An algorithm for finding signals of unknown length in DNA sequences

Pattern discovery in unaligned DNA sequences is a challenging problem in both computer science and molecular biology. Several different methods and techniques have been proposed so far, but in most of the cases signals in DNA sequences are very complicated and avoid detection. Exact exhaustive methods can solve the problem only for short signals with a limited number of mutations. In this work, we extend exhaustive enumeration also to longer patterns. More in detail, the basic version of algorithm presented in this paper, given as input a set of sequences and an error ratio epsilon < 1, finds all patterns that occur in at least q sequences of the set with at most epsilonm mutations, where m is the length of the pattern. The only restriction is imposed on the location of mutations along the signal. That is, a valid occurrence of a pattern can present at most [epsiloni] mismatches in the first i nucleotides, and so on. However, we show how the algorithm can be used also when no assumption can be made on the position of mutations. In this case, it is also possible to have an estimate of the probability of finding a signal according to the signal length, the error ratio, and the input parameters. Finally, we discuss some significance measures that can be used to sort the patterns output by the algorithm.

Lacidipine and blood pressure variability in diabetic hypertensive patients

The aim of our study was to assess the effects of lacidipine, a long-acting calcium antagonist, on 24-hour average blood pressure, blood pressure variability, and baroreflex sensitivity. In 10 mildly to moderately hypertensive patients with type II diabetes mellitus (aged 18 to 65 years), 24-hour ambulatory blood pressure was continuously monitored noninvasively (Portapres device) after a 3-week pretreatment with placebo and a subsequent 4-week once daily lacidipine (4 mg) or placebo treatment (double-blind crossover design). Systolic blood pressure, diastolic blood pressure, and heart rate means were computed each hour for 24 hours (day and night) at the end of each treatment period. Similar assessments were also made for blood pressure and heart rate variability (standard deviation and variation coefficient) and for 24-hour baroreflex sensitivity, which was quantified (1) in the time domain by the slope of the spontaneous sequences characterized by progressive increases or reductions of systolic blood pressure and RR interval and (2) in the frequency domain by the squared ratio of RR interval and systolic blood pressure spectral power approximately 0.1 and 0.3 Hz over the 24 hours. Compared with placebo, lacidipine reduced the 24-hour, daytime, and nighttime systolic and diastolic blood pressure (P<0.05) with no significant change in heart rate. It also reduced 24-hour, daytime, and nighttime standard deviation (-19.6%, -14.4%, and -24.0%, respectively; P<0.05) and their variation coefficient. The 24-hour average slope of all sequences (7.7+/-1.7 ms/mm Hg) seen during placebo was significantly increased by lacidipine (8.7+/-1.8 ms/mm Hg, P<0.01), with a significant increase being obtained also for the 24-hour average alpha coefficient at 0.1 Hz (from 5.7+/-1.5 to 6.4+/-1.3 ms/mm Hg, P<0.01). Thus, in diabetic hypertensive patients, lacidipine reduced not only 24-hour blood pressure means but also blood pressure variability. This reduction was accompanied by an improvement of baroreflex sensitivity. Computer analysis of beat-to-beat 24-hour noninvasive blood pressure monitoring may offer valuable information about the effects of antihypertensive drugs on hemodynamic and autonomic parameters in daily life.

Time and frequency domain estimates of spontaneous baroreflex sensitivity provide early detection of autonomic dysfunction in diabetes mellitus

Diabetic autonomic dysfunction is associated with a high risk of mortality which makes its early identification clinically important. The aim of our study was to compare the detection of autonomic dysfunction provided by classical laboratory autonomic function tests with that obtained through computer assessment of the spontaneous sensitivity of the baroreceptor-heart rate reflex (BRS) by time domain and frequency domain techniques. In 20 normotensive diabetic patients (mean age +/- SD 41.9 +/- 8.1 years) with no evidence of autonomic dysfunction on laboratory autonomic testing (D0) blood pressure (BP) and ECG were continuously monitored over 15 min in the supine position. BRS was assessed as the slope of the regression line between spontaneous increases or reductions in systolic BP and linearly related lengthening or shortening in RR interval over sequences of at least 4 consecutive beats (sequence method), or as the squared ratio between RR interval and systolic BP spectral powers around 0.1 Hz. We compared the results with those of 32 age-matched normotensive diabetic patients with abnormal autonomic function tests (D1) and with those of 24 healthy age-matched control subjects with normal autonomic function tests (C). Compared to C, BRS was markedly less in D1 when assessed by both the slope of the two types of sequences (data pooled) and by the spectral method (-71.3% and -60.2% respectively, both p < 0.01). However, BRS was consistently although somewhat less markedly reduced in D0, the reduction being clearly evident for all the estimates (-57.0% and -43.5%, both p < 0.01). The effects were more evident than those obtained by the simple quantification of the RR interval variability. These data suggest that time and frequency domain estimates of spontaneous BRS allow earlier detection of diabetic autonomic dysfunction than classical laboratory autonomic tests. The estimates can be obtained by short non-invasive recording of the BP and RR interval signals in the supine patient, i.e. under conditions suitable for routine outpatient evaluation.

[Hemorheologic characteristics in beta-thalassemic homozygotes before and after splenectomy]

In a group of 36 homozigous beta-thalassaemic children we studied the effect of splenectomy on hemorheologic characteristics. The aim of the work was to evaluate the importance of such operation either on anemia or on erythrocyte deformability. Whole blood viscosity was measured with a Brookfield Microviscometer (LVT) and erythrocyte deformability was evaluated with the erythrocyte filtration technique using policarbonate membranes. The more the erythrocyte deformability decreases, the more the erythrocyte filtration rate decreases. Our data show that splenectomized children, have worse hemorheologic characteristics according to the longer survival time of pathological red blood cells in spite of their reduced deformability. This behaviour can be modified only by blood transfusion that we have seen to be able to reduce whole blood viscosity and to increase erythrocyte filtration rate in splenectomized children. We think that splenectomy must be delayed as long as possible so that hemodinamyc conditions cannot be worsened. An hemorheologic monitorage could be useful for diagnostic and prognostic evaluations both in splenectomized and not splenectomized children.

[Osteopetrosis ( Albers-Schönberg disease ). II. Personal contribution]

Five cases of marble bones in two families living near Brescia are presented. Case 1 (42-yr-old female) was a typical malignant form with deep and extensive eburnation, many pathological fractures, concomitant osteitis and the formation of many fistulae, massive spleen enlargement and infarct, and marked anaemia with clear signs of extra-medullary haemopoiesis. The patient died 5 yr after her first admission. Two of her brothers had had an identical, fatal form. Case 4 (28-yr-old male) was much the same: virtually general osteosclerosis despite the difference in age, marked spleen enlargement, a history of fractures, serious anaemia and extramedullary haemopoiesis. Benign pictures were seen in cases 2 and 3 (73- and 68-yr-old females). In case 5 (25-yr-old male), typical bone condensation was the only significant pathological sign. It is suggested that this, too, may be seen as a "benign" form.