Search PubMed⌕ Search

Biomedical subjects

A J Shepherd

Publications and source records attributed to A J Shepherd.

At least 19 recordsLinked to original sources
PubMed2006

Local and global motion after-effects are both enhanced in migraine, and the underlying mechanisms differ across cortical areas.

Visual after-effects are illusions that occur after prolonged viewing of visual displays (pattern adaptation). The motion after-effect (MAE), for example, is an illusory impression of motion that is seen after viewing moving displays. After-effects have been used extensively in basic vision research as well as in clinical settings, and have been reported to be enhanced in migraine. Pattern adaptation is a cortical phenomenon that reflects both cellular mechanisms acting within individual neurons and specific interactions between groups of neurons activated by the adapting display. A remarkable feature of the MAE is that its duration is only slightly reduced if a delay is inserted between the end of the adaptation and the test display ('storage'). The reduction is consistent with recovery of the cellular component, and the residual with network changes that are maintained during the delay. This study aimed (i) to assess explanations for prolonged MAEs in migraine by teasing apart the proposed cellular and network components of adaptation using storage; (ii) to determine the extent of cortical abnormality in migraine using local and global MAEs, which reflect adaptation at different stages of the visual system. Fifty migraine (22 with, 28 without aura) and 50 control participants adapted to motion before viewing a stationary or dynamic (random motion) test, which consequently appeared to move in the opposite direction (local and global MAEs, respectively). Half of the trials included a delay between the adapting and test displays. The results extend those reported previously, as both local and global MAEs lasted longer in migraine compared with the control group. Global MAEs survived delays almost completely for both groups, whereas local MAEs were reduced to a greater extent in migraine. There were no significant differences between migraine subgroups classified according to the presence or absence of visual aura. These results suggest that cellular recovery is slowed in migraine for early but not later visual cortical areas. Sustained network changes following adaptation are implicated across cortical areas. Differences between people with and without migraine on various measures of visual perception have been attributed to abnormal cortical processing in migraine, variously described by hyperexcitability, heightened responsiveness and/or a lack of intra-cortical inhibition. The results are not consistent with hyperexcitability resulting from a lack of inhibition in migraine, but are consistent with extended suppression of intra-cortical excitation. The implications of these results for alternative models of hyperexcitability are discussed.

Adaptation, Physiological↗
PubMed2005

Colour vision in migraine: selective deficits for S-cone discriminations.

Three studies are reported that explore colour perception in migraine. In each, sensitivity for colours detected selectively by the S-cones and the L- and M-cones was assessed separately. The first study assessed the discrimination of small colour differences using the Farnsworth-Munsell 100-hue test. The second assessed threshold detection for purple, yellow, red and green targets on five equiluminant background colours. The third examined supra-threshold colour scaling using two colour series, purple-yellow and red-green. Each study indicated that differences in colour perception between migraine and control groups were restricted to colours detected by the S-cones, there were no differences in performance for colours detected by the L- and M-cones. The results are discussed in terms of possible pathologies in the early visual pathways.

Adolescent↗
PubMed2004

Childhood H. pylori: disappearing disease or chronic infection?

Helicobacter pylori is one of the commonest chronic bacterial infections worldwide. It is acquired during childhood and its persistence has implications for health in later life. In adults, it is the principle cause of duodenal ulcer disease and there is evidence of an association between H. pylori and gastric cancer. However, most colonized people are asymptomatic. The prevalence of H. pylori increases with age but there is a striking difference between the rates in developed and developing countries. As no significant non-human or environmental source for this infection has been identified, person to person spread is almost certainly the main mode of transmission. Community nurses should be aware of this micro-organism as a potential cause of illness in children, and that they can play a role in promoting hygiene practices and educating families so that the risk of acquisition may be reduced. This review discusses the clinical features, prevalence, risk factors for transmission, diagnosis and treatment of H. pylori.

Age Distribution↗
PubMed2003

Comparison of electron microscopic techniques for enumeration of endogenous retrovirus in mouse and Chinese hamster cell lines used for production of biologics.

Murine myeloma and Chinese hamster ovary cells are used widely in the manufacture of recombinant proteins for biopharmaceuticals. However, rodent cell lines express endogenous retrovirus, which necessitates appropriate design of purification processes to remove virus in excess of the calculated maximum retroviral load. Currently, electron microscopy is the method of choice for determination of retroviral titre in bulk harvest. In this study we compared three electron microscopy techniques to determine retroviral titre in bulk harvest. These were direct negative stain, negative stain after sucrose-density purification and thin section electron microscopy of pelleted supernatant. The study demonstrated that the level of C-type retrovirus associated with cells was predictive of the viral load in cell culture supernatants. The most accurate method for quantifying viral load was direct counting, followed by thin section of pelleted supernatant and negative stain after sucrose concentration. The most practical method was thin section of resuspended pelleted supernatant, which gave improved detection limits.

Animals↗
PubMed2003

Characterisation of endogenous retrovirus in rodent cell lines used for production of biologicals.

Rodent cells are used widely to manufacture recombinant proteins for pharmaceutical use in humans and animals. However, all rodent cell lines express endogenous retroviruses that require appropriate testing regimes for identification and characterisation. In this communication we report the results of transmission electron microscopy, reverse transcriptase assay and infectious virus assays for retrovirus in 185 manufacturer cell banks of mouse, rat or hamster origin. The results indicated considerable variability of retroviral expression levels by transmission electron microscopy and reverse transcriptase assay, but nevertheless characteristic features of each cell type were observed. Infectious retrovirus was detected in mouse myeloma and hybridoma cell lines, but not in cell lines of hamster or rat origin. There was no evidence of contamination of cell banks with exogenous retrovirus. The results of retroviral characterisation of the parental mouse cell lines NS0, NS-1 and Sp2/0Ag14 by the above assays were consistent with the results of the survey. Co-cultivation of the above parental mouse cell lines with mouse and human cell lines suggested that the ability to infect human cells was related to threshold susceptibility of cell types and the levels of expression of infectious xenotropic retrovirus by mouse cells.

Animals↗
PubMed2003

Evaluation of protocol using gene capture and PCR for detection of Helicobacter pylori DNA in feces.

The route of transmission of Helicobacter pylori, which is usually acquired in childhood and is one of the most common bacterial infections in humans, remains undetermined. Mapping the distribution of H. pylori genotypes within families could help to determine the routes of transmission and risk factors. Here we describe a noninvasive method for obtaining H. pylori DNA isolates from the feces of children. Children presenting with gastrointestinal symptoms at the Royal Hospital for Sick Children were tested for gastric H. pylori colonization by using the 13C-urea breath test (UBT) and were asked to provide fecal samples, which were tested for H. pylori by using the HpSA fecal antigen test. DNA was purified from fecal samples by using a novel method of gene capture with subsequent H. pylori PCR analysis. Fifteen UBT-positive and 15 UBT-negative children participated in the study. The positive and negative predictive values for the assay were 80 and 100%, respectively. Fecal DNA purification followed by H. pylori PCR analysis is an effective tool for harvesting H. pylori DNA isolates from the feces of children. This technique may be developed to allow the diagnosis and noninvasive genotyping of H. pylori in children and their families.

Antigens, Bacterial↗
PubMed2002

Pattern-reversal visual evoked potentials in infants: gender differences during early visual maturation.

This paper investigates gender differences in the peak latency and amplitude of the P1 component of the pattern-reversal visual evoked potential (pattern-reversal VEP) recorded in healthy term infants. Pattern-reversal VEPs in response to a series of high contrast black and white checks (check widths 120', 60', 30', 24', 12', 6') were recorded in 50 infants (20 males, 30 females) at 50 weeks post-conceptional age (PCA) and in 49 infants (22 males, 27 females) at 66 weeks PCA. Peak latency of the major component, P1, was considerably shorter in female compared with male infants. Differences in head circumference do not entirely account for the gender differences in peak latency reported here. A gender difference in P1 amplitude was not detected. These findings stress the importance of considering gender norms as well as age-matched norms when utilizing the pattern-reversal VEP in clinical investigations. Studies including a wider range of ages are clearly necessary in order to establish whether the earlier peak latencies in female infants represents a difference in the onset or rate of visual maturation.

Age Factors↗
PubMed2002

Emmetropisation following preterm birth.

BACKGROUND/AIMS: Even in the absence of retinopathy of prematurity (ROP), premature birth signals increased risk for abnormal refractive development. The present study examined the relation between clinical risk factors and refractive development among preterm infants without ROP. METHODS: Cycloplegic refraction was measured at birth, term, 6, 12, and 48 months corrected age in a cohort of 59 preterm infants. Detailed perinatal history and cranial ultrasound data were collected. 40 full term (plus or minus 2 weeks) subjects were tested at birth, 6, and 12 months old. RESULTS: Myopia and anisometropia were associated with prematurity (p<0.05). More variation in astigmatic axis was found among preterm infants (p<0.05) and a trend for more astigmatism (p<0.1). Emmetropisation occurred in the preterm infants so that at term age they did not differ from the fullterm group in astigmatism or anisometropia. However, preterm infants remained more myopic (less hyperopic) than the fullterm group at term (p<0.05) and those infants born <1500 g remained more anisometropic than their peers until 6 months (p<0.05). Infants with abnormal cranial ultrasound were at risk for higher hyperopia (p<0.05). Other clinical risk factors were not associated with differences in refractive development. At 4 years of age 19% of the preterm group had clinically significant refractive errors. CONCLUSION: Preterm infants without ROP had high rates of refractive error. The early emmetropisation process differed from that of the fullterm group but neither clinical risk factors nor measures of early refractive error were predictive of refractive outcome at 4 years.

Anisometropia↗
PubMed2002

Increased visual after-effects in migraine following pattern adaptation extend to simultaneous tilt illusion.

Much previous research into visual processing in migraine supports a model of abnormal cortical processing, in between the headache attacks, that is characterised by hyperexcitability, heightened responsiveness, a lack of habituation and/or a lack of intra-cortical inhibition. Shepherd (2001) reported two adaptation studies that challenged this view, one using the tilt after-effect, the second using the motion after-effect. Models of cortical function in migraine based on hyperexcitability and a lack of inhibition lead to specific predictions in an adaptation study: there should have been smaller after-effects in people with migraine than in people without. Both experiments, however, revealed larger after-effects in the migraine group than in the control group. Here, these results are extended to the simultaneous tilt illusion and an identical pattern of results was obtained: there were consistently larger effects in the migraine group than in the control group. The results from the three experiments are not consistent with a lack of inhibition in migraine. The results are discussed in terms of alternative models of cortical function, including a lack of excitation and reduced central energy reserves.

Adaptation, Ocular↗
PubMed2001

VIDA: a virus database system for the organization of animal virus genome open reading frames.

VIDA is a new virus database that organizes open reading frames (ORFs) from partial and complete genomic sequences from animal viruses. Currently VIDA includes all sequences from GenBank for Herpesviridae, Coronaviridae and Arteriviridae. The ORFs are organized into homologous protein families, which are identified on the basis of sequence similarity relationships. Conserved sequence regions of potential functional importance are identified and can be retrieved as sequence alignments. We use a controlled taxonomical and functional classification for all the proteins and protein families in the database. When available, protein structures that are related to the families have also been included. The database is available for online search and sequence information retrieval at http://www.biochem.ucl.ac.uk/bsm/virus_database/ VIDA.html.

Animals↗
PubMed2001

A rapid classification protocol for the CATH Domain Database to support structural genomics.

In order to support the structural genomic initiatives, both by rapidly classifying newly determined structures and by suggesting suitable targets for structure determination, we have recently developed several new protocols for classifying structures in the CATH domain database (http://www.biochem.ucl.ac.uk/bsm/cath). These aim to increase the speed of classification of new structures using fast algorithms for structure comparison (GRATH) and to improve the sensitivity in recognising distant structural relatives by incorporating sequence information from relatives in the genomes (DomainFinder). In order to ensure the integrity of the database given the expected increase in data, the CATH Protein Family Database (CATH-PFDB), which currently includes 25,320 structural domains and a further 160,000 sequence relatives has now been installed in a relational ORACLE database. This was essential for developing more rigorous validation procedures and for allowing efficient querying of the database, particularly for genome analysis. The associated Dictionary of Homologous Superfamilies [Bray,J.E., Todd,A.E., Pearl,F.M.G., Thornton,J.M. and Orengo,C.A. (2000) Protein Eng., 13, 153-165], which provides multiple structural alignments and functional information to assist in assigning new relatives, has also been expanded recently and now includes information for 903 homologous superfamilies. In order to improve coverage of known structures, preliminary classification levels are now provided for new structures at interim stages in the classification protocol. Since a large proportion of new structures can be rapidly classified using profile-based sequence analysis [e.g. PSI-BLAST: Altschul,S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Nucleic Acids Res., 25, 3389-3402], this provides preliminary classification for easily recognisable homologues, which in the latest release of CATH (version 1.7) represented nearly three-quarters of the non-identical structures.

Computational Biology↗
PubMed2001

Increased visual after-effects following pattern adaptation in migraine: a lack of intracortical excitation?

Much research on visual function in migraine has examined early aspects of visual processing, often using detection or discrimination measures and stimuli reported to trigger an attack, e.g. striped patterns or flickering lights. Differences between people with and without migraine have been attributed to abnormal cortical processing in migraine, variously described by interictal hyperexcitability, heightened responsiveness, a lack of habituation and/or a lack of intra-cortical inhibition. Here, two experiments are presented that explore a uniquely cortical phenomenon, pattern or contrast adaptation, one using the motion after-effect, one the tilt after-effect. Pattern adaptation reflects specific interactions between groups of neurones and is therefore ideally suited to address proposed models of cortical function in migraine. These models lead to specific predictions in an adaptation study: there should be smaller effects in people with migraine than in people without. The results from both adaptation experiments, however, revealed larger effects in migraine sufferers than in headache-free control subjects. There were no differences between migraine subgroups classified according to the presence or absence of aura. These results are discussed in terms of models of cortical function in migraine.

Adaptation, Psychological↗
PubMed2000

Visual contrast processing in migraine.

Some migraine sufferers report certain visual patterns can reliably trigger a migraine attack, such as high contrast striped patterns or flickering lights. Differences between people with and without migraine on tasks that involve these patterns have been attributed to abnormal cortical processing in migraine, although the locus and extent of the abnormality remains unclear, as is any relationship between impairment on various visual tasks. In this study 58 migraine sufferers and 61 control subjects participated in three visual tasks involving striped patterns. One assessed pattern sensitivity with high contrast patterns, the second detection thresholds for low contrast patterns and the third supra-threshold contrast scaling. With each measure, the performance of migraine sufferers as a group differed to the performance of non-migraine control subjects. There were no significant differences between the migraine subgroups when classified according to the presence or absence of aura. Cross-correlating the results from the three tasks, however, revealed consistent associations: impaired or extreme responses on one task were associated with impaired or extreme responses on the others. There were no overall effects due to migraine duration, the frequency of migraine attacks or the time since the last attack. These results are discussed in the context of visually induced migraine, proposed causes of abnormal cortical function in migraine and the prospects for developing clinically useful tests of visual function.

Adolescent↗
PubMed2000

Comparison of an enzyme immunoassay for the detection of Helicobacter pylori antigens in the faeces with the urea breath test.

BACKGROUND: Current diagnostic tests for Helicobacter pylori are invasive (endoscopy) or indirect (urea breath test, serology). AIMS: To evaluate a new enzyme immunoassay (EIA) which detects H pylori antigens in faeces, by comparing its sensitivity and specificity in children with the (13)C urea breath test (UBT). METHODS: A total of 119 children underwent a UBT and provided a faecal sample for antigen testing within seven days. After an overnight fast each child provided a pretest breath sample, and samples at 30 and 40 minutes after ingestion of 100 mg (13)C labelled urea. (13)C enrichment of breath was measured by isotope ratio mass spectrometry. Faeces were stored at -70 degrees C until antigen testing, using the EIA. Samples were read spectrophotometrically at 450 nm and results were interpreted using recommended cut offs of optical density <0.14 as negative, >/=0.16 as positive, with >/=0.14 and <0. 16 representing equivocal results. Sensitivity and specificity were calculated using the manufacturer's cut off compared with UBT. RESULTS: Sensitivity and specificity were 88% and 82%, respectively. Negative and positive predictive values were 97% and 58%. CONCLUSIONS: The EIA is an alternative, non-invasive, and easy to use method for the detection of H pylori in children. Its high negative predictive value suggests a role in screening out uninfected children.

Adolescent↗
PubMed2000

Identification of risk factors in blood donors found to have HIV infection.

To ascertain whether current screening procedures for human immunodeficiency virus (HIV) infected blood can be improved, a study of blood donors found by Mersey and North Wales Blood Centre to be HIV positive was made. In total 22 donors were identified, of which 16 were referred to the Department of Genito-Urinary Medicine (GUM) in Liverpool. Most (9/16) should have been excluded from donating because of recognized risk factors. However, in 7 cases no such identifiable factors were found. Although the risk of transfusion transmitted infection is small, there is an argument for testing donated blood for HIV RNA by nucleic acid technology.

Adult↗
PubMed1999

Remodelling colour contrast: implications for visual processing and colour representation.

Colour contrast describes the influence of one colour on the perception of colours in neighbouring areas. This study addresses two issues: (i) the accurate representation of the colour changes; (ii) the underlying visual mechanisms. Observers viewed a haploscopic display in which a standard display was presented to one eye and a matching display to the other. The matches could be represented accurately using a diagram that is a logarithmic transformation of the MacLeod-Boynton (r, b) (1979) chromaticity diagram. Since haploscopic presentation has been described as isolating retinal processes (Whittle, P., & Challands, P.D.C. (1969). The effect of background luminance on the brightness of flashes. Vision Research, 9, 1095-1110; Chichilnisky, E.J., & Wandell, B.A. (1995). Photoreceptor sensitivity changes explain color appearance shifts induced by large uniform backgrounds in dichoptic matching. Vision Research, 35, 239-254), the results are discussed in terms of receptor sensitivity changes and the ratio of receptor contrasts.

Adult↗
PubMed1999

High throughput detection of retrovirus-associated reverse transcriptase using an improved fluorescent product enhanced reverse transcriptase assay and its comparison to conventional detection methods.

The development and application of a novel, sensitive TaqMan fluorescent probe-based product enhanced RT test (F-PERT) for the detection of retrovirus are described. The assay allows discrimination between the amplification signals generated by genuine positive signals that result from retroviral RT activity and the RT-like activity from DNA polymerases. The RT-like activity from DNA polymerases was suppressed by the addition of activated calf-thymus DNA with no reduction in the RT activity. A linear relationship between threshold cycle (C(T)) and the number of virus particles was demonstrated, allowing quantification of retroviruses in unknown samples. The F-PERT assay was able to detect a wide range of retroviral RT activities, including that from porcine endogenous retrovirus (PoERV), murine leukaemia virus (MLV), simian foamy virus (SFV), simian immunodeficiency virus (SIVmac) and squirrel monkey retrovirus (SMRV). The detection limit of SMRV, MLV and PoERV was approximately 100 virion particles and the test was able to detect at least 10(2) molecules of purified RT enzyme. RT activity was not detected in cellular lysates and supernatants from MRC-5, BT, VERO, or Raji cells, whereas RT activity was detected in C1271, Mus dunni, K-Balb, BHK-21, CHO-K1, SP2/0-Ag14 and NSO cell supernatants. RT activity was also detected in the Spodoptera cell line Sf9.

Animals↗