: strategy, indications, and technique.

Endovascular occlusion of a cerebral aneurysm refers to the induction of thrombosis within the aneurysm by any of several methods, all of which make use of devices delivered through the bloodstream of the parent vessel. The type of endovascular treatment most commonly used today for aneurysm treatment is the detachable platinum microcoil designed by Guglielmi, known as the GDC. The GDC has been used more frequently and successfully over the last decade as a treatment alternative to microneurosurgical clip ligation. A continual and rapid technological evolution and increasing clinical experience of neurosurgeons and neuroradiologists using this technology have been important contributors to its success. Endovascular coil embolization may hold advantages over microneurosurgical clip ligation under selected clinical circumstances. It is also necessary to acknowledge and outline the disadvantages of this form of treatment in an unbiased manner.

Cerebral Angiography↗
PubMed1999

Characterisation of a virus from Australia that is closely related to papaya mosaic potexvirus.

We have isolated a previously undescribed potexvirus from Alternanthera pungens (Amaranthaceae) in southern Queensland, Australia. This virus was shown to have a moderately wide experimental host range, infecting plants in nine of the twelve families tested. Using specific antibodies, a plate trapped antigen ELISA was developed, allowing detection of virions down to 0.8 microgram/ml of leaf extract. Virions averaged 554 nm long and had a capsid protein with a M(r) of 23.1 x 10(3). A portion of the genome containing the capsid protein ORF and 3' untranslated region was cloned and sequenced. From both serological and amino acid sequence comparisons, the virus was shown to be closely related to papaya mosaic potexvirus (PMV). To determine the taxonomic status of the virus, we assessed variation in the amino acid sequence of capsid proteins of distinct species within the potexvirus genus, as well as variation between strains of the same virus. When the core region of the capsid proteins were compared, distinct species had a maximum of 62.2% sequence identity, whereas strains had a minimum of 88.8% identity. By comparison, the core region of the capsid proteins of the Alternanthera virus and PMV had 79.8% identity. We have concluded that the Alternanthera virus is a different species from PMV, and its relationship with PMV resembles that of potyvirus subgroup members.

Amino Acid Sequence↗