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PubMed1998

Pearls and pitfalls in clinical neuroradiology.

Imaging technology continues to advance at a rapid pace. Central nervous system imaging, in particular, is an invaluable tool for the practicing clinical neurologist. Although computed tomography (CT) was once the procedure of choice for neuroimaging, CT has been surpassed by magnetic resonance imaging (MRI) because of the latter's greater sensitivity. MRI exquisitely demonstrates brain and spine pathology by means of its multiplanar capability and its ability to generate different tissue contrast with various pulse sequences. However, artifacts as well as normal anatomic variants can mimic significant CNS pathology. An understanding of the technology involved in producing and interpreting these images is necessary in order that protocols can be tailored for each individual patient and that unimportant findings are not misinterpreted as being pathologic. This article will present cases illustrating some of the common neuroimaging artifacts and normal variants as well as important differential diagnoses of certain imaging findings.

Adult↗

PubMed2004

Incipient evolution of Wolbachia compatibility types.

Cytoplasmic incompatibility (CI) is induced in arthropods by the maternally inherited bacterium Wolbachia. When infected males mate with uninfected females or with females bearing a different Wolbachia variant, paternal chromosomes behave abnormally and embryos die. This pattern can be interpreted as resulting from two bacterial effects: One (usually termed mod, for modification) would affect sperm and induce embryo death, unless Wolbachia is also present in the egg, which implies the existence of a second effect, usually termed resc, for rescue. The fact that CI can occur in crosses between males and females infected by different Wolbachia shows that mod and resc interact in a specific manner. In other words, different compatibility types, or mod/resc pairs seem to have diverged from one (or a few) common ancestor(s). We are interested in the process allowing the evolution of mod/resc pairs. Here this question is addressed experimentally after cytoplasmic injection into a single host species (Drosophila simulans) by investigating compatibility relationships between closely related Wolbachia variants naturally evolving in different dipteran hosts: D. simulans, Drosophila melanogaster, and Rhagoletis cerasi. Our results suggest that closely related bacteria can be totally or partially incompatible. The compatibility relationships observed can be explained using a formal description of the mod and resc functions, implying both qualitative and quantitative variations.

Animals↗

PubMed1999

Light-scattering study of a supercooled epoxy resin.

The dynamics of the fragile glass-forming liquid diglycidyl ether of bisphenol-A was studied by depolarized Rayleigh-Brillouin light-scattering and photon correlation spectroscopy above the glass transition, in the temperature range from 261 to 473 K and in the frequency range from 1 Hz to 300 GHz. The structural (alpha-) relaxation process was revealed and no signature of the secondary relaxation previously evidenced by dielectric spectroscopy at about 0.1 GHz was observed. The characteristic time of the alpha process differs from that determined by dielectric spectroscopy of an amount, which increases with increasing temperature. The relaxation times were compared with viscosity data to test the predictions of the classic Stokes-Einstein-Debye model. The tau proportional, variant eta behavior was verified for dielectric data, while a fractional power law of viscosity tau proportional, variant eta(0.89) was obtained for light-scattering relaxation times, extending over more than seven decades in viscosity and time. This deviation of light scattering from viscosity data could be interpreted in terms of cooperative motion in the supercooled liquid with a characteristic length xi(a) proportional, variant(T-T0)(-v) where T(0)=229 K is the Vogel temperature and v is close to 2 / 3 which is consistent with the prediction of the fluctuation theory of glass transition.

Journal Article↗

PubMed2006

Replacement of isobutyl by trifluoromethyl in pepstatin A selectively affects inhibition of aspartic proteinases.

Two bis-trifluoromethyl pepstatin A analogues, carboxylic acid 1 and its methyl ester 2, have been synthesised in order to probe the properties and size of the trifluoromethyl (Tfm) group and compare it to the "bigger" isobutyl that is present in pepstatin A. The results demonstrate that Tfm can effectively replace the isobutyl chain as far as inhibitory activity against plasmepsin II (PM II), an aspartic proteinase from Plasmodium falciparum, is concerned. On the other hand, replacement of isobutyl by Tfm selectively affected activity against other aspartic proteinases tested. Two lines of evidence led to these conclusions. Firstly, compounds 1 and 2 retained single-digit nanomolar inhibitory activity against PM II, but were markedly less active against PM IV, cathepsin D and cathepsin E. Secondly, the X-ray crystal structures of the three complexes of PM II with 1, 2 and pepstatin A were obtained at 2.8, 2.4 and 1.7 A resolution, respectively. High overall similarity among the three complexes indicated that the central Tfm was well accommodated in the lipophilic S1 pocket of PM II, where it was involved in tight hydrophobic contacts. The interaction of PM II with Phe111 appeared to be crucial. Comparison of the crystal structures presented here, with X-ray structures or structural models of PM IV and cathepsin D, allowed an interpretation of the inhibition profiles of pepstatin A and its Tfm variants against these three enzymes. Interactions of the P1 side chain with amino acids that point into the S1 pocket appear to be critical for inhibitory activity. In summary, Tfm can be used to replace an isobutyl group and can affect the selectivity profile of a compound. These findings have implications for the design of novel bioactive molecules and synthetic mimics of natural compounds.

Animals↗

PubMed1991

Parametric method for the detection of inter- and intrasweep variability in VEP processing.

The paper introduces a Kalman filter procedure for the processing of single-sweep visual evoked potentials (VEPs). The identification of the filter coefficients is based on a model of signal and noise interaction which considers the generating process as the superposition of the true evoked response to an AR process (the background EEG) and a broader spectrum noise. Intersweep variability is thus evident on the filtered response and a functional parameter of the filter (VP(t), namely variability path) is proposed for the automatic determination of the latencies associated with the main peaks of the response. Finally, the time-variant algorithm allows the quantification of the intrasweep variability for possible interpretation of the physiological mechanism involved.

Adult↗

PubMed2005

Vascular diseases of the thorax: evaluation with multidetector CT.

The list of vascular diseases in the thorax has been narrowed to three, which are considered essential information for radiologists interpreting CT scans of the thorax: (1) aortic dissection and its variants, intramural hematoma and penetrating atherosclerotic ulcer; (2) acute pulmonary embolism; and (3) coronary artery disease. The spatial resolution of multidetector CT is such that CT has become the imaging modality of choice for aortic dissection and pulmonary embolism. This move away from angiography has transpired over the last decade; perhaps the next decade will see the same occur for evaluation of coronary artery disease.

Aortic Dissection↗

PubMed2000

Lumbar spine imaging. Normal variants, imaging pitfalls, and artifacts.

Accurate recognition and reporting of spine abnormalities on MRI requires knowledge of normal anatomy and its variants. This article deals with common normal variants, points out pitfalls which may be sources of errors in interpretation and describes imaging artifacts which are essential to be recognized and not mistaken for true pathologies.

Artifacts↗

PubMed1995

A heuristic approach to the analysis of enzymic catalysis: reaction of delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-alpha-aminobutyrate and delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-allylglycine catalyzed by isopenicillin N synthase isozymes.

Isopenicillin N synthase (IPNS) catalyzes the oxidative cyclization of delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-valine to isopenicillin N. It is proposed that the multiple products produced from certain substrate analogues result from pathway branching after formation of a ferryl oxene intermediate. We have been interested in ascertaining the reasons for multiple product formation. One possibility is that the products are predisposed toward formation once the beta-lactam ring and the ferryl oxene are produced. Alternately, the products may be persuaded into being by the enzyme restricting conformations such that otherwise less favorable chemistry can take place. With the existing description of the IPNS catalytic cycle, this fundamental question has not been answerable. We describe here the application of a heuristic method to resolve this key issue. It was reasoned that by comparing the ratios of products formed by a set of perturbed IPNS variants it might be possible to generate qualitative information about the relative magnitude of certain activation parameters. If certain product ratios are affected but others are not, then it should be possible to say which steps in the reaction are dictated merely by chemical fundamentals and which steps are directly effected by the enzyme. In this paper we report the high-level expression, purification, and characterization of four IPNS isozymes. Comparison of the product ratios obtained on incubation of unnatural substrate analogues with four IPNS isozymes corresponding to perturbed active site variants shows substantial variation in some cases and little in others. Interpretation of the results obtained with delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-alpha-aminobutyrate (ACAB) allows conclusions to be drawn regarding the role of the enzyme in restricting available conformations of the natural substrate to disfavor certain otherwise chemically favorable pathways and hence products. The results obtained with delta-(L-alpha-aminoadipoyl)-L-cysteinyl-D-allylglycine, while rather more complex, substantiate the conclusions drawn from the ACAB data. A major conclusion is that, in the oxidation of ACV, IPNS is a negative catalyst of cepham formation but a positive catalyst of penam formation.

Acremonium↗

PubMed2002

Mexican waves in an excitable medium.

The Mexican wave, or La Ola, which rose to fame during the 1986 World Cup in Mexico, surges through the rows of spectators in a stadium as those in one section leap to their feet with their arms up, and then sit down again as the next section rises to repeat the motion. To interpret and quantify this collective human behaviour, we have used a variant of models that were originally developed to describe excitable media such as cardiac tissue. Modelling the reaction of the crowd to attempts to trigger the wave reveals how this phenomenon is stimulated, and may prove useful in controlling events that involve groups of excited people.

Computer Simulation↗

PubMed2004

High variability of chloroplast DNA in three Mediterranean evergreen oaks indicates complex evolutionary history.

Chloroplast DNA variation was studied in three evergreen Quercus species (Q. suber L., Q. ilex L. and Q. coccifera L.) from the Western Mediterranean Basin using PCR-RFLP. We studied five primer pair/enzyme combinations, four of them previously used in other European Quercus, obtaining a large number of haplotypes (81) grouped in three main types (suber type, ilex-coccifera I type and ilex-coccifera II type). Such level of haplotype diversity is higher than previously reported for the genus. Remarkable differences in haplotype richness between species have been found. Q. ilex and Q. coccifera usually share the same haplotypes, while a number of Q. suber populations possesses variants of the ilex-coccifera I type. This fact is interpreted as a result of genetic introgression between Q. suber and Q. ilex. Reproductive factors that could determine this exchange are discussed, as well as the influence of different species histories on the present structure of evergreen Quercus in the Western Mediterranean Basin.

DNA, Chloroplast↗

PubMedDate not supplied

Comparative genomics analysis of human sequence variation in the UGT1A gene cluster.

Common polymorphisms within the human UGT1A gene locus are associated with irinotecan and tranilast toxicity. To uncover additional functional variation across this gene cluster, cross-species sequence comparisons were performed. Evolutionarily conserved segments (a total of 47.1 kb) were re-sequenced in 24 African-American, 24 European-American, and 24 Asian individuals, and 381 segregating sites (including 123 singletons) were identified. Highly conserved coding sites were less likely to be polymorphic than diverged sites (P<0.0001) but this pattern was not observed at non-coding sites (P=0.1025). Among coding variants, the distribution of those computationally predicted to affect function was skewed toward low frequencies. Some alleles occurred at similar frequencies in each population; others had wide disparities. Although strong linkage disequilibrium was detected among the hepatically expressed genes, the degree of linkage disequilibrium varied among populations. These results suggest that rare functional gene variants and inter-population variability must be considered in the interpretation of association studies between UGT1A and drug metabolism/toxicity phenotypes.

Animals↗

PubMed2001

Azotobacter vinelandii ferredoxin I: a sequence and structure comparison approach to alteration of [4Fe-4S]2+/+ reduction potential.

The reduction potential (E(0)') of the [4Fe-4S](2+/+) cluster of Azotobacter vinelandii ferredoxin I (AvFdI) and related ferredoxins is approximately 200 mV more negative than the corresponding clusters of Peptostreptococcus asaccharolyticus ferredoxin and related ferredoxins. Previous studies have shown that these differences in E(0)' do not result from the presence or absence of negatively charged surface residues or in differences in the types of hydrophobic residues found close to the [4Fe-4S](2+/+) clusters. Recently, a third, quite distinct class of ferredoxins (represented by the structurally characterized Chromatium vinosum ferredoxin) was shown to have a [4Fe-4S](2+/+) cluster with a very negative E(0)' similar to that of AvFdI. The observation that the sequences and structures surrounding the very negative E(0)' clusters in quite dissimilar proteins were almost identical inspired the construction of three additional mutations in the region of the [4Fe-4S](2+/+) cluster of AvFdI. The three mutations, V19E, P47S, and L44S, that incorporated residues found in the higher E(0)' P. asaccharolyticus ferredoxin all led to increases in E(0)' for a total of 130 mV with a 94-mV increase in the case of L44S. The results are interpreted in terms of x-ray structures of the FdI variants and show that the major determinant for the large increase in L44S is the introduction of an OH-S bond between the introduced Ser side chain and the Sgamma atom of Cys ligand 42 and an accompanying movement of water.

Amino Acid Sequence↗

PubMed2006

The missense genetic polymorphisms of human CYP2A13: functional significance in carcinogen activation and identification of a null allelic variant.

Cytochrome P450 2A13 (CYP2A13), an enzyme predominantly expressed in human respiratory tissues, is highly efficient for the metabolic activation of two suspected human lung carcinogens 4-(methylnitrosamino)-1-(3-pyridyl)-1-butanone (NNK) and aflatoxin B1 (AFB1). Functional genetic polymorphisms of CYP2A13 may therefore be an important factor in human susceptibility to related lung cancers. Among the reported CYP2A13 polymorphisms with missense variations, only CYP2A13*2 variant (containing either a single or double variation of R25Q and R257C) was studied for its NNK-metabolizing activity. The present study demonstrated that there was no remarkable difference in AFB1- and NNK-induced toxicity between the Flp-In Chinese Hamster Ovary (CHO) cells stably expressing wild-type CYP2A13 and the cells expressing the individual polymorphic variants R25Q, D158E, R257C, R25Q/R257C, V323L, F453Y, and R494C. In contrast, cells transfected with R101Q variant complementary DNA (cDNA), same as the vector control cells, showed no significant death even at highest concentrations of AFB1 (10microM) and NNK (200microM). This result correlated with the lack of CYP2A13 protein in the R101Q-CHO cells, although the genomic integration of transfected R101Q cDNA and the expression of R101Q messenger RNA were clearly demonstrated in these stable transfectants. Consistent with the possibility that the variation might reduce the protein stability, R101Q variant protein expressed in insect cells showed a loss of P450 peak and coumarin 7-hydroxylase activity as well as an increased susceptibility to limited protein digestion. Thus, the R101Q polymorphic change results in a null allelic variant of CYP2A13. Our results should be useful in designing and interpreting molecular epidemiological studies related to CYP2A13 genetic polymorphisms.

Aflatoxin B1↗

PubMedDate not supplied

Hepatic segments II and III mimicking a lung mass: diagnosis of a normal variant using reformatted multiplanar CT images.

We describe a patient misinterpreted to have a lung mass on CT owing to extension of hepatic segments II and III between the diaphragm and spleen. This report underscores the importance of being aware of this normal anatomic variant and the utility of two-dimensional multiplanar reformation in interpretation of abnormalities in the region of the thoracoabdominal junction.

Aged↗

PubMed2025

Genomic Language Model for Predicting Enhancers and Their Allele-Specific Activity in the Human Genome.

Predicting and deciphering the regulatory logic of enhancers is a challenging problem, due to the intricate sequence features and lack of consistent genetic or epigenetic signatures that can accurately discriminate enhancers from other genomic regions. Recent machine-learning based methods have spotlighted the importance of extracting nucleotide composition of enhancers but failed to learn the sequence context and perform suboptimally. Motivated by advances in genomic language models, we developed DNABERT-Enhancer, a novel enhancer prediction method, by applying DNABERT pre-trained language model on the human genome. We trained two different models, using large collection of enhancers curated from the ENCODE registry of candidate cis-Regulatory Elements. The best fine-tuned model achieved 88.05% accuracy with Matthews correlation coefficient of 76% on independent set aside data. Further, we present the analysis of the predicted enhancers for all chromosomes of the human genome by comparing with the enhancer regions reported in publicly available databases. Finally, we applied DNABERT-Enhancer along with other DNABERT based regulatory genomic region prediction models to predict candidate SNPs with allele-specific enhancer and transcription factor binding activity. The genome-wide enhancer annotations and candidate loss-of-function genetic variants predicted by DNABERT-Enhancer provide valuable resources for genome interpretation in functional and clinical genomics studies.

Journal Article↗

PubMed2005

Subtelomeric chromosome aberrations: still a lot to learn.

Subtelomeric chromosome aberrations: still a lot to learn.Cryptic subtelomeric chromosome aberrations are a significant cause of mental retardation (MR). More than 4000 patients have been investigated, and the mean overall prevalence of subtelomeric rearrangements has been found to be 5.2%. In order to contribute to knowledge on the clinical presentation of subtelomeric rearrangements, we retrospectively studied patients with unexplained MR who had been evaluated for subtelomeric abnormalities by different fluorescence in situ hybridization (FISH) techniques. Hundred and two patients had an unexplained combination of MR with dysmorphism, congenital anomalies, and/or a positive family history and were investigated by total subtelomeric (TS) FISH (89/102), or by total painting (TP) in an obligate carrier in the case of familial MR (13/102). In 59 additional patients, a sequence-specific FISH was performed on clinical indication. In the 102 patients studied by TS or TP, six pathogenic aberrations (5.9%) were found in addition to one polymorphism. In total, eight clinically significant subtelomeric aberrations were found in the 161 index patients; four of these eight aberrations were familial. We report on the clinical presentation of all patients with an aberration and review the relevant literature. Factors complicating the interpretation of subtelomeric rearrangements are discussed, such as the occurrence of variants, clinical variability, and limited knowledge of the phenotype.

Chromosome Aberrations↗

PubMed1985

Complex partial seizures in childhood.

A clinical and electroencephalographic study was undertaken on 215 children with complex partial seizures as selected on the basis of the International Classification of Epileptic Seizures (1981). Complex partial seizures were noted in 7.8% of the epileptic children. The ictal symptoms of complex partial seizures closely resembled those of psychomotor triad described by Lennox. Interictal EEG revealed seizure discharges from the temporal or frontal focus in 57.2%. There existed a group with automatism as a main symptom having both diffuse slow spike-waves and focal temporal spikes. This type should be interpreted to be one of secondary generalized epilepsies and be a variant of the Lennox syndrome.

Adolescent↗

PubMed1999

Different frequencies of inducible nitric oxide synthase genotypes in older hypertensives.

A locus for essential hypertension has been found recently on chromosome 17 in the general vicinity of the inducible nitric oxide synthase (iNOS) gene (NOS2A at 17cen-q11.2). We therefore tested NOS2A markers for association and linkage with hypertension in affected Australian Anglo-Caucasians. Patients for the association study (n=112) were from our cohort of hypertensives (systolic/diastolic=175+/-25 SD/112+/-19 mm Hg) who were the offspring of 2 hypertensive parents; control subjects (n=164) were normotensives whose parents were both normotensive. The linkage study involved 156 hypertensive sib-pairs. Genotypes for an 8-allele pentameric repeat located 2.6 kb upstream of NOS2A and of a biallelic tetranucleotide repeat 0.7 kb upstream were determined by polymerase chain reaction and automated gene scan analysis. In the association study, the frequency of the minor allele of the biallelic marker was 0.18 in the hypertensives and 0.14 in the normotensives (chi21 df=1.1, P=0.3). Allele frequencies for the multiallelic marker were also similar in each group (chi2 7 df=9.8, P=0.2). Furthermore, no genotypic differences in blood pressure were apparent. In the sib-pair study, SPLINK APM, and MAPMAKERS/SIBS did not indicate excess allele sharing. We also examined genotype as a function of age. In the younger (< 60 years) hypertensives as well as younger or older normotensives, genotype and allele frequency of the biallelic marker was similar (0.12 to 0.14). However, in hypertensives >/=60 years of age, frequency of the minor allele was 0.28 (chi2=7.4, P=0.006). Homozygotes for this allele were rare. Frequency of heterozygotes was 0.19 for normotensives but 0.39 for the older hypertensives (chi2=8.0, P=0.018) and was 0.40 for hypertensive sibs >/=60 years of age with a diastolic pressure >/=100 mm Hg. Furthermore, homozygotes for the major allele were 7 years younger than heterozygotes (P=0.05 by ANOVA). In conclusion, the present study shows (1) no evidence for a role of NOS2A in hypertension and (2) a genotypic difference in frequency of a NOS2A promoter variant in older hypertensives, seen in 2 different cohorts. A possible interpretation of the latter observation is that NOS2A genotype could affect longevity, at least in patients at high risk by having moderate to severe hypertension.

Adult↗