Isolated mild white matter signal changes in preterm infants: a regional approach for comparison of cranial ultrasound and MRI findings

OBJECTIVE

To compare echogenicity detected using cranial ultrasound (cUS) and diffuse excessive high signal intensity (DEHSI) detected using magnetic resonance imaging (MRI) by identical region-based scoring criteria in preterm infants. To explore the association between these white matter (WM) signal changes with early neurobehavior.

STUDY DESIGN

Forty-nine pre-selected premature infants with only echogenicity on a first routine cUS1 underwent MRI and a repeated cUS2 at term equivalent age. Echogenicity and DEHSI were graded in various brain areas and diffusivity values were calculated. Neurobehavior was assessed using the Rapid Neonatal Neurobehavioral Assessment Procedure.

RESULT

WM signal changes were significantly higher on cUS1 than cUS2; and higher in MRI than cUS2 in posterior regions. Infants with DEHSI demonstrated reduced tissue integrity. Imaging findings were not correlated with early neurobehavior.

CONCLUSION

Echogenicity and DEHSI likely represent the same phenomenon. Reduction of over-interpretation of WM signal changes may help define criteria for the judicious use of imaging in routine follow-up of premature infants.

Naturally occurring circular permutations in proteins

A pair of proteins is defined to be related by a circular permutation if the N-terminal region of one protein has significant sequence similarity to the C-terminal of the other and vice versa. To detect pairs of proteins that might be related by circular permutation, we implemented a procedure based on a combination of a fast screening algorithm that we had designed and manual verification of candidate pairs. The screening algorithm is a variation of a dynamic programming string matching algorithm, in which one of the sequences is doubled. This algorithm, although not guaranteed to identify all cases of circular permutation, is a good first indicator of protein pairs related by permutation events. The candidate pairs were further validated first by application of an exhaustive string matching algorithm and then by manual inspection using the dotplot visual tool. Screening the whole Swissprot database, a total of 25 independent protein pairs were identified. These cases are presented here, divided into three categories depending on the level of functional similarity of the related proteins. To validate our approach and to confirm further the small number of circularly permuted protein pairs, a systematic search for cases of circular permutation was carried out in the Pfam database of protein domains. Even with this more inclusive definition of a circular permutation, only seven additional candidates were found. None of these fitted our original definition of circular permutations. The small number of cases of circular permutation suggests that there is no mechanism of local genetic manipulation that can induce circular permutations; most examples observed seem to result from fusion of functional units.

A simple algorithm for detecting circular permutations in proteins

MOTIVATION

Circular permutation of a protein is a genetic operation in which part of the C-terminal of the protein is moved to its N-terminal. Recently, it has been shown that proteins that undergo engineered circular permutations generally maintain their three dimensional structure and biological function. This observation raises the possibility that circular permutation has occurred in Nature during evolution. In this scenario a protein underwent circular permutation into another protein, thereafter both proteins further diverged by standard genetic operations. To study this possibility one needs an efficient algorithm that for a given pair of proteins can detect the underlying event of circular permutations. A possible formal description of the question is: given two sequences, find a circular permutation of one of them under which the edit distance between the proteins is minimal. A naive algorithm might take time proportional to N3 or even N4, which is prohibitively slow for a large-scale survey. A sophisticated algorithm that runs in asymptotic time of N2 was recently suggested, but it is not practical for a large-scale survey.

RESULTS

A simple and efficient algorithm that runs in time N2 is presented. The algorithm is based on duplicating one of the two sequences, and then performing a modified version of the standard dynamic programming algorithm. While the algorithm is not guaranteed to find the optimal results, we present data that indicate that in practice the algorithm performs very well.

AVAILABILITY

A Fortran program that calculates the optimal edit distance under circular permutation is available upon request from the authors.

CONTACT

ron@biocom1.ls.biu.ac.il.

Acoustic reflex measurements and the loudness function in sensorineural hearing loss

The suprathreshold acoustic reflex responses of forty two ears affected by sensorineural hearing loss of cochlear origin and fifty-eight ears demonstrating normal hearing, were recorded by means of an electro-acoustic impedance meter and attached X-Y recorder. The recordings were done in ascending and descending fashion,  at successively increasing and decreasing 5dB intensity levels from 90-120-90 dB HL respectively, for the individual pure-tone frequencies of 500, 1 000, 2 000 and 4 000 Hz. The contralateral mode of measurement was employed. Analysis of  these recordings indicated that the acoustic reflex  responses could be differentiated into five  characteristic patterns of  growth, which could be depicted upon a continuum of peaked, peaked-rounded, rounded, rounded-flat,  and flat  shapes. The peaked and peaked-rounded patterns were found  to predominate at all four pure-tone frequencies  in the normal ears, while the rounded-fiat  and flat  patterns were found  to predominate only at the higher pure-tone frequencies of 2 000 and 4 000 Hz in the ears affected  by sensorineural hearing loss. This latter relationship was also able to be applied to two disorders of  the loudness functio— loudness recruitment and hyperacusis. It was concluded that the flattened  acoustic reflex  patterns at the higher pure-tone frequencies  constituted a potential diagnostic cue related to the differential  diagnosis of sensorineural hearing loss, and to disorders of  the loudness function.