Key-string segmentation algorithm and higher-order repeat 16mer (54 copies) in human alpha satellite DNA in chromosome 7.

A new key-string segmentation algorithm for identification of alpha satellite DNAs and higher-order repeat (HOR) units was introduced and exemplified. Starting with an initial key string, we determine the dominant key string and HOR. Our key-string algorithm was used to scan the recent GenBank data for human alpha satellite DNA sequence AC017075.8 (193 277 bp) from the centromeric region of chromosome 7. The sequence was computationally segmented into one HOR domain (super-repeat domain) and two non-HOR domains. Dominant key-string GTTTCT provided segmentation in terms of alpha monomers. The HOR is tandemly repeated in 54 copies in the super-repeat (HOR) domain. Five insertions and three deletions in the HOR structure associated with a dominant key string were identified. Concensus HOR was constructed. Divergence of individual HOR copies from concensus amounts to 0.7% on the average, while divergence between 16 monomer variants within each HOR is on the average 20%. In the front and back domain, 199 monomer variants were identified that are not organized in HOR and diverge by 20-40%.

Quantification of Helicobacter pylori resistance in functional and organic dyspepsia.

OBJECTIVE: To compare the efficacy of Helicobacter pylori eradication in patients with functional and organic dyspepsia. METHODS: The study included a cohort of 160 patients (115 with organic and 45 with functional dyspepsia) with dyspeptic symptoms and gastroscopically confirmed H. pylori infection. Triple therapy with omeprazole 20 mg, amoxicillin 1000 mg and metronidazole 400 mg (OAM) was administered twice a day for a week. Minimal inhibition concentration (MIC) was estimated on cultures from 41 patients with positive H. pylori for determination of antimicrobial sensitivity and primary resistance to amoxicillin and metronidazole. RESULTS: Endoscopic examination at least 6 weeks after therapy showed that 116 (72.5%) patients had H. pylori eradicated, whereas 44 (27.5%) were not. From the latter patients, 10 (23%) had functional dyspepsia and from 116 eradicated patients 35 (30%) had functional dyspepsia. Difference in efficacy of OAM therapy between patients with organic and functional dyspepsia was not significant (P > 0.5). Percentages of non-eradicated patients with organic and functional dyspepsia were 29.6 and 22.2%, respectively (ratio 1.3 : 1). MIC from 41 samples showed 18 (44%) in vitro resistant strains. There was no resistance to amoxicillin. CONCLUSIONS: There is no significant difference in H. pylori resistance to the same antibiotic between patients having functional or organic dyspepsia.

Link between truncated fractals and coupled oscillators in biological systems.

This article aims at providing a new theoretical insight into the fundamental question of the origin of truncated fractals in biological systems. It is well known that fractal geometry is one of the characteristics of living organisms. However, contrary to mathematical fractals which are self-similar at all scales, the biological fractals are truncated, i.e. their self-similarity extends at most over a few orders of magnitude of separation. We show that nonlinear coupled oscillators, modeling one of the basic features of biological systems, may generate truncated fractals: a truncated fractal pattern for basin boundaries appears in a simple mathematical model of two coupled nonlinear oscillators with weak dissipation. This fractal pattern can be considered as a particular hidden fractal property. At the level of sufficiently fine precision technique the truncated fractality acts as a simple structure, leading to predictability, but at a lower level of precision it is effectively fractal, limiting the predictability of the long-term behavior of biological systems. We point out to the generic nature of our result.

Antibiotic-resistance patterns of Helicobacter pylori in Croatia: cohort study.

AIM: To provide information on regional sensitivity of H. pylori to antibiotic treatment by investigating the rate of H. pylori eradication in Croatia. METHODS: The study included 217 outpatients (107 women and 110 men), with gastrointestinal symptoms and H. pylori positive finding. They received the first-line and second-line treatments. The first-line treatment included triple therapies with either omeprazole (omeprazole, amoxicillin, and metronidazole - OAM), or pantoprazole (pantoprazole, amoxicillin, and metronidazole - PAM), or a combination of ranitidine bismuth citrate, amoxicillin, and azithromycin (RBAAz). If this therapy failed, clarithromycin was used in the second-line treatment. RESULTS: H. pylori was eradicated in 93% of the patients, whereas in 7% it was resistant to all administered therapies. The efficacy of OAM or PAM first-line treatments in H. pylori eradication, including resistant patients, was 70%, and of RBAAz treatment 95%. The RBAAz treatment had the highest eradication rate. In the second-line treatment, clarithromycin eradicated 45% of the remaining H. pylori strains that had not reacted to metronidazole and azithromycin administered either alone or in combination with ranitidine bismuth citrate. CONCLUSION: Optimal therapy for the eradication of H. pylori infection is the RBAAz treatment, whereas metronidazole cannot be recommended because of the high rate of resistance of H. pylori to that antibiotic.

Quantitative tissue carcinoembryonic antigen (T CEA) assay as a screening test for severe dysplasia in colorectal adenomas.

Relationship between the serum (S CEA) and the tissue (T CEA) carcinoembryonic antigen concentrations with regard to the degree of dysplasia in colorectal adenomas was investigated. Our study included 56 single or multiple colorectal adenomas in 46 patients. The measurements of T CEA concentrations were performed using the quantitative CEA-EIA method (Abbott) modified for wet tissue, obtained from heads of the adenomas. As a control point the mucosa near adenoma and the rectal mucosa were used. Our results suggest that the T CEA concentrations from the head of the adenoma demonstrate a highly significant difference between mild and severe dysplasia (P < 0.001), between mild dysplasia and invasive adenocarcinoma (P < 0.001) and a significant difference between mild and moderate dysplasia (P < 0.05). On the other hand, the S CEA concentrations corresponding to these cases showed no such differences. In conclusion, we suggest the quantitative measurement of T CEA concentrations as a screening test for severe dysplasia in colorectal adenomas.

Prognostic and therapeutic score for colorectal adenomas and the role of serum and tissue carcinoembryonic antigen.

OBJECTIVE: To study the tissue carcinoembryonic antigen (TCEA) concentrations with regard to multiplicity, diameter, pathohistological finding, degree of dysplasia and serum CEA (SCEA) concentrations. METHODS: Our study included 46 patients with single or multiple adenomas. For 56 adenomas TCEA concentrations were measured in addition to standard determinations of multiplicity, diameter, pathohistology, degree of dysplasia and SCEA. The measurements of TCEA concentrations were performed using the CEA-EIA method (Abbott) modified for wet tissue obtained from the head of the adenoma (TCEA-A), margin of resection at the neck or base of the adenoma (TCEA-B), mucosa near the adenoma (TCEA-C) and rectal mucosa (TCEA-D). The Mann-Whitney test and M estimates were used to differentiate CEA distribution between various classes of adenomas within each characterization. RESULTS: TCEA concentrations from the head of the adenoma (TCEA-A) demonstrated highly significant difference between mild and severe dysplasia (P = 0.0003), between mild dysplasia and invasive adenocarcinoma (P = 0.001) and significant difference between mild and moderate dysplasia (P = 0.04). There was a statistically significant difference in TCEA-A also between tubular and villous adenomas (P = 0.04). On the other hand, no significant correlations with regard to multiplicity, diameter and pathohistological features were found. CONCLUSION: These results suggest that there is a highly significant difference between the tissue CEA concentration from the head of the adenoma (TCEA-A) in the presence or absence of severe dysplasia. Furthermore, combining a number of pathological variables together with TCEA and routine SCEA, a new score was proposed to be used as a guide to the frequency of follow-up colonoscopy following polypectomy.

[Palliative treatment of malignant esophageal obstruction with a new endoscopically administered self-expanding nitinol stent: case report]. / Palijativni pristup malignoj opstrukciji jednjaka endoskopskom primjenom novog samosireceg (self-expanding) nitinolskog stenta; prikaz bolesnice.

The endoscopic methods of palliative treatment in malignant esophageal stenoses caused by neoplasm which have been performed so far unfortunately do not provide permanently satisfying results. The implantation of self-expanding stents with the purpose of removing malignant esophageal obstructions has recently become the most acceptable method of treatment. By using that method it is possible to reduce or even completely remove difficulties in swallowing. In that way a significant improvement in life quality of patients with inoperable esophageal cancer is possible. The various types of metal endoprostheses used for the palliative treatment of esophageal malignant stenoses are described in this paper. Here is also presented a case of nitinol stent implantation in a 50 year old woman suffering from esophageal cancer. This type of therapeutic treatment has been applied in Croatia for first time.

Comparison of injection sclerotherapy and laser photocoagulation for bleeding peptic ulcers.

BACKGROUND AND STUDY AIMS: The most widely used endoscopic procedures in the management of patients with bleeding peptic ulcer are at present sclerotherapy and thermal methods. In an attempt to assess the most effective method of achieving hemostasis, we compared injection sclerotherapy and laser photocoagulation in terms of the efficacy of initial hemostasis, rebleeding, need for surgery, mortality, and the appearance of the ulcer after the hemostatic procedure. PATIENTS AND METHODS: In this prospective, randomized trial, 160 patients were treated with injection sclerotherapy (1% polidocanol), and 155 patients with laser photocoagulation (Nd:YAG laser) in cases of Forrest I, Forrest IIa, and Forrest IIb hemorrhage. The bleeding activity was classified according to the modified Forrest criteria. Polidocanol injection and Nd:YAG laser photocoagulation were not preceded by epinephrine administration. RESULTS: There were no significant overall differences between the groups in the outcome in terms of definitive hemostasis, rebleeding, urgent surgery, and death (p = 0.487). In the case of the subgroup with Forrest I lesions, laser photocoagulation was more efficacious than sclerotherapy (p = 0.0078). In the Forrest IIa and Forrest IIb subgroups, the two methods were equally effective (p = 0.202 and 0.513 respectively). In the sclerotherapy patients, definitive initial hemostasis in Forrest IIa was achieved in 100%, whereas in the laser group this rate was 92%, with 28% of patients initially developing hemorrhage after one or two laser pulses. Ulcer healing was slower following sclerotherapy than after photocoagulation. CONCLUSION: Injection sclerotherapy and laser photocoagulation are equally effective in achieving definitive hemostasis in bleeding peptic ulcers. Laser photocoagulation is more efficacious in patients with active bleeding, whereas injection sclerotherapy is more effective in patients with a nonbleeding visible vessel.