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At least 343 records · Page 19Linked to original sources
PubMed2002

[Amplification of bacterial heat shock protein 60 gene using inverse PCR method].

A method is presented for rapid in vitro amplification of DNA sequences of bacterial HSP60 gene. In our previous work, using degenerate oligonucleotide primers for conserved regions of HSP60 gene, a 600 bp fragment was amplified by PCR, cloned and sequenced. An inverse PCR method, with the primers oriented in the reversed direction of the usual orientation, is used to amplify the DNA sequences that flank the 600 bp known region. The feasibility of this method is shown by amplifying the complete HSP60 gene sequences of 4 bacterial strains, namely Bifidobacterium denticolens, Bifidobacterium inopinatum, Bifidobacterium adolescentis and Gardnerella vaginalis.

Base Sequence↗
PubMed1990

New aspects of lumbar disc disease. MR imaging and histological findings.

Magnetic resonance imaging (MRI) and plain X-ray and CT studies were performed in patients with a history of lumbar back pain due to spinal disc disease. Spin-echo pulse sequences (SE), phase-contrast techniques (partial saturation sequences with delayed readout, PS), and fat-suppressing inversion recovery sequences (STIR) were employed. In 74 of 325 patients, PS and STIR images displayed vertebral marrow changes adjacent to the end-plates of the affected segments. Bacterial infection, however, could be excluded. In six patients histological diagnosis showed substitution of hematopoietic marrow by fatty tissue, cartilaginous particles, degeneration of fat cells, and an increase in extracellular fluid with different components. The etiology is still unclear, but a correlation with lumbar disc disease is demonstrated. These vertebral marrow changes were best displayed with STIR and phase-contrast MR sequences, both providing contrast changes superior to T2-weighted SE techniques.

Adolescent↗
PubMedDate not supplied

A quantitative index of ventricular and extraventricular intracranial CSF volumes using MR imaging.

A new technique is described that utilises a novel magnetic resonance pulse sequence to produce a quantitative index both for ventricular and, for the first time, extraventricular intracranial CSF volumes. The pulse sequence is a combination of a null-point inversion recovery sequence with an extended spin-echo read (echo time = 400 ms), which produces a contrast of CSF to white or grey matter of approximately 120:1. A series of experiments are performed on phantoms representing CSF filled ventricles and sulci over a wide range of volume values, and it is found that the standard deviation of differences between true and estimated values is 3.9% for ventricles, 4.6% for total cranial CSF, and 7.9% for CSF within the sulci. Normal volunteer reproducibility studies revealed corresponding standard deviations of less than 5.5%. Using the technique to produce absolute estimates of CSF volumes in normal subjects and patients produced results in good agreement with previously published necropsy studies. The technique has wide neurological and neurosurgical applicability particularly in terms of differential diagnosis and as an objective monitor of therapy or progression in conditions such as hydrocephalus, atrophy, and benign intracranial hypertension.

Adolescent↗
PubMedDate not supplied

Use of nutritional support formula as a gastrointestinal contrast agent for MRI.

The objective of this study was to evaluate the potential utility of a nutritional support formula to serve as a practical means of enhancing the gastrointestinal tract on abdominal MR images. Nutritional support formula (Ensure Plus) was administered to 29 patients prior to abdominal MRI. Standard T1-weighted and T2-weighted pulse sequences were performed, in addition to fat suppression and inversion recovery sequences in selected patients. Images in these patients were evaluated for degree and uniformity of gastrointestinal tract enhancement and delineation of the bowel wall and pancreas. Results were compared with those obtained in 10 control patients. Marked enhancement of gastric contents was present in nearly all patients who received nutritional support formula on both T1-weighted and T2-weighted sequences, with mild to moderate enhancement of small bowel and colon in most patients. Although gastrointestinal and respiratory motion artifacts often limited bowel wall delineation, excellent delineation of the gastric wall and pancreas was provided. Phantom experiments demonstrated that gastrointestinal tract enhancement with nutritional support formula is due to the paramagnetic trace elements, corn syrup, and lipid material it contains. Such a formula requires no preparation, is safe, inexpensive, palatable, readily available, and represents a practical means of enhancing the gastrointestinal tract on MRI.

Adipose Tissue↗
PubMed2006

[The chromosomal polymorphism and divergence of populations in Chironomus nuditarsis Str. (Diptera, Chironomidae)].

The karyotype structure and chromosomal polymorphisms were investigated in 6 natural and 2 laboratory populations of Chironomus nuditarsis from Europe and Asia. The pool of rearranged polytene chromosome banding sequences of this species was determined that includes 16 inversion banding sequences and sequences with giant DNA-knobs (ndtG1k, ndtG2k). Obvious differences were demonstrated in the level of chromosomal polymorphism between European and Asian (Siberian) populations: the former were highly polymorphic, while the latter were practically monomorphic. It was suggested to consider the Siberian populations as marginal one. Cytogenetic distances between populations of C. nuditarsis as well between C. nuditarsis and the related species C. plumosus were estimated. The data obtained show that chromosomal rearrangements play a very important role in cytogenetic divergence of populations.

Animals↗
PubMed1986

[Plain imaging of meningioma in NMR tomography--retrospective contrast optimization by image synthesis].

Synthetic images of the tumour region were computed in the case of ten meningiomas for the purpose of determining retrospectively pulse sequences and sequence parameters supplying an optimal contrast between tumour and adjacent tissue in plain imaging. It was found that best results were obtained via the partial saturation/spin-echo sequence with a long recovery time (TR approximately greater than 2,000 msec) and a long maximum echo delay (TE max approximately greater than 200 msec). A comparable contrast quality can be attained by using the inversion-recovery sequence with an inversion time T1 approximately 450 msec. Nevertheless, it was not possible in our study to identify two small meningiomas with a diameter of just below one centimetre by studying the MR tomogram.

Brain↗
PubMed2003

Computer assessment of neurodegeneration in Parkinson disease using data fusion techniques with MR images.

RATIONALE AND OBJECTIVES: Recently developed MR imaging techniques using inversion recovery are a sensitive tool to identify and quantify morphologic changes in the substantia nigra due to neurodegeneration. Using a semi-automated computer segmentation technique to isolate the substantia nigra pars compacta (SN(c)), we propose a colored image fusion technique to visually assess the sites of damage in the SN(c) and integrate the information obtained from two implemented inversion-recovery sequences. PATIENTS AND METHODS: Six patients and six age-matched control subjects were scanned using a combination of two MR imaging inversion-recovery (IR) pulse sequences. A subgroup of them was used to develop our technique. Images were blended together into a final (RGBA) image, where A stands for the alpha channel describing transparency. RESULTS: Abnormalities in the SN(c) can be accurately assessed in location, shape, and variations of signal intensities within the segmented SN(c) by varying the transparency (alpha) channel of the color fusion image. Several previous findings such as the lateral-medial gradient of signal change and a ventral-dorsal broadening of the pars compacta are accompanied by an overall mild-to-severe heterogeneity of neurodegeneration patterns. CONCLUSION: Color fusion techniques revealed subtle changes in the neurodegeneration of the substantia nigra in Parkinson disease, which can be helpful for an objective and hence effective visual assessment of disease progression.

Aged↗
PubMed1990

[Magnetic resonance imaging of ovarian cystic teratoma].

Two patients with ovarian cystic teratoma were imaged using real-time ultrasound and 1.0-T magnetic resonance imaging (MRI) devices. The ultrasound appearance of cystic teratoma varies with the internal contents. If bone or teeth is present, highly echogenic foci with posterior shadow will be identified. The cysts may contain solid areas, septa and fluid-fluid levels. The dermoid cyst filled with fat showing characteristic echogenic appearance might confused with the pelvic fact tissue. MRI is well suited to the evaluation of pelvic disorders. The T1 and T2 relaxation times in different tissues might present with different signal intensities by changing the pulse sequences. Fat, with its relatively short T1 and long T2 times, appears bright on the T1-weighted images (short TE and TR) and T2-weighted images (long TE and TR). However, old hemorrhage has the MRI characteristics of short T1 and long T2 times as fat. The inversion recovery sequence with short inversion time (STIR) will suppress signal from fat tissue and this is of particular value in differentiating dermoid from hemorrhagic cyst. MRI is quite efficient in cases where ultrasound study is equivocal or difficult in the technique.

Adult↗
PubMed2001

Diffusion and relaxation effects in general stray field NMR experiments.

We analyze the evolution of magnetization following any series of radiofrequency pulses in strongly inhomogeneous fields, with particular attention to diffusion and relaxation effects. When the inhomogeneity of the static magnetic field approaches or exceeds the strength of the RF field, the magnetization has contributions from different coherence pathways. The diffusion or relaxation induced decay of the signal amplitude is in general nonexponential, even if the sample has single relaxation times T(1), T(2) and a single diffusion coefficient D. In addition, the shape of the echo depends on diffusion and relaxation. It is possible to separate contributions from different coherence pathways by phase cycling of the RF pulses. The general analysis is tested on stray field measurements using two different pulse sequences. We find excellent agreement between measurements and calculations. The inversion recovery sequence is used to study the relaxation effects. We demonstrate two different approaches of data analysis to extract the relaxation time T(1). Finite pulse width effects on the timing of the echo formation are also studied. Diffusion effects are analyzed using the Carr--Purcell--Meiboom--Gill sequence. In a stray field of a constant gradient g, we find that unrestricted diffusion leads to nonexponential signal decay versus echo number N, but within experimental error the diffusion attenuation is still only a function of g(2)Dt(3)(E)N, where t(E) is the echo spacing.

Journal Article↗
PubMed1986

Primary glioma: diagnosis with magnetic resonance imaging.

Seventeen patients with surgically documented primary glial-origin brain tumors were evaluated by magnetic resonance imaging and high-resolution computed tomography. The exclusion of CT ring-enhancing lesions directed the focus of this study toward lower grade tumors that were more difficult to diagnose. The computed tomography abnormalities were often subtle and included areas of low attenuation, mass effect, and focal enhancement. Spin-echo sequences with both heavy T1 and T2 weighting were utilized. Prolonged T1 and T2 values were observed in all tumors. The T2-weighted spin-echo 1000/120 sequence was the most sensitive in tumor detection and was positive in all cases. Magnetic resonance imaging was superior to computed tomography in tumor detection, tumor localization, assessment of tumor extent, and determination of associated changes, ie, brain stem encroachment. All the magnetic resonance sequences used showed an increase in severity of imaging changes with increasing tumor grade. The T2-weighted sequence showed progressive margin irregularity, whereas the T1-weighted (inversion recovery) sequence showed increasing severity of internal tissue changes. The superior resolution of these changes by magnetic resonance imaging may have implications for better assessment of tumor grade in the future than is currently possible with computed tomography.

Adolescent↗
PubMed2004

Evolution of resistance to drugs in HIV-1-infected patients failing antiretroviral therapy.

BACKGROUND AND OBJECTIVE: The optimal time for changing failing antiretroviral therapy (ART) is not known. It involves balancing the risk of exhausting future treatment options against the risk of developing increased drug resistance. The frequency with which new drug-resistance mutations (DRM) developed and their potential consequences in patients continuing unchanged treatment despite persistent viremia were assessed. DESIGN: A retrospective study of consecutive sequence samples from 106 patients at one institution with viral load (VL) of more than 400 copies/ml, with no change in ART for more than 2 months despite virologic failure. METHODS: Two consecutive pol sequences, CD4 cell counts and VL were analyzed to quantify the development of new DRM and to identify changes in immunologic and virologic parameters. Genotypic susceptibility scores (GSS) and viral drug susceptibilities were calculated by a computer program (HIVDB). Poisson log-linear regression models were used to predict the expected number of mutations at the second time point. RESULTS: : After a median of 14 months of continued ART, 75% (80 of 106) of patients acquired new DRM and were assigned a significantly lower GSS, potentially limiting the success of future ART. The development of new DRM was proportional to the time between the two sequences and inversely proportional to the number of DRM in the first sequence. However, the development of DRM was not associated with significant changes in CD4 or VL counts. CONCLUSIONS: Despite stable levels of CD4 and VL over time, maintaining a failing therapeutic regimen increases drug resistance and may limit future treatment options.

Adult↗
PubMed1989

[Magnetic resonance imaging of diseased cervical and lumbar intervertebral discs].

Magnetic resonance images (MRI) of diseased cervical and lumbar intervertebral discs involving both intrinsic and extrinsic cord lesions were examined using either a 0.15 T resistive or a 0.5 T superconductive magnetic imaging system. High resolution images were obtained by means of a surface coil in most cases. The vertebrae, intervertebral discs, and spinal cord were delineated in greatest detail on spin-echo (SE) images with a long repetition time (TR) and a short echo time (proton density-weighted image), on which the spinal cord was appreciated without overshadowing by the cerebrospinal fluid-filled subarachnoid space. Protrusion of degenerated intervertebral discs into the spinal canal was clearly demonstrated not only on sagittal but also on parasagittal and transverse views. The location of protruded discs and compression of the spinal cord, caudal sac, and nerve roots were well visualized three-dimensionally. Pathological features of intervertebral discs were better appreciated on T2-weighted images with long TR and SE pulse sequences. Degeneration of intervertebral discs resulted in decreased signal intensity in cases involving lumbar disc lesions but not those involving cervical disc lesions. In a case of suspected myelomalacia, the intrinsic cord lesion resulting from traumatic disc protrusion appeared as focal low signal intensity on T1-weighted images and as somewhat high intensity on T2-weighted images. The inversion recovery sequence with median inversion time displayed an inferior image of low contrast and was judged uninformative in comparison to SE images. The authors' observations demonstrate that MRI is an essential diagnostic technique for spinal cord disorders.(ABSTRACT TRUNCATED AT 250 WORDS)

Cervical Vertebrae↗
PubMed2004

Simultaneous bilateral breast and high-resolution axillary MRI of patients with breast cancer: preliminary results.

OBJECTIVE: The aims of this study were to develop a standardized one-step procedure for simultaneous high-resolution MRI of the axilla and bilateral breast MRI and to identify nodal features suggestive of metastatic involvement. SUBJECTS AND METHODS. We studied 16 women undergoing axillary lymph node dissection after combined bilateral breast MRI and high-resolution MRI of the axilla with a maximum in-plane resolution of 0.6 x 0.4 mm. MRI was performed using a standard double breast coil and a 15-cm round flexible surface coil adapted to the axilla. High-resolution axillary sequences, including inversion recovery T2- and spin-echo T1-weighted sequences, were performed before and after gadolinium chelates bolus injection. Axillary image analysis focused on nodal morphology including size, contour regularity, cortex and hilar appearance, signal intensity, and enhancement parameters. Axillary MRI findings were compared with the final pathogic results from axillary lymph node dissection in all patients. Patients were divided into groups according to the final pathologic axillary status. Differences in MRI lymph node features across the groups were tested using a t test for quantitative data and the chisquare test or Fisher's exact test for binary data. RESULTS: The features of the axilla on high-resolution MRI that best discriminated between patients with positive pathologic findings and those with negative pathologic findings were the presence of nodes with irregular contours (p < 10(-4)), high signal intensity on T2 sequences (p < 10(-3)), marked gadolinium enhancement (p < 10(-3)), and round hila and abnormal cortexes (p < 0.05). CONCLUSION: Breast tissue and axillary lymph nodes both can be analyzed on MRI in a one-step process using a bilateral breast coil combined with a surface coil. Morphologic features observed on high-resolution MRI of the axilla can improve the identification of metastatic nodes.

Adult↗
PubMed1994

Tn10-mediated inversions fuse uridine phosphorylase (udp) and rRNA genes of Escherichia coli.

Two strains carrying metE::Tn10 insertions (upstream of the udp gene) were used to isolate mutants of Escherichia coli overexpressing udp. These strains differ in their gene order; one contains an inversion between the rrnD and rrnE rRNA operons. Selection was based on the ability of overexpressed Udp to complement thymine auxotrophy. Chromosomal rearrangements that connect the udp gene and promoters of different rrn operons were obtained by this selection. Seven of 14 independent mutants selected in one of the initial strains contained similar inversions of the metE-rrnD segment of the chromosome (about 12% of its length). Another mutant contained traces of a more complicated event, inversion between rrnB and rrnG operons, which was followed by reinversion of the segment between metE and the hybrid rrnG/B operon. Similar inversions (udp-rrn) in a strain already carrying an rrnE-rrnD inversion flip the chromosomal segment between metE and rrnD/E in the opposite direction. In this case, inversions are also accompanied by duplications of the chromosomal region between the rrnA and hybrid udp-rrnD/E operons. PCR amplification with a set of oligonucleotides from the rrn, Tn5, and met genes was used for more detailed mapping. Amplified fragments of the rearranged chromosomes connecting rrnD sequences and insertion elements were sequenced, and inversion endpoints were established.

Base Sequence↗
PubMed1994

[Fat-suppressing STIR sequences with and without contrast media in the MRT of ENT tumors].

Fat-suppressed STIR (short TI inversion recovery) sequences were compared to plain and contrast-enhanced T1-weighted SE sequences of head and neck tumors. 19 patients underwent MR imaging on a 0.5 Telsa system (T5-II, Philips). STIR imaging parameters: TR/TE = 1000/20 ms, inversion pulse 100 ms. All films were read by four radiologists. The image quality was graded: score from 0 to 5, by means that grade 5 = optimal quality. Sensitivity was 89% in STIR, 96% in SE sequences. Tumor delineation was graded good in the enhanced T1-weighted and enhanced fat suppression images. The unenhanced imaging was superior in STIR (STIR/T1 = 2.8/2.43). The tumor contrast was best in contrast enhanced and plain STIR sequences (STIR contrast = 3.41), and in the contrast enhanced T1-weighted SE (3.33). STIR almost equaled T1 post-contrast in respect of tumour conspicuity, but the sensitivity was lower. STIR can be a supplement to SE, but cannot substitute T1 postcontrast. The combined use is expected to have the highest assessment value.

Adipose Tissue↗
PubMed1997

Sequence-structure specificity--how does an inverse folding approach work?

The inverse folding approach is a powerful tool in protein structure prediction when the native state of a sequence adopts one of the known protein folds. This is because some proteins show strong sequence-structure specificity in inverse folding experiments that allow gaps and insertions in the sequence-structure alignment. In those cases when structures similar to their native folds are included in the structure database, the z-scores (which measure the sequence-structure specificity) of these folds are well separated from those of other alternative structures. In this paper, we seek to understand the origin of this sequence-structure specificity and to identify how the specificity arises on passing from a short peptide chain to the entire protein sequence. To accomplish this objective, a simplified version of inverse folding, gapless inverse folding, is performed using sequence fragments of different sizes from 53 proteins. The results indicate that usually a significant portion of the entire protein sequence is necessary to show sequence-structure specificity, but there are regions in the sequence that begin to show this specificity at relatively short fragment size (15-20 residues). An island picture, in which the regions in the sequence that recognize their own native structure grow from some seed fragments, is observed as the fragment size increases. Usually, more similar structures to the native states are found in the top-scoring structural fragments in these high-specificity regions.

Amino Acid Sequence↗
PubMed1985

IS50-mediated inverse transposition: specificity and precision.

The IS50 elements, which are present as inverted repeats in the kanamycin-resistance transposon, Tn5, can move in unison carrying with them any interstitial DNA segment. In consequence, DNA molecules such as a lambda::Tn5 phage genome are composed of two overlapping transposons - the kan segment bracketed by IS50 elements (Tn5), and lambda bracketed by IS50 elements. During direct transposition, mediated by IS50 "O" (outside) ends, the kan gene is moved and the lambda vector is left behind. During inverse transposition, mediated by the "I" (inside) ends of the IS50 elements, the lambda vector segment is moved and the kan gene is left behind. Direct transposition is several orders of magnitude more frequent than inverse transposition (Isberg and Syvanen, 1981; Sasakawa and Berg, 1982). We assessed the specificity and precision of the rare events mediated by pairs of I ends by mapping and sequencing independent inverse transpositions from a lambda::Tn5 phage into the amp and tet genes of plasmid pBR322. Using restriction analyses, 32 and 40 distinct sites of insertion were found among 46 and 72 independent inverse transpositions into the amp and tet genes, respectively. Eleven sites were used in two or more insertion events, and the two sites in tet used most frequently corresponded to major hotspots for the insertion of the Tn5 (by direct transposition). The sequences of 22 sites of inverse transposition (including each of the sites used more than once) were determined, in eleven cases by analyzing both pBR322-IS50 junctions, and in eleven others by sequencing one junction. The sequence of the "I" end of IS50 was preserved and 9-bp target sequence duplications were present in every case analyzed. GC pairs were found at each end of the target sequence duplication in ten of the eleven sites used more than once, and also in seven of the other eleven sites. Our data indicate that transposition mediated by pairs of "I" ends is similar in its specificity and precision to the more frequent transposition mediated by IS50 "O" ends.

Base Sequence↗